From 54f24930180861cf649c0f05669e9e9dc1a7bb7d Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Tue, 28 Nov 2017 14:53:44 -0700
Subject: [PATCH 001/332] Added ReductionView to Kokkos ReaxFF
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 74 ++++++-------
src/KOKKOS/fix_qeq_reax_kokkos.h | 3 +
src/KOKKOS/pair_kokkos.h | 15 ++-
src/KOKKOS/pair_reaxc_kokkos.cpp | 169 +++++++++++++++++++++++------
src/KOKKOS/pair_reaxc_kokkos.h | 11 ++
5 files changed, 199 insertions(+), 73 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 5d2f6a0438..764b2f9191 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -254,12 +254,18 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_t.template modify<LMPHostType>();
k_t.template sync<DeviceType>();
+ if (neighflag != FULL)
+ red_o = Kokkos::Experimental::create_reduction_view<> (k_o.d_view); // allocate duplicated memory
+
// 1st cg solve over b_s, s
cg_solve1();
// 2nd cg solve over b_t, t
cg_solve2();
+ if (neighflag != FULL)
+ red_o = decltype(red_o)(); // free duplicated memory
+
// calculate_Q();
calculate_q();
@@ -494,13 +500,9 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse12_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- if (neighflag == HALF) {
- FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
- Kokkos::parallel_for(inum,sparse13_functor);
- } else {
- FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
- Kokkos::parallel_for(inum,sparse13_functor);
- }
+ FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
+ Kokkos::parallel_for(inum,sparse13_functor);
+ Kokkos::Experimental::contribute(k_o.d_view, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec1> (inum, teamsize), *this);
}
@@ -548,18 +550,14 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- if (neighflag == HALF) {
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
- } else {
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
- }
+ red_o.reset_except(d_o);
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ Kokkos::Experimental::contribute(k_o.d_view, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
-
if (neighflag != FULL) {
k_o.template modify<DeviceType>();
k_o.template sync<LMPHostType>();
@@ -625,13 +623,10 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse32_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- if (neighflag == HALF) {
- FixQEqReaxKokkosSparse33Functor<DeviceType,HALF> sparse33_functor(this);
- Kokkos::parallel_for(inum,sparse33_functor);
- } else {
- FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
- Kokkos::parallel_for(inum,sparse33_functor);
- }
+ red_o.reset_except(d_o);
+ FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
+ Kokkos::parallel_for(inum,sparse33_functor);
+ Kokkos::Experimental::contribute(k_o.d_view, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec3> (inum, teamsize), *this);
}
@@ -679,13 +674,10 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- if (neighflag == HALF) {
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
- } else {
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
- }
+ red_o.reset_except(d_o);
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ Kokkos::Experimental::contribute(k_o.d_view, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
@@ -797,8 +789,8 @@ template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
{
- // The q array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
+ // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto a_o = red_o.access();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -806,9 +798,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_s[j];
- a_o[j] += d_val(jj) * d_s[i];
+ a_o(j) += d_val(jj) * d_s[i];
}
- a_o[i] += tmp;
+ a_o(i) += tmp;
}
}
@@ -849,8 +841,8 @@ template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
{
- // The q array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
+ // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto a_o = red_o.access();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -858,9 +850,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_d[j];
- a_o[j] += d_val(jj) * d_d[i];
+ a_o(j) += d_val(jj) * d_d[i];
}
- a_o[i] += tmp;
+ a_o(i) += tmp;
}
}
@@ -908,8 +900,8 @@ template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
{
- // The q array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
+ // The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto a_o = red_o.access();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -917,9 +909,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_t[j];
- a_o[j] += d_val(jj) * d_t[i];
+ a_o(j) += d_val(jj) * d_t[i];
}
- a_o[i] += tmp;
+ a_o(i) += tmp;
}
}
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h
index 9014e20b8e..dd7b4073c2 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.h
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.h
@@ -22,6 +22,7 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos<LMPHostType>)
#ifndef LMP_FIX_QEQ_REAX_KOKKOS_H
#define LMP_FIX_QEQ_REAX_KOKKOS_H
+#include <Kokkos_ReductionView.hpp>
#include "fix_qeq_reax.h"
#include "kokkos_type.h"
#include "neigh_list.h"
@@ -192,6 +193,8 @@ class FixQEqReaxKokkos : public FixQEqReax {
HAT::t_ffloat_2d h_s_hist, h_t_hist;
typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist;
+ Kokkos::Experimental::ReductionView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType> red_o;
+
void init_shielding_k();
void init_hist();
void allocate_matrix();
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index f0e357270c..c8e926a721 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -19,9 +19,10 @@
#define LMP_PAIR_KOKKOS_H
#include "Kokkos_Macros.hpp"
+#include "Kokkos_Vectorization.hpp"
+#include "Kokkos_ReductionView.hpp"
#include "pair.h"
#include "neigh_list_kokkos.h"
-#include "Kokkos_Vectorization.hpp"
namespace LAMMPS_NS {
@@ -58,6 +59,18 @@ struct AtomicF<HALFTHREAD> {
enum {value = Kokkos::Atomic|Kokkos::Unmanaged};
};
+// Determine memory traits for force array
+// Do atomic trait when running HALFTHREAD neighbor list style
+template<int NEIGHFLAG>
+struct AtomicDup {
+ enum {value = Kokkos::Experimental::ReductionNonAtomic};
+};
+
+template<>
+struct AtomicDup<HALFTHREAD> {
+ enum {value = Kokkos::Experimental::ReductionAtomic};
+};
+
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
struct PairComputeFunctor {
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index d5f83f4537..79d9241ea4 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -711,6 +711,15 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
+ // allocate duplicated memory
+ if (neighflag != FULL) {
+ dup_f = Kokkos::Experimental::create_reduction_view<>(f);
+ dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom);
+ dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom);
+ dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
+ }
+
if (eflag_global) {
for (int i = 0; i < 14; i++)
pvector[i] = 0.0;
@@ -802,7 +811,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf_LessAtomics<HALFTHREAD> >(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALFTHREAD> >(0,ignum),*this);
else //(neighflag == FULL)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsFull>(0,ignum),*this);
@@ -817,14 +826,32 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (resize_hb) maxhb++;
resize = resize_bo || resize_hb;
- if (resize) allocate_array();
+ if (resize) {
+ allocate_array();
+ if (neighflag != FULL) {
+ dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
+ }
+ }
}
+ // allocate duplicated memory
+ if (neighflag != FULL) {
+ dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta);
+ dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
+ dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
+ dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
+ }
+
+ // reduction over duplicated memory
+ if (neighflag != FULL)
+ Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
+
// Bond order
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
} else if (neighflag == HALFTHREAD) {
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1_LessAtomics>(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
}
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder2>(0,ignum),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder3>(0,ignum),*this);
@@ -923,9 +950,29 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
pvector[7] = ev.ereax[8];
ev_all.evdwl += ev.ereax[8];
+ // reduction over duplicated memory
+ if (neighflag != FULL) {
+ Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
+
+ Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
+ Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
+ Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
+ dup_Cdbo.reset_except(d_Cdbo);
+ dup_Cdbopi.reset_except(d_Cdbopi);
+ dup_Cdbopi2.reset_except(d_Cdbopi2);
+ }
+
// Bond force
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALF> >(0,ignum),*this);
+
+ // reduction over duplicated memory
+ if (neighflag != FULL) {
+ Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ }
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALF,1> >(0,ignum),*this,ev);
else
@@ -934,6 +981,13 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
pvector[0] += ev.evdwl;
} else { //if (neighflag == HALFTHREAD) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALFTHREAD> >(0,ignum),*this);
+
+ // reduction over duplicated memory
+ if (neighflag != FULL) {
+ Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ }
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALFTHREAD,1> >(0,ignum),*this,ev);
else
@@ -942,6 +996,10 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
pvector[0] += ev.evdwl;
}
+ // reduction over duplicated memory
+ if (neighflag != FULL)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) {
eng_vdwl += ev_all.evdwl;
eng_coul += ev_all.ecoul;
@@ -958,11 +1016,15 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
+ if (neighflag != FULL)
+ Kokkos::Experimental::contribute(v_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (neighflag != FULL)
+ Kokkos::Experimental::contribute(v_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -970,6 +1032,19 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (fixspecies_flag)
FindBondSpecies();
+ // free duplicated memory
+ if (neighflag != FULL) {
+ dup_f = decltype(f)();
+ dup_dDeltap_self = decltype(d_dDeltap_self)();
+ dup_total_bo = decltype(d_total_bo)();
+ dup_CdDelta = decltype(d_CdDelta)();
+ dup_Cdbo = decltype(d_Cdbo)();
+ dup_Cdbopi = decltype(d_Cdbopi)();
+ dup_Cdbopi2 = decltype(d_Cdbopi2)();
+ dup_eatom = decltype(v_eatom)();
+ dup_vatom = decltype(v_vatom)();
+ }
+
copymode = 0;
}
@@ -1010,7 +1085,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
// The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto a_f = dup_f.access();
F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp;
F_FLOAT evdwl, fvdwl;
@@ -1169,7 +1245,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
// The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto a_f = dup_f.access();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -1548,8 +1625,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
if (d_resize_bo() || d_resize_hb())
return;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
+ //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
+ auto a_dDeltap_self = dup_dDeltap_self.access();
+ auto a_total_bo = dup_total_bo.access();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -2236,10 +2315,14 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ auto a_CdDelta = dup_CdDelta.access();
+ auto a_Cdbo = dup_Cdbo.access();
+ auto a_Cdbopi = dup_Cdbopi.access();
+ auto a_Cdbopi2 = dup_Cdbopi2.access();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2390,9 +2473,13 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ auto a_f = dup_f.access();
+ auto a_Cdbo = dup_Cdbo.access();
+ auto a_CdDelta = dup_CdDelta.access();
+
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2699,9 +2786,12 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ auto a_f = dup_f.access();
+ auto a_CdDelta = dup_CdDelta.access();
+ auto a_Cdbo = dup_Cdbo.access();
// in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3071,7 +3161,8 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto a_f = dup_f.access();
int hblist[MAX_BONDS];
F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
@@ -3218,9 +3309,12 @@ template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, const int &ii) const {
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
+ //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ auto a_Cdbo = dup_Cdbo.access();
+ auto a_Cdbopi = dup_Cdbopi.access();
+ auto a_Cdbopi2 = dup_Cdbopi2.access();
const int i = d_ilist[ii];
const tagint itag = tag(i);
@@ -3267,8 +3361,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ auto a_f = dup_f.access();
+ auto a_CdDelta = dup_CdDelta.access();
F_FLOAT delij[3];
F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3405,7 +3501,8 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto a_f = dup_f.access();
F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3];
F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3];
@@ -3618,8 +3715,10 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
const int VFLAG = vflag_either;
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ auto a_eatom = dup_eatom.access();
+ auto a_vatom = dup_vatom.access();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
@@ -3685,7 +3784,9 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const
// The eatom array is atomic for Half/Thread neighbor style
if (eflag_atom) {
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
+ auto a_eatom = dup_eatom.access();
+
const E_FLOAT epairhalf = 0.5 * epair;
a_eatom[i] += epairhalf;
a_eatom[j] += epairhalf;
@@ -3701,7 +3802,8 @@ void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i
const F_FLOAT &epair) const
{
// The eatom array is atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
+ auto a_eatom = dup_eatom.access();
a_eatom[i] += epair;
}
@@ -3734,7 +3836,9 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i,
}
if (vflag_atom) {
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ auto a_vatom = dup_vatom.access();
+
a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
}
@@ -3750,7 +3854,8 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons
{
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ auto a_vatom = dup_vatom.access();
F_FLOAT v[6];
@@ -3810,7 +3915,9 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
}
if (vflag_atom) {
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
+ auto a_vatom = dup_vatom.access();
+
a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2];
a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5];
a_vatom(j,0) += 0.25 * v[0]; a_vatom(j,1) += 0.25 * v[1]; a_vatom(j,2) += 0.25 * v[2];
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index 95fd7ced38..e25077f2cf 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -24,6 +24,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
#define LMP_PAIR_REAXC_KOKKOS_H
#include <stdio.h>
+#include <Kokkos_ReductionView.hpp>
#include "pair_kokkos.h"
#include "pair_reaxc.h"
#include "neigh_list_kokkos.h"
@@ -411,6 +412,16 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2;
typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self;
+ Kokkos::Experimental::ReductionView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_total_bo;
+ Kokkos::Experimental::ReductionView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_CdDelta;
+ Kokkos::Experimental::ReductionView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType> dup_eatom;
+ Kokkos::Experimental::ReductionView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType> dup_f;
+ Kokkos::Experimental::ReductionView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType> dup_vatom;
+ Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_dDeltap_self;
+ Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbo;
+ Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi;
+ Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi2;
+
typedef Kokkos::DualView<F_FLOAT**[7],typename DeviceType::array_layout,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7;
--
GitLab
From 41202c3627bb2ea5a4a8bf725b679484edc58ed5 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Tue, 28 Nov 2017 16:28:17 -0700
Subject: [PATCH 002/332] Turn atomics back on for some views in
pair_reaxc_kokkos
---
src/KOKKOS/pair_reaxc_kokkos.cpp | 80 ++++++++++++++++----------------
1 file changed, 40 insertions(+), 40 deletions(-)
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 79d9241ea4..8a1f1291e5 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -811,7 +811,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALFTHREAD> >(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf_LessAtomics<HALFTHREAD> >(0,ignum),*this);
else //(neighflag == FULL)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsFull>(0,ignum),*this);
@@ -838,9 +838,9 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// allocate duplicated memory
if (neighflag != FULL) {
dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta);
- dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
- dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
- dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
+ //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
+ //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
+ //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
}
// reduction over duplicated memory
@@ -851,7 +851,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
} else if (neighflag == HALFTHREAD) {
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1_LessAtomics>(0,ignum),*this);
}
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder2>(0,ignum),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder3>(0,ignum),*this);
@@ -955,12 +955,12 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
- Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
- Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
- dup_Cdbo.reset_except(d_Cdbo);
- dup_Cdbopi.reset_except(d_Cdbopi);
- dup_Cdbopi2.reset_except(d_Cdbopi2);
+ //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
+ //dup_Cdbo.reset_except(d_Cdbo);
+ //dup_Cdbopi.reset_except(d_Cdbopi);
+ //dup_Cdbopi2.reset_except(d_Cdbopi2);
}
// Bond force
@@ -968,11 +968,11 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALF> >(0,ignum),*this);
// reduction over duplicated memory
- if (neighflag != FULL) {
- Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
- }
+ //if (neighflag != FULL) {
+ // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //}
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALF,1> >(0,ignum),*this,ev);
else
@@ -983,11 +983,11 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALFTHREAD> >(0,ignum),*this);
// reduction over duplicated memory
- if (neighflag != FULL) {
- Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
- }
+ //if (neighflag != FULL) {
+ // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //}
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALFTHREAD,1> >(0,ignum),*this,ev);
else
@@ -1038,9 +1038,9 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
dup_dDeltap_self = decltype(d_dDeltap_self)();
dup_total_bo = decltype(d_total_bo)();
dup_CdDelta = decltype(d_CdDelta)();
- dup_Cdbo = decltype(d_Cdbo)();
- dup_Cdbopi = decltype(d_Cdbopi)();
- dup_Cdbopi2 = decltype(d_Cdbopi2)();
+ //dup_Cdbo = decltype(d_Cdbo)();
+ //dup_Cdbopi = decltype(d_Cdbopi)();
+ //dup_Cdbopi2 = decltype(d_Cdbopi2)();
dup_eatom = decltype(v_eatom)();
dup_vatom = decltype(v_vatom)();
}
@@ -2316,13 +2316,13 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
auto a_CdDelta = dup_CdDelta.access();
- auto a_Cdbo = dup_Cdbo.access();
- auto a_Cdbopi = dup_Cdbopi.access();
- auto a_Cdbopi2 = dup_Cdbopi2.access();
+ //auto a_Cdbo = dup_Cdbo.access();
+ //auto a_Cdbopi = dup_Cdbopi.access();
+ //auto a_Cdbopi2 = dup_Cdbopi2.access();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2474,10 +2474,10 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
auto a_f = dup_f.access();
- auto a_Cdbo = dup_Cdbo.access();
+ //auto a_Cdbo = dup_Cdbo.access();
auto a_CdDelta = dup_CdDelta.access();
@@ -2788,10 +2788,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
auto a_f = dup_f.access();
auto a_CdDelta = dup_CdDelta.access();
- auto a_Cdbo = dup_Cdbo.access();
+ //auto a_Cdbo = dup_Cdbo.access();
// in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3309,12 +3309,12 @@ template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, const int &ii) const {
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
- auto a_Cdbo = dup_Cdbo.access();
- auto a_Cdbopi = dup_Cdbopi.access();
- auto a_Cdbopi2 = dup_Cdbopi2.access();
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
+ Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
+ //auto a_Cdbo = dup_Cdbo.access();
+ //auto a_Cdbopi = dup_Cdbopi.access();
+ //auto a_Cdbopi2 = dup_Cdbopi2.access();
const int i = d_ilist[ii];
const tagint itag = tag(i);
--
GitLab
From ee9ba99cde572c5146cfa8569cc3626219ff41dd Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Wed, 29 Nov 2017 11:11:20 -0700
Subject: [PATCH 003/332] Fix some bugs in pair_reaxc_kokkos
---
src/KOKKOS/pair_reaxc_kokkos.cpp | 30 +++++++++++++++++-------------
1 file changed, 17 insertions(+), 13 deletions(-)
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 8a1f1291e5..6791690cf0 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -716,8 +716,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
dup_f = Kokkos::Experimental::create_reduction_view<>(f);
dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom);
dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom);
- dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
}
if (eflag_global) {
@@ -789,6 +787,12 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
allocate_array();
}
+ // allocate duplicated memory
+ if (neighflag != FULL) {
+ dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
+ }
+
// Neighbor lists for bond and hbond
// try, resize if necessary
@@ -811,7 +815,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf_LessAtomics<HALFTHREAD> >(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALFTHREAD> >(0,ignum),*this);
else //(neighflag == FULL)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsFull>(0,ignum),*this);
@@ -851,7 +855,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
} else if (neighflag == HALFTHREAD) {
- Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1_LessAtomics>(0,ignum),*this);
+ Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
}
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder2>(0,ignum),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder3>(0,ignum),*this);
@@ -1034,15 +1038,15 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// free duplicated memory
if (neighflag != FULL) {
- dup_f = decltype(f)();
- dup_dDeltap_self = decltype(d_dDeltap_self)();
- dup_total_bo = decltype(d_total_bo)();
- dup_CdDelta = decltype(d_CdDelta)();
- //dup_Cdbo = decltype(d_Cdbo)();
- //dup_Cdbopi = decltype(d_Cdbopi)();
- //dup_Cdbopi2 = decltype(d_Cdbopi2)();
- dup_eatom = decltype(v_eatom)();
- dup_vatom = decltype(v_vatom)();
+ dup_f = decltype(dup_f)();
+ dup_dDeltap_self = decltype(dup_dDeltap_self)();
+ dup_total_bo = decltype(dup_total_bo)();
+ dup_CdDelta = decltype(dup_CdDelta)();
+ //dup_Cdbo = decltype(dup_Cdbo)();
+ //dup_Cdbopi = decltype(dup_Cdbopi)();
+ //dup_Cdbopi2 = decltype(dup_Cdbopi2)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
}
copymode = 0;
--
GitLab
From d2da1f5797faa0b752b7408822f361e565ea8d64 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Wed, 6 Dec 2017 09:41:29 -0700
Subject: [PATCH 004/332] Template out atomics for full neighbor list
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 6 ++--
src/KOKKOS/pair_reaxc_kokkos.cpp | 56 +++++++++++++++---------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 764b2f9191..e5f1901c1b 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -790,7 +790,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.access();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -842,7 +842,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.access();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -901,7 +901,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.access();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 27cf18b02e..07d17408ca 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -1090,7 +1090,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp;
F_FLOAT evdwl, fvdwl;
@@ -1250,7 +1250,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -1633,8 +1633,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
//Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
- auto a_dDeltap_self = dup_dDeltap_self.access();
- auto a_total_bo = dup_total_bo.access();
+ auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -2329,10 +2329,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
- auto a_CdDelta = dup_CdDelta.access();
- //auto a_Cdbo = dup_Cdbo.access();
- //auto a_Cdbopi = dup_Cdbopi.access();
- //auto a_Cdbopi2 = dup_Cdbopi2.access();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2486,9 +2486,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.access();
- //auto a_Cdbo = dup_Cdbo.access();
- auto a_CdDelta = dup_CdDelta.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
@@ -2799,9 +2799,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- auto a_f = dup_f.access();
- auto a_CdDelta = dup_CdDelta.access();
- //auto a_Cdbo = dup_Cdbo.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
// in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3172,7 +3172,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
int hblist[MAX_BONDS];
F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
@@ -3322,9 +3322,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, cons
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
- //auto a_Cdbo = dup_Cdbo.access();
- //auto a_Cdbopi = dup_Cdbopi.access();
- //auto a_Cdbopi2 = dup_Cdbopi2.access();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();
const int i = d_ilist[ii];
const tagint itag = tag(i);
@@ -3373,8 +3373,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFL
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
//Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.access();
- auto a_CdDelta = dup_CdDelta.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
F_FLOAT delij[3];
F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3512,7 +3512,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.access();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3];
F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3];
@@ -3727,8 +3727,8 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_eatom = dup_eatom.access();
- auto a_vatom = dup_vatom.access();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
@@ -3795,7 +3795,7 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const
if (eflag_atom) {
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.access();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
const E_FLOAT epairhalf = 0.5 * epair;
a_eatom[i] += epairhalf;
@@ -3813,7 +3813,7 @@ void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i
{
// The eatom array is atomic for Half/Thread neighbor style
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.access();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
a_eatom[i] += epair;
}
@@ -3847,7 +3847,7 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i,
if (vflag_atom) {
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.access();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
@@ -3865,7 +3865,7 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.access();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
F_FLOAT v[6];
@@ -3926,7 +3926,7 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
if (vflag_atom) {
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.access();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2];
a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5];
--
GitLab
From 8a9a7f4e504ef6b59536cba3e48297d29222ea14 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Wed, 6 Dec 2017 14:06:35 -0700
Subject: [PATCH 005/332] Fix issues
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 10 +--
src/KOKKOS/pair_kokkos.h | 4 +-
src/KOKKOS/pair_reaxc_kokkos.cpp | 100 ++++++++++++-----------------
3 files changed, 48 insertions(+), 66 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index e5f1901c1b..638837e265 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -255,7 +255,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_t.template sync<DeviceType>();
if (neighflag != FULL)
- red_o = Kokkos::Experimental::create_reduction_view<> (k_o.d_view); // allocate duplicated memory
+ red_o = Kokkos::Experimental::create_reduction_view<> (d_o); // allocate duplicated memory
// 1st cg solve over b_s, s
cg_solve1();
@@ -502,7 +502,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
- Kokkos::Experimental::contribute(k_o.d_view, red_o);
+ Kokkos::Experimental::contribute(d_o, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec1> (inum, teamsize), *this);
}
@@ -553,7 +553,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
red_o.reset_except(d_o);
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
- Kokkos::Experimental::contribute(k_o.d_view, red_o);
+ Kokkos::Experimental::contribute(d_o, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
@@ -626,7 +626,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
red_o.reset_except(d_o);
FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
Kokkos::parallel_for(inum,sparse33_functor);
- Kokkos::Experimental::contribute(k_o.d_view, red_o);
+ Kokkos::Experimental::contribute(d_o, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec3> (inum, teamsize), *this);
}
@@ -677,7 +677,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
red_o.reset_except(d_o);
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
- Kokkos::Experimental::contribute(k_o.d_view, red_o);
+ Kokkos::Experimental::contribute(d_o, red_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index c8e926a721..04c56d0aa7 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -19,10 +19,10 @@
#define LMP_PAIR_KOKKOS_H
#include "Kokkos_Macros.hpp"
-#include "Kokkos_Vectorization.hpp"
-#include "Kokkos_ReductionView.hpp"
#include "pair.h"
#include "neigh_list_kokkos.h"
+#include "Kokkos_Vectorization.hpp"
+#include "Kokkos_ReductionView.hpp"
namespace LAMMPS_NS {
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 07d17408ca..7a45c068be 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -712,11 +712,9 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
// allocate duplicated memory
- if (neighflag != FULL) {
- dup_f = Kokkos::Experimental::create_reduction_view<>(f);
- dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom);
- dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom);
- }
+ dup_f = Kokkos::Experimental::create_reduction_view<>(f);
+ dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom);
+ dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom);
if (eflag_global) {
for (int i = 0; i < 14; i++)
@@ -788,10 +786,8 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// allocate duplicated memory
- if (neighflag != FULL) {
- dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
- }
+ dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
// Neighbor lists for bond and hbond
@@ -832,24 +828,19 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
resize = resize_bo || resize_hb;
if (resize) {
allocate_array();
- if (neighflag != FULL) {
- dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
- }
+ dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
}
}
// allocate duplicated memory
- if (neighflag != FULL) {
- dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta);
- //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
- //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
- //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
- }
+ dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta);
+ //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
+ //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
+ //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
// reduction over duplicated memory
- if (neighflag != FULL)
- Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
+ Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
// Bond order
if (neighflag == HALF) {
@@ -955,28 +946,25 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all.evdwl += ev.ereax[8];
// reduction over duplicated memory
- if (neighflag != FULL) {
- Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
-
- //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
- //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
- //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
- //dup_Cdbo.reset_except(d_Cdbo);
- //dup_Cdbopi.reset_except(d_Cdbopi);
- //dup_Cdbopi2.reset_except(d_Cdbopi2);
- }
+ Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
+
+ //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
+ //dup_Cdbo.reset_except(d_Cdbo);
+ //dup_Cdbopi.reset_except(d_Cdbopi);
+ //dup_Cdbopi2.reset_except(d_Cdbopi2);
// Bond force
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALF> >(0,ignum),*this);
// reduction over duplicated memory
- //if (neighflag != FULL) {
- // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
- //}
+ //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALF,1> >(0,ignum),*this,ev);
else
@@ -987,11 +975,10 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALFTHREAD> >(0,ignum),*this);
// reduction over duplicated memory
- //if (neighflag != FULL) {
- // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
- //}
+ //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALFTHREAD,1> >(0,ignum),*this,ev);
else
@@ -1001,8 +988,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// reduction over duplicated memory
- if (neighflag != FULL)
- Kokkos::Experimental::contribute(f, dup_f);
+ Kokkos::Experimental::contribute(f, dup_f);
if (eflag_global) {
eng_vdwl += ev_all.evdwl;
@@ -1020,15 +1006,13 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
- if (neighflag != FULL)
- Kokkos::Experimental::contribute(v_eatom, dup_eatom);
+ Kokkos::Experimental::contribute(v_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
- if (neighflag != FULL)
- Kokkos::Experimental::contribute(v_vatom, dup_vatom);
+ Kokkos::Experimental::contribute(v_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -1037,17 +1021,15 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
FindBondSpecies();
// free duplicated memory
- if (neighflag != FULL) {
- dup_f = decltype(dup_f)();
- dup_dDeltap_self = decltype(dup_dDeltap_self)();
- dup_total_bo = decltype(dup_total_bo)();
- dup_CdDelta = decltype(dup_CdDelta)();
- //dup_Cdbo = decltype(dup_Cdbo)();
- //dup_Cdbopi = decltype(dup_Cdbopi)();
- //dup_Cdbopi2 = decltype(dup_Cdbopi2)();
- dup_eatom = decltype(dup_eatom)();
- dup_vatom = decltype(dup_vatom)();
- }
+ dup_f = decltype(dup_f)();
+ dup_dDeltap_self = decltype(dup_dDeltap_self)();
+ dup_total_bo = decltype(dup_total_bo)();
+ dup_CdDelta = decltype(dup_CdDelta)();
+ //dup_Cdbo = decltype(dup_Cdbo)();
+ //dup_Cdbopi = decltype(dup_Cdbopi)();
+ //dup_Cdbopi2 = decltype(dup_Cdbopi2)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
copymode = 0;
}
--
GitLab
From a5790ef68f564b3b6fc3c120fd4e530213944ca1 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 11 Dec 2017 08:38:54 -0700
Subject: [PATCH 006/332] Rename to ScatterView
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 +-
src/KOKKOS/fix_qeq_reax_kokkos.h | 4 ++--
src/KOKKOS/pair_kokkos.h | 6 +++---
src/KOKKOS/pair_reaxc_kokkos.cpp | 22 +++++++++++-----------
src/KOKKOS/pair_reaxc_kokkos.h | 20 ++++++++++----------
5 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index d8723339ad..aefc2ea130 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -255,7 +255,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_t.template sync<DeviceType>();
if (neighflag != FULL)
- red_o = Kokkos::Experimental::create_reduction_view<> (d_o); // allocate duplicated memory
+ red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory
// 1st cg solve over b_s, s
cg_solve1();
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h
index dd7b4073c2..64f81b9141 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.h
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.h
@@ -22,7 +22,7 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos<LMPHostType>)
#ifndef LMP_FIX_QEQ_REAX_KOKKOS_H
#define LMP_FIX_QEQ_REAX_KOKKOS_H
-#include <Kokkos_ReductionView.hpp>
+#include <Kokkos_ScatterView.hpp>
#include "fix_qeq_reax.h"
#include "kokkos_type.h"
#include "neigh_list.h"
@@ -193,7 +193,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
HAT::t_ffloat_2d h_s_hist, h_t_hist;
typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist;
- Kokkos::Experimental::ReductionView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType> red_o;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType> red_o;
void init_shielding_k();
void init_hist();
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 3243af26e7..a409035dc6 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -23,7 +23,7 @@
#include "neighbor_kokkos.h"
#include "neigh_list_kokkos.h"
#include "Kokkos_Vectorization.hpp"
-#include "Kokkos_ReductionView.hpp"
+#include "Kokkos_ScatterView.hpp"
namespace LAMMPS_NS {
@@ -64,12 +64,12 @@ struct AtomicF<HALFTHREAD> {
// Do atomic trait when running HALFTHREAD neighbor list style
template<int NEIGHFLAG>
struct AtomicDup {
- enum {value = Kokkos::Experimental::ReductionNonAtomic};
+ enum {value = Kokkos::Experimental::ScatterNonAtomic};
};
template<>
struct AtomicDup<HALFTHREAD> {
- enum {value = Kokkos::Experimental::ReductionAtomic};
+ enum {value = Kokkos::Experimental::ScatterAtomic};
};
//Specialisation for Neighborlist types Half, HalfThread, Full
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index c3197e222f..3a3faefc24 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -713,9 +713,9 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
// allocate duplicated memory
- dup_f = Kokkos::Experimental::create_reduction_view<>(f);
- dup_eatom = Kokkos::Experimental::create_reduction_view<>(v_eatom);
- dup_vatom = Kokkos::Experimental::create_reduction_view<>(v_vatom);
+ dup_f = Kokkos::Experimental::create_scatter_view<>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom);
if (eflag_global) {
for (int i = 0; i < 14; i++)
@@ -787,8 +787,8 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// allocate duplicated memory
- dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
// Neighbor lists for bond and hbond
@@ -829,16 +829,16 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
resize = resize_bo || resize_hb;
if (resize) {
allocate_array();
- dup_dDeltap_self = Kokkos::Experimental::create_reduction_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_reduction_view<>(d_total_bo);
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
}
}
// allocate duplicated memory
- dup_CdDelta = Kokkos::Experimental::create_reduction_view<>(d_CdDelta);
- //dup_Cdbo = Kokkos::Experimental::create_reduction_view<>(d_Cdbo);
- //dup_Cdbopi = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi);
- //dup_Cdbopi2 = Kokkos::Experimental::create_reduction_view<>(d_Cdbopi2);
+ dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta);
+ //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo);
+ //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi);
+ //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2);
// reduction over duplicated memory
Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index e25077f2cf..70aef2d608 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -24,7 +24,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
#define LMP_PAIR_REAXC_KOKKOS_H
#include <stdio.h>
-#include <Kokkos_ReductionView.hpp>
+#include <Kokkos_ScatterView.hpp>
#include "pair_kokkos.h"
#include "pair_reaxc.h"
#include "neigh_list_kokkos.h"
@@ -412,15 +412,15 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2;
typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self;
- Kokkos::Experimental::ReductionView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_total_bo;
- Kokkos::Experimental::ReductionView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_CdDelta;
- Kokkos::Experimental::ReductionView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType> dup_eatom;
- Kokkos::Experimental::ReductionView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType> dup_f;
- Kokkos::Experimental::ReductionView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType> dup_vatom;
- Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_dDeltap_self;
- Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbo;
- Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi;
- Kokkos::Experimental::ReductionView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi2;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_total_bo;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_CdDelta;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType> dup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_dDeltap_self;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbo;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi2;
typedef Kokkos::DualView<F_FLOAT**[7],typename DeviceType::array_layout,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
--
GitLab
From 2b99a26b47781bd59bdff63a10f0be0e9d7ad0dc Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 18 Dec 2017 13:57:56 -0700
Subject: [PATCH 007/332] Fix issue in fix_qeq_reax_kokkos, can't call child
function from base constructor
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index b251c634b6..ca14159b55 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -64,6 +64,10 @@ FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) :
nmax = nmax = m_cap = 0;
allocated_flag = 0;
nprev = 4;
+
+ memory->destroy(s_hist);
+ memory->destroy(t_hist);
+ grow_arrays(atom->nmax);
}
/* ---------------------------------------------------------------------- */
--
GitLab
From 5886cadeef893d114570e50cd33b51f9b7f82198 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 18 Dec 2017 14:09:39 -0700
Subject: [PATCH 008/332] Fix compiler warnings in atom_vec_hybrid_kokkos
---
src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
index b5aadb18d6..67dce07b80 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
@@ -255,6 +255,7 @@ int AtomVecHybridKokkos::pack_comm_kokkos(const int &n, const DAT::tdual_int_2d
const int &pbc_flag, const int pbc[])
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
+ return 0;
}
void AtomVecHybridKokkos::unpack_comm_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf)
@@ -266,12 +267,14 @@ int AtomVecHybridKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &l
const int &pbc_flag, const int pbc[])
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
+ return 0;
}
int AtomVecHybridKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
+ return 0;
}
void AtomVecHybridKokkos::unpack_border_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf,
@@ -286,12 +289,14 @@ int AtomVecHybridKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat
X_FLOAT lo, X_FLOAT hi)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
+ return 0;
}
int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
ExecutionSpace space)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
+ return 0;
}
/* ---------------------------------------------------------------------- */
--
GitLab
From dbbfacc5985b1b8bb19c126bc9d997a7f92adc99 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Wed, 20 Dec 2017 16:13:28 -0700
Subject: [PATCH 009/332] Fix atomic issues
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 18 +++++-----
src/KOKKOS/pair_kokkos.h | 6 ++--
src/KOKKOS/pair_reaxc_kokkos.cpp | 56 +++++++++++++++---------------
3 files changed, 41 insertions(+), 39 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 0f578707a4..d7632fe793 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -777,7 +777,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -785,9 +785,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_s[j];
- a_o(j) += d_val(jj) * d_s[i];
+ a_o[j] += d_val(jj) * d_s[i];
}
- a_o(i) += tmp;
+ a_o[i] += tmp;
}
}
@@ -829,7 +829,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -837,9 +837,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_d[j];
- a_o(j) += d_val(jj) * d_d[i];
+ a_o[j] += d_val(jj) * d_d[i];
}
- a_o(i) += tmp;
+ a_o[i] += tmp;
}
}
@@ -888,7 +888,7 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -896,9 +896,9 @@ void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_t[j];
- a_o(j) += d_val(jj) * d_t[i];
+ a_o[j] += d_val(jj) * d_t[i];
}
- a_o(i) += tmp;
+ a_o[i] += tmp;
}
}
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index a409035dc6..445583c455 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -62,15 +62,17 @@ struct AtomicF<HALFTHREAD> {
// Determine memory traits for force array
// Do atomic trait when running HALFTHREAD neighbor list style
-template<int NEIGHFLAG>
+template<int NEIGHFLAG, class DeviceType>
struct AtomicDup {
enum {value = Kokkos::Experimental::ScatterNonAtomic};
};
+#ifdef KOKKOS_ENABLE_CUDA
template<>
-struct AtomicDup<HALFTHREAD> {
+struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {
enum {value = Kokkos::Experimental::ScatterAtomic};
};
+#endif
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 3a3faefc24..1cbe8933e9 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -1073,7 +1073,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp;
F_FLOAT evdwl, fvdwl;
@@ -1233,7 +1233,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -1616,8 +1616,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
//Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
- auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG>::value>();
- auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -2312,10 +2312,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2469,9 +2469,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
@@ -2782,9 +2782,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
// in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3155,7 +3155,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
int hblist[MAX_BONDS];
F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
@@ -3305,9 +3305,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, cons
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG>::value>();
- //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG>::value>();
+ //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const tagint itag = tag(i);
@@ -3356,8 +3356,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFL
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
//Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT delij[3];
F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3495,7 +3495,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3];
F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3];
@@ -3710,8 +3710,8 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
@@ -3778,7 +3778,7 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const
if (eflag_atom) {
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const E_FLOAT epairhalf = 0.5 * epair;
a_eatom[i] += epairhalf;
@@ -3796,7 +3796,7 @@ void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i
{
// The eatom array is atomic for Half/Thread neighbor style
//Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_eatom[i] += epair;
}
@@ -3830,7 +3830,7 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i,
if (vflag_atom) {
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
@@ -3848,7 +3848,7 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT v[6];
@@ -3909,7 +3909,7 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
if (vflag_atom) {
//Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2];
a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5];
--
GitLab
From 81331e2a34fb79dbc15cf00f5e17c1d90821163b Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 21 Dec 2017 11:07:06 -0700
Subject: [PATCH 010/332] Better load balance fix_qeq_reax_kokkos for half
neigh list
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index d7632fe793..28838f27b6 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -398,19 +398,19 @@ void FixQEqReaxKokkos<DeviceType>::compute_h_item(int ii, int &m_fill, const boo
const X_FLOAT delz = x(j,2) - ztmp;
if (neighflag != FULL) {
+ // skip half of the interactions
const tagint jtag = tag(j);
- flag = 0;
- if (j < nlocal) flag = 1;
- else if (itag < jtag) flag = 1;
- else if (itag == jtag) {
- if (delz > SMALL) flag = 1;
- else if (fabs(delz) < SMALL) {
- if (dely > SMALL) flag = 1;
- else if (fabs(dely) < SMALL && delx > SMALL)
- flag = 1;
+ if (j >= nlocal) {
+ if (itag > jtag) {
+ if ((itag+jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag+jtag) % 2 == 1) continue;
+ } else {
+ if (x(j,2) < ztmp) continue;
+ if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
+ if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
}
}
- if (!flag) continue;
}
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
--
GitLab
From dbc308f35233d1a88ae6dbeb6b3330280d29fc0c Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 1 Mar 2018 10:06:43 -0700
Subject: [PATCH 011/332] Add warning
---
src/KOKKOS/kokkos.cpp | 6 ++++
src/KOKKOS/pair_kokkos.h | 47 +++++++++++++++++++++++++++++++-
src/KOKKOS/pair_reaxc_kokkos.cpp | 39 ++++++++++++++------------
src/KOKKOS/pair_reaxc_kokkos.h | 18 ++++++------
4 files changed, 83 insertions(+), 27 deletions(-)
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 5a74223353..2f9fbdb28b 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -119,6 +119,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
Kokkos::Cuda::initialize(select_device);
#else
LMPHostType::initialize(num_threads,numa);
+
+#ifndef KOKKOS_HAVE_SERIAL
+ if (num_threads == 1)
+ error->warning(FLERR,"Using Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) performs better with 1 thread");
+#endif
+
#endif
// default settings for package kokkos command
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index d9288cb7e8..4f10a4eb2f 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -61,7 +61,7 @@ struct AtomicF<HALFTHREAD> {
};
// Determine memory traits for force array
-// Do atomic trait when running HALFTHREAD neighbor list style
+// Do atomic trait when running HALFTHREAD neighbor list style with CUDA
template<int NEIGHFLAG, class DeviceType>
struct AtomicDup {
enum {value = Kokkos::Experimental::ScatterNonAtomic};
@@ -74,6 +74,51 @@ struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {
};
#endif
+#ifdef LMP_KOKKOS_USE_ATOMICS
+
+#ifdef KOKKOS_ENABLE_OPENMP
+template<>
+struct AtomicDup<HALFTHREAD,Kokkos::OpenMP> {
+ enum {value = Kokkos::Experimental::ScatterAtomic};
+};
+#endif
+
+#ifdef KOKKOS_ENABLE_THREADS
+template<>
+struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
+ enum {value = Kokkos::Experimental::ScatterAtomic};
+};
+#endif
+
+#endif
+
+
+// Determine duplication traits for force array
+// Use duplication when running threaded and not using atomics
+template<class DeviceType>
+struct DupF {
+ enum {value = Kokkos::Experimental::ScatterNonDuplicated};
+};
+
+#ifndef LMP_KOKKOS_USE_ATOMICS
+
+#ifdef KOKKOS_ENABLE_OPENMP
+template<>
+struct DupF<Kokkos::OpenMP> {
+ enum {value = Kokkos::Experimental::ScatterDuplicated};
+};
+#endif
+
+#ifdef KOKKOS_ENABLE_THREADS
+template<>
+struct DupF<Kokkos::Threads> {
+ enum {value = Kokkos::Experimental::ScatterDuplicated};
+};
+#endif
+
+#endif
+
+
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
struct PairComputeFunctor {
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 1cbe8933e9..f34549bc8c 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -73,6 +73,14 @@ PairReaxCKokkos<DeviceType>::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp)
k_error_flag = DAT::tdual_int_scalar("pair:error_flag");
k_nbuf_local = DAT::tdual_int_scalar("pair:nbuf_local");
+
+ static double t1 = 0.0;
+ static double t2 = 0.0;
+ static double t3 = 0.0;
+ static double t4 = 0.0;
+ static double t5 = 0.0;
+ static double t6 = 0.0;
+ static double t7 = 0.0;
}
/* ---------------------------------------------------------------------- */
@@ -674,6 +682,8 @@ void PairReaxCKokkos<DeviceType>::LR_vdW_Coulomb( int i, int j, double r_ij, LR_
template<class DeviceType>
void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
+ Kokkos::Timer timer;
+
copymode = 1;
bocnt = hbcnt = 0;
@@ -809,6 +819,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// zero
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxZero>(0,nmax),*this);
+
if (neighflag == HALF)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
@@ -2309,13 +2320,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi = d_Cdbopi;
- Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbopi2 = d_Cdbopi2;
auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //auto a_Cdbopi = dup_Cdbopi.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //auto a_Cdbopi2 = dup_Cdbopi2.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2714,10 +2719,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
// Forces
- a_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- a_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- a_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
- a_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ d_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ d_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ d_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ d_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
CdDelta_i += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
CdDelta_j += CEcoa4;
@@ -2732,7 +2737,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
temp = temp_bo_jt * temp_bo_jt * temp_bo_jt;
pBOjt7 = temp * temp * temp_bo_jt;
- a_Cdbo(i,l_index) += (CEval6 * pBOjt7);
+ d_Cdbo(i,l_index) += (CEval6 * pBOjt7);
d_Cdbopi(i,l_index) += CEval5;
d_Cdbopi2(i,l_index) += CEval5;
}
@@ -3085,9 +3090,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV
CdDelta_i += CEtors3;
CdDelta_j += CEtors3;
- a_Cdbo(i,k_index) += CEtors4 + CEconj1;
- a_Cdbo(i,j_index) += CEtors5 + CEconj2;
- a_Cdbo(j,l_index) += CEtors6 + CEconj3; // trouble
+ d_Cdbo(i,k_index) += CEtors4 + CEconj1;
+ d_Cdbo(i,j_index) += CEtors5 + CEconj2;
+ d_Cdbo(j,l_index) += CEtors6 + CEconj3; // trouble
// dcos_theta_ijk
const F_FLOAT coeff74 = CEtors7 + CEconj4;
@@ -3340,9 +3345,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, cons
}
if (flag) {
- a_Cdbo(j,k_index) += Cdbo_i;
- a_Cdbopi(j,k_index) += Cdbopi_i;
- a_Cdbopi2(j,k_index) += Cdbopi2_i;
+ d_Cdbo(j,k_index) += Cdbo_i;
+ d_Cdbopi(j,k_index) += Cdbopi_i;
+ d_Cdbopi2(j,k_index) += Cdbopi2_i;
}
}
}
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index 70aef2d608..f341da84c4 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -412,15 +412,15 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2;
typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_total_bo;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType> dup_CdDelta;
- Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType> dup_eatom;
- Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType> dup_f;
- Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType> dup_vatom;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_dDeltap_self;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbo;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType> dup_Cdbopi2;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_total_bo;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_CdDelta;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_dDeltap_self;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbo;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbopi;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbopi2;
typedef Kokkos::DualView<F_FLOAT**[7],typename DeviceType::array_layout,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
--
GitLab
From ed494b295fab613fbc83d49e8236105a337f574d Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 1 Mar 2018 11:52:39 -0700
Subject: [PATCH 012/332] WIP
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 +-
src/KOKKOS/fix_qeq_reax_kokkos.h | 3 +-
src/KOKKOS/kokkos_type.h | 74 ++++++++++++++++++++++++++++++
src/KOKKOS/neigh_list_kokkos.h | 2 +-
src/KOKKOS/pair_kokkos.h | 70 ----------------------------
src/KOKKOS/pair_reaxc_kokkos.cpp | 22 ++++-----
src/KOKKOS/pair_reaxc_kokkos.h | 1 -
7 files changed, 88 insertions(+), 86 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 28838f27b6..7fa7f7f05a 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -250,7 +250,7 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_t.template sync<DeviceType>();
if (neighflag != FULL)
- red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory
+ red_o = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> (d_o); // allocate duplicated memory
// 1st cg solve over b_s, s
cg_solve1();
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h
index 27be712ad8..9920325cf1 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.h
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.h
@@ -22,7 +22,6 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxKokkos<LMPHostType>)
#ifndef LMP_FIX_QEQ_REAX_KOKKOS_H
#define LMP_FIX_QEQ_REAX_KOKKOS_H
-#include <Kokkos_ScatterView.hpp>
#include "fix_qeq_reax.h"
#include "kokkos_type.h"
#include "neigh_list.h"
@@ -193,7 +192,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
HAT::t_ffloat_2d h_s_hist, h_t_hist;
typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType> red_o;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> red_o;
void init_shielding_k();
void init_hist();
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index 6b6fc8610a..de0dab8eb1 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -20,6 +20,9 @@
#include <Kokkos_DualView.hpp>
#include <impl/Kokkos_Timer.hpp>
#include <Kokkos_Vectorization.hpp>
+#include <Kokkos_ScatterView.hpp>
+
+enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in neigh_list_kokkos.h
#if defined(KOKKOS_HAVE_CXX11)
#undef ISFINITE
@@ -205,6 +208,77 @@ struct ExecutionSpaceFromDevice<Kokkos::Cuda> {
};
#endif
+
+// Determine memory traits for force array
+// Do atomic trait when running HALFTHREAD neighbor list style
+template<int NEIGHFLAG>
+struct AtomicF {
+ enum {value = Kokkos::Unmanaged};
+};
+
+template<>
+struct AtomicF<HALFTHREAD> {
+ enum {value = Kokkos::Atomic|Kokkos::Unmanaged};
+};
+
+// Determine memory traits for force array
+// Do atomic trait when running HALFTHREAD neighbor list style with CUDA
+template<int NEIGHFLAG, class DeviceType>
+struct AtomicDup {
+ enum {value = Kokkos::Experimental::ScatterNonAtomic};
+};
+
+#ifdef KOKKOS_ENABLE_CUDA
+template<>
+struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {
+ enum {value = Kokkos::Experimental::ScatterAtomic};
+};
+#endif
+
+#ifdef LMP_KOKKOS_USE_ATOMICS
+
+#ifdef KOKKOS_ENABLE_OPENMP
+template<>
+struct AtomicDup<HALFTHREAD,Kokkos::OpenMP> {
+ enum {value = Kokkos::Experimental::ScatterAtomic};
+};
+#endif
+
+#ifdef KOKKOS_ENABLE_THREADS
+template<>
+struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
+ enum {value = Kokkos::Experimental::ScatterAtomic};
+};
+#endif
+
+#endif
+
+
+// Determine duplication traits for force array
+// Use duplication when running threaded and not using atomics
+template<class DeviceType>
+struct DupF {
+ enum {value = Kokkos::Experimental::ScatterNonDuplicated};
+};
+
+#ifndef LMP_KOKKOS_USE_ATOMICS
+
+#ifdef KOKKOS_ENABLE_OPENMP
+template<>
+struct DupF<Kokkos::OpenMP> {
+ enum {value = Kokkos::Experimental::ScatterDuplicated};
+};
+#endif
+
+#ifdef KOKKOS_ENABLE_THREADS
+template<>
+struct DupF<Kokkos::Threads> {
+ enum {value = Kokkos::Experimental::ScatterDuplicated};
+};
+#endif
+
+#endif
+
// define precision
// handle global precision, force, energy, positions, kspace separately
diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h
index 1c433f321c..993543157b 100644
--- a/src/KOKKOS/neigh_list_kokkos.h
+++ b/src/KOKKOS/neigh_list_kokkos.h
@@ -20,7 +20,7 @@
namespace LAMMPS_NS {
-enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u};
+enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in kokkos_type.h
class AtomNeighbors
{
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 4f10a4eb2f..be4eb574e2 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -48,76 +48,6 @@ struct DoCoul<1> {
typedef CoulTag type;
};
-// Determine memory traits for force array
-// Do atomic trait when running HALFTHREAD neighbor list style
-template<int NEIGHFLAG>
-struct AtomicF {
- enum {value = Kokkos::Unmanaged};
-};
-
-template<>
-struct AtomicF<HALFTHREAD> {
- enum {value = Kokkos::Atomic|Kokkos::Unmanaged};
-};
-
-// Determine memory traits for force array
-// Do atomic trait when running HALFTHREAD neighbor list style with CUDA
-template<int NEIGHFLAG, class DeviceType>
-struct AtomicDup {
- enum {value = Kokkos::Experimental::ScatterNonAtomic};
-};
-
-#ifdef KOKKOS_ENABLE_CUDA
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#ifdef LMP_KOKKOS_USE_ATOMICS
-
-#ifdef KOKKOS_ENABLE_OPENMP
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::OpenMP> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#ifdef KOKKOS_ENABLE_THREADS
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#endif
-
-
-// Determine duplication traits for force array
-// Use duplication when running threaded and not using atomics
-template<class DeviceType>
-struct DupF {
- enum {value = Kokkos::Experimental::ScatterNonDuplicated};
-};
-
-#ifndef LMP_KOKKOS_USE_ATOMICS
-
-#ifdef KOKKOS_ENABLE_OPENMP
-template<>
-struct DupF<Kokkos::OpenMP> {
- enum {value = Kokkos::Experimental::ScatterDuplicated};
-};
-#endif
-
-#ifdef KOKKOS_ENABLE_THREADS
-template<>
-struct DupF<Kokkos::Threads> {
- enum {value = Kokkos::Experimental::ScatterDuplicated};
-};
-#endif
-
-#endif
-
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index f34549bc8c..55354f7c93 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -723,9 +723,9 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
// allocate duplicated memory
- dup_f = Kokkos::Experimental::create_scatter_view<>(f);
- dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom);
- dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom);
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(v_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(v_vatom);
if (eflag_global) {
for (int i = 0; i < 14; i++)
@@ -797,8 +797,8 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// allocate duplicated memory
- dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_total_bo);
// Neighbor lists for bond and hbond
@@ -840,16 +840,16 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
resize = resize_bo || resize_hb;
if (resize) {
allocate_array();
- dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_total_bo);
}
}
// allocate duplicated memory
- dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta);
- //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo);
- //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi);
- //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2);
+ dup_CdDelta = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_CdDelta);
+ //dup_Cdbo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_Cdbo);
+ //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_Cdbopi);
+ //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value>(d_Cdbopi2);
// reduction over duplicated memory
Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index f341da84c4..23a5c79b24 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -24,7 +24,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
#define LMP_PAIR_REAXC_KOKKOS_H
#include <stdio.h>
-#include <Kokkos_ScatterView.hpp>
#include "pair_kokkos.h"
#include "pair_reaxc.h"
#include "neigh_list_kokkos.h"
--
GitLab
From 6dd8efd0b479ba3648798765fe1d8a294b3000e4 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Wed, 21 Mar 2018 17:20:45 -0600
Subject: [PATCH 013/332] Add if statements
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 46 +++++--
src/KOKKOS/fix_qeq_reax_kokkos.h | 4 +-
src/KOKKOS/kokkos.h | 13 ++
src/KOKKOS/pair_kokkos.h | 29 +++-
src/KOKKOS/pair_reaxc_kokkos.cpp | 212 ++++++++++++++++++-----------
src/KOKKOS/pair_reaxc_kokkos.h | 35 +++--
6 files changed, 230 insertions(+), 109 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 28838f27b6..be04d305cb 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -249,8 +249,12 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_t.template modify<LMPHostType>();
k_t.template sync<DeviceType>();
- if (neighflag != FULL)
- red_o = Kokkos::Experimental::create_scatter_view<> (d_o); // allocate duplicated memory
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+
+ if (need_dup)
+ dup_o = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated> (d_o); // allocate duplicated memory
+ else
+ ndup_o = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated> (d_o);
// 1st cg solve over b_s, s
cg_solve1();
@@ -258,8 +262,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
// 2nd cg solve over b_t, t
cg_solve2();
- if (neighflag != FULL)
- red_o = decltype(red_o)(); // free duplicated memory
+ if (need_dup)
+ dup_o = decltype(dup_o)(); // free duplicated memory
// calculate_Q();
calculate_q();
@@ -489,7 +493,9 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
- Kokkos::Experimental::contribute(d_o, red_o);
+ if (need_dup)
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec1> (inum, teamsize), *this);
}
@@ -537,10 +543,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- red_o.reset_except(d_o);
+ if (need_dup)
+ dup_o.reset_except(d_o);
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
- Kokkos::Experimental::contribute(d_o, red_o);
+ if (need_dup)
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
@@ -610,10 +619,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse32_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- red_o.reset_except(d_o);
+ if (need_dup)
+ dup_o.reset_except(d_o);
FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
Kokkos::parallel_for(inum,sparse33_functor);
- Kokkos::Experimental::contribute(d_o, red_o);
+ if (need_dup)
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec3> (inum, teamsize), *this);
}
@@ -661,10 +673,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse22_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- red_o.reset_except(d_o);
+ if (need_dup)
+ dup_o.reset_except(d_o);
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
- Kokkos::Experimental::contribute(d_o, red_o);
+ if (need_dup)
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
@@ -777,7 +792,8 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_o = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o);
+ auto a_o = v_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -829,7 +845,8 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_o = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o);
+ auto a_o = v_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
@@ -888,7 +905,8 @@ KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
{
// The q array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- auto a_o = red_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_o = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_o),decltype(ndup_o)>::get(dup_o,ndup_o);
+ auto a_o = v_o.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h
index 27be712ad8..4caacdf8a8 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.h
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.h
@@ -149,6 +149,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
private:
int inum;
int allocated_flag;
+ int need_dup;
typedef Kokkos::DualView<int***,DeviceType> tdual_int_1d;
Kokkos::DualView<params_qeq*,Kokkos::LayoutRight,DeviceType> k_params;
@@ -193,7 +194,8 @@ class FixQEqReaxKokkos : public FixQEqReax {
HAT::t_ffloat_2d h_s_hist, h_t_hist;
typename AT::t_ffloat_2d_randomread r_s_hist, r_t_hist;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType> red_o;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType, Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated> dup_o;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename AT::t_ffloat_1d::array_layout, DeviceType, Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated> ndup_o;
void init_shielding_k();
void init_hist();
diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h
index 7b7848f1f0..6ecb27eb32 100644
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@@ -16,6 +16,7 @@
#include "pointers.h"
#include "kokkos_type.h"
+#include "pair_kokkos.h"
namespace LAMMPS_NS {
@@ -39,6 +40,18 @@ class KokkosLMP : protected Pointers {
~KokkosLMP();
void accelerator(int, char **);
int neigh_count(int);
+
+ template<class DeviceType>
+ int need_dup()
+ {
+ int value = 0;
+
+ if (neighflag == HALFTHREAD)
+ value = NeedDup<HALFTHREAD,DeviceType>::value;
+
+ return value;
+ };
+
private:
static void my_signal_handler(int);
};
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 4f10a4eb2f..1ec5dff0c8 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -95,8 +95,8 @@ struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
// Determine duplication traits for force array
// Use duplication when running threaded and not using atomics
-template<class DeviceType>
-struct DupF {
+template<int NEIGHFLAG, class DeviceType>
+struct NeedDup {
enum {value = Kokkos::Experimental::ScatterNonDuplicated};
};
@@ -104,20 +104,41 @@ struct DupF {
#ifdef KOKKOS_ENABLE_OPENMP
template<>
-struct DupF<Kokkos::OpenMP> {
+struct NeedDup<HALFTHREAD,Kokkos::OpenMP> {
enum {value = Kokkos::Experimental::ScatterDuplicated};
};
#endif
#ifdef KOKKOS_ENABLE_THREADS
template<>
-struct DupF<Kokkos::Threads> {
+struct NeedDup<HALFTHREAD,Kokkos::Threads> {
enum {value = Kokkos::Experimental::ScatterDuplicated};
};
#endif
#endif
+template<int value, typename T1, typename T2>
+class ScatterViewHelper {};
+
+template<typename T1, typename T2>
+class ScatterViewHelper<Kokkos::Experimental::ScatterDuplicated,T1,T2> {
+public:
+ KOKKOS_INLINE_FUNCTION
+ static T1 get(const T1 &dup, const T2 &nondup) {
+ return dup;
+ }
+};
+
+template<typename T1, typename T2>
+class ScatterViewHelper<Kokkos::Experimental::ScatterNonDuplicated,T1,T2> {
+public:
+ KOKKOS_INLINE_FUNCTION
+ static T2 get(const T1 &dup, const T2 &nondup) {
+ return nondup;
+ }
+};
+
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index f34549bc8c..842aeeea43 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -722,10 +722,18 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+
// allocate duplicated memory
- dup_f = Kokkos::Experimental::create_scatter_view<>(f);
- dup_eatom = Kokkos::Experimental::create_scatter_view<>(v_eatom);
- dup_vatom = Kokkos::Experimental::create_scatter_view<>(v_vatom);
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
if (eflag_global) {
for (int i = 0; i < 14; i++)
@@ -797,9 +805,13 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// allocate duplicated memory
- dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
-
+ if (need_dup) {
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_total_bo);
+ } else {
+ ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_dDeltap_self);
+ ndup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_total_bo);
+ }
// Neighbor lists for bond and hbond
// try, resize if necessary
@@ -840,19 +852,32 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
resize = resize_bo || resize_hb;
if (resize) {
allocate_array();
- dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<>(d_dDeltap_self);
- dup_total_bo = Kokkos::Experimental::create_scatter_view<>(d_total_bo);
+ if (need_dup) {
+ dup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_dDeltap_self);
+ dup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_total_bo);
+ } else {
+ ndup_dDeltap_self = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_dDeltap_self);
+ ndup_total_bo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_total_bo);
+ }
}
}
// allocate duplicated memory
- dup_CdDelta = Kokkos::Experimental::create_scatter_view<>(d_CdDelta);
- //dup_Cdbo = Kokkos::Experimental::create_scatter_view<>(d_Cdbo);
- //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi);
- //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<>(d_Cdbopi2);
+ if (need_dup) {
+ dup_CdDelta = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_CdDelta);
+ //dup_Cdbo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbo);
+ //dup_Cdbopi = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbopi);
+ //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_Cdbopi2);
+ } else {
+ ndup_CdDelta = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_CdDelta);
+ //ndup_Cdbo = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_Cdbo);
+ //ndup_Cdbopi = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_Cdbopi);
+ //ndup_Cdbopi2 = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_Cdbopi2);
+ }
// reduction over duplicated memory
- Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
// Bond order
if (neighflag == HALF) {
@@ -958,24 +983,28 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all.evdwl += ev.ereax[8];
// reduction over duplicated memory
- Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
- Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
-
- //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
- //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
- //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
- //dup_Cdbo.reset_except(d_Cdbo);
- //dup_Cdbopi.reset_except(d_Cdbopi);
- //dup_Cdbopi2.reset_except(d_Cdbopi2);
+ if (need_dup) {
+ Kokkos::Experimental::contribute(d_dDeltap_self, dup_dDeltap_self); // needed in ComputeBond2
+ Kokkos::Experimental::contribute(d_CdDelta, dup_CdDelta); // needed in ComputeBond2
+
+ //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in UpdateBond, but also used in UpdateBond
+ //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in UpdateBond, but also used in UpdateBond
+ //dup_Cdbo.reset_except(d_Cdbo);
+ //dup_Cdbopi.reset_except(d_Cdbopi);
+ //dup_Cdbopi2.reset_except(d_Cdbopi2);
+ }
// Bond force
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALF> >(0,ignum),*this);
// reduction over duplicated memory
- //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //if (need_dup) {
+ // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //}
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALF,1> >(0,ignum),*this,ev);
@@ -987,9 +1016,11 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxUpdateBond<HALFTHREAD> >(0,ignum),*this);
// reduction over duplicated memory
- //Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
- //Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
- //Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //if (need_dup) {
+ // Kokkos::Experimental::contribute(d_Cdbo, dup_Cdbo); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi, dup_Cdbopi); // needed in ComputeBond2
+ // Kokkos::Experimental::contribute(d_Cdbopi2, dup_Cdbopi2); // needed in ComputeBond2
+ //}
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeBond2<HALFTHREAD,1> >(0,ignum),*this,ev);
@@ -1000,7 +1031,8 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
// reduction over duplicated memory
- Kokkos::Experimental::contribute(f, dup_f);
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
if (eflag_global) {
eng_vdwl += ev_all.evdwl;
@@ -1018,13 +1050,15 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
- Kokkos::Experimental::contribute(v_eatom, dup_eatom);
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
- Kokkos::Experimental::contribute(v_vatom, dup_vatom);
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -1033,15 +1067,17 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
FindBondSpecies();
// free duplicated memory
- dup_f = decltype(dup_f)();
- dup_dDeltap_self = decltype(dup_dDeltap_self)();
- dup_total_bo = decltype(dup_total_bo)();
- dup_CdDelta = decltype(dup_CdDelta)();
- //dup_Cdbo = decltype(dup_Cdbo)();
- //dup_Cdbopi = decltype(dup_Cdbopi)();
- //dup_Cdbopi2 = decltype(dup_Cdbopi2)();
- dup_eatom = decltype(dup_eatom)();
- dup_vatom = decltype(dup_vatom)();
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_dDeltap_self = decltype(dup_dDeltap_self)();
+ dup_total_bo = decltype(dup_total_bo)();
+ dup_CdDelta = decltype(dup_CdDelta)();
+ //dup_Cdbo = decltype(dup_Cdbo)();
+ //dup_Cdbopi = decltype(dup_Cdbopi)();
+ //dup_Cdbopi2 = decltype(dup_Cdbopi2)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
copymode = 0;
}
@@ -1084,7 +1120,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT powr_vdw, powgi_vdw, fn13, dfn13, exp1, exp2, etmp;
F_FLOAT evdwl, fvdwl;
@@ -1244,7 +1281,8 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
// The f array is atomic for Half/Thread neighbor style
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -1444,18 +1482,18 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxZero, const int &n) const {
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxZeroEAtom, const int &i) const {
- v_eatom(i) = 0.0;
+ d_eatom(i) = 0.0;
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxZeroVAtom, const int &i) const {
- v_vatom(i,0) = 0.0;
- v_vatom(i,1) = 0.0;
- v_vatom(i,2) = 0.0;
- v_vatom(i,3) = 0.0;
- v_vatom(i,4) = 0.0;
- v_vatom(i,5) = 0.0;
+ d_vatom(i,0) = 0.0;
+ d_vatom(i,1) = 0.0;
+ d_vatom(i,2) = 0.0;
+ d_vatom(i,3) = 0.0;
+ d_vatom(i,4) = 0.0;
+ d_vatom(i,5) = 0.0;
}
/* ---------------------------------------------------------------------- */
@@ -1626,9 +1664,11 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
return;
//Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
+ auto v_dDeltap_self = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_dDeltap_self),decltype(ndup_dDeltap_self)>::get(dup_dDeltap_self,ndup_dDeltap_self);
+ auto a_dDeltap_self = v_dDeltap_self.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
- auto a_dDeltap_self = dup_dDeltap_self.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- auto a_total_bo = dup_total_bo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_total_bo = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_total_bo),decltype(ndup_total_bo)>::get(dup_total_bo,ndup_total_bo);
+ auto a_total_bo = v_total_bo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -2320,7 +2360,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
+ auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2472,12 +2513,13 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
//auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
-
+ //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
+ auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const int itype = type(i);
@@ -2785,10 +2827,12 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
//Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+ auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
+ auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
//auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
// in reaxc_torsion_angles: j = i, k = j, i = k;
@@ -3160,7 +3204,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
int hblist[MAX_BONDS];
F_FLOAT theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
@@ -3360,9 +3405,12 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
//Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- auto a_CdDelta = dup_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
+ auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
F_FLOAT delij[3];
F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3500,7 +3548,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
//Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
- auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT delij[3], delik[3], deljk[3], tmpvec[3];
F_FLOAT dBOp_i[3], dBOp_k[3], dln_BOp_pi[3], dln_BOp_pi2[3];
@@ -3713,10 +3762,12 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
const int VFLAG = vflag_either;
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
@@ -3782,8 +3833,9 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const
// The eatom array is atomic for Half/Thread neighbor style
if (eflag_atom) {
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const E_FLOAT epairhalf = 0.5 * epair;
a_eatom[i] += epairhalf;
@@ -3800,8 +3852,9 @@ void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i
const F_FLOAT &epair) const
{
// The eatom array is atomic for Half/Thread neighbor style
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = v_eatom;
- auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_eatom[i] += epair;
}
@@ -3834,8 +3887,9 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i,
}
if (vflag_atom) {
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
@@ -3852,8 +3906,9 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons
{
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT v[6];
@@ -3913,8 +3968,9 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
}
if (vflag_atom) {
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = v_vatom;
- auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
a_vatom(i,0) += 0.25 * v[0]; a_vatom(i,1) += 0.25 * v[1]; a_vatom(i,2) += 0.25 * v[2];
a_vatom(i,3) += 0.25 * v[3]; a_vatom(i,4) += 0.25 * v[4]; a_vatom(i,5) += 0.25 * v[5];
@@ -4012,13 +4068,13 @@ void PairReaxCKokkos<DeviceType>::ev_setup(int eflag, int vflag)
maxeatom = atom->nmax;
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
- v_eatom = k_eatom.view<DeviceType>();
+ d_eatom = k_eatom.view<DeviceType>();
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
- v_vatom = k_vatom.view<DeviceType>();
+ d_vatom = k_vatom.view<DeviceType>();
}
// zero accumulators
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index f341da84c4..aefa63a03d 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -391,11 +391,10 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_tagint_1d_randomread molecule;
DAT::tdual_efloat_1d k_eatom;
- typename AT::t_efloat_1d v_eatom;
+ typename AT::t_efloat_1d d_eatom;
DAT::tdual_virial_array k_vatom;
- typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
- typename AT::t_virial_array v_vatom;
+ typename AT::t_virial_array d_vatom;
HAT::t_virial_array h_vatom;
DAT::tdual_float_1d k_tap;
@@ -412,15 +411,27 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_C1dbopi2, d_C2dbopi2, d_C3dbopi2, d_C4dbopi2;
typename AT::t_ffloat_2d_dl d_Cdbo, d_Cdbopi, d_Cdbopi2, d_dDeltap_self;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_total_bo;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_CdDelta;
- Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_eatom;
- Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_f;
- Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_vatom;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_dDeltap_self;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbo;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbopi;
- Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,DupF<DeviceType>::value> dup_Cdbopi2;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_total_bo;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_CdDelta;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_dDeltap_self;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_Cdbo;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_Cdbopi;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_Cdbopi2;
+
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_total_bo;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_CdDelta;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_dDeltap_self;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_Cdbo;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_Cdbopi;
+ Kokkos::Experimental::ScatterView<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_Cdbopi2;
+
+ int need_dup;
typedef Kokkos::DualView<F_FLOAT**[7],typename DeviceType::array_layout,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
--
GitLab
From 2dcee75ae4deb58117cddcc65adbd1091fd544c4 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 22 Mar 2018 10:01:50 -0600
Subject: [PATCH 014/332] Add data duplication to pair_kokkos.h
---
src/KOKKOS/kokkos_type.h | 31 +++++-
src/KOKKOS/pair_kokkos.h | 197 ++++++++++++++-------------------------
2 files changed, 99 insertions(+), 129 deletions(-)
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index de0dab8eb1..c870bac31c 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -221,6 +221,7 @@ struct AtomicF<HALFTHREAD> {
enum {value = Kokkos::Atomic|Kokkos::Unmanaged};
};
+
// Determine memory traits for force array
// Do atomic trait when running HALFTHREAD neighbor list style with CUDA
template<int NEIGHFLAG, class DeviceType>
@@ -256,8 +257,8 @@ struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
// Determine duplication traits for force array
// Use duplication when running threaded and not using atomics
-template<class DeviceType>
-struct DupF {
+template<int NEIGHFLAG, class DeviceType>
+struct NeedDup {
enum {value = Kokkos::Experimental::ScatterNonDuplicated};
};
@@ -265,20 +266,42 @@ struct DupF {
#ifdef KOKKOS_ENABLE_OPENMP
template<>
-struct DupF<Kokkos::OpenMP> {
+struct NeedDup<HALFTHREAD,Kokkos::OpenMP> {
enum {value = Kokkos::Experimental::ScatterDuplicated};
};
#endif
#ifdef KOKKOS_ENABLE_THREADS
template<>
-struct DupF<Kokkos::Threads> {
+struct NeedDup<HALFTHREAD,Kokkos::Threads> {
enum {value = Kokkos::Experimental::ScatterDuplicated};
};
#endif
#endif
+template<int value, typename T1, typename T2>
+class ScatterViewHelper {};
+
+template<typename T1, typename T2>
+class ScatterViewHelper<Kokkos::Experimental::ScatterDuplicated,T1,T2> {
+public:
+ KOKKOS_INLINE_FUNCTION
+ static T1 get(const T1 &dup, const T2 &nondup) {
+ return dup;
+ }
+};
+
+template<typename T1, typename T2>
+class ScatterViewHelper<Kokkos::Experimental::ScatterNonDuplicated,T1,T2> {
+public:
+ KOKKOS_INLINE_FUNCTION
+ static T2 get(const T1 &dup, const T2 &nondup) {
+ return nondup;
+ }
+};
+
+
// define precision
// handle global precision, force, energy, positions, kspace separately
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 1ec5dff0c8..ab616d2c07 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -48,125 +48,48 @@ struct DoCoul<1> {
typedef CoulTag type;
};
-// Determine memory traits for force array
-// Do atomic trait when running HALFTHREAD neighbor list style
-template<int NEIGHFLAG>
-struct AtomicF {
- enum {value = Kokkos::Unmanaged};
-};
-
-template<>
-struct AtomicF<HALFTHREAD> {
- enum {value = Kokkos::Atomic|Kokkos::Unmanaged};
-};
-
-// Determine memory traits for force array
-// Do atomic trait when running HALFTHREAD neighbor list style with CUDA
-template<int NEIGHFLAG, class DeviceType>
-struct AtomicDup {
- enum {value = Kokkos::Experimental::ScatterNonAtomic};
-};
-
-#ifdef KOKKOS_ENABLE_CUDA
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::Cuda> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#ifdef LMP_KOKKOS_USE_ATOMICS
-
-#ifdef KOKKOS_ENABLE_OPENMP
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::OpenMP> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#ifdef KOKKOS_ENABLE_THREADS
-template<>
-struct AtomicDup<HALFTHREAD,Kokkos::Threads> {
- enum {value = Kokkos::Experimental::ScatterAtomic};
-};
-#endif
-
-#endif
-
-
-// Determine duplication traits for force array
-// Use duplication when running threaded and not using atomics
-template<int NEIGHFLAG, class DeviceType>
-struct NeedDup {
- enum {value = Kokkos::Experimental::ScatterNonDuplicated};
-};
-
-#ifndef LMP_KOKKOS_USE_ATOMICS
-
-#ifdef KOKKOS_ENABLE_OPENMP
-template<>
-struct NeedDup<HALFTHREAD,Kokkos::OpenMP> {
- enum {value = Kokkos::Experimental::ScatterDuplicated};
-};
-#endif
-
-#ifdef KOKKOS_ENABLE_THREADS
-template<>
-struct NeedDup<HALFTHREAD,Kokkos::Threads> {
- enum {value = Kokkos::Experimental::ScatterDuplicated};
-};
-#endif
-
-#endif
-
-template<int value, typename T1, typename T2>
-class ScatterViewHelper {};
-
-template<typename T1, typename T2>
-class ScatterViewHelper<Kokkos::Experimental::ScatterDuplicated,T1,T2> {
-public:
- KOKKOS_INLINE_FUNCTION
- static T1 get(const T1 &dup, const T2 &nondup) {
- return dup;
- }
-};
-
-template<typename T1, typename T2>
-class ScatterViewHelper<Kokkos::Experimental::ScatterNonDuplicated,T1,T2> {
-public:
- KOKKOS_INLINE_FUNCTION
- static T2 get(const T1 &dup, const T2 &nondup) {
- return nondup;
- }
-};
-
//Specialisation for Neighborlist types Half, HalfThread, Full
template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
struct PairComputeFunctor {
typedef typename PairStyle::device_type device_type ;
+ typedef ArrayTypes<device_type> AT;
// Reduction type, contains evdwl, ecoul and virial[6]
typedef EV_FLOAT value_type;
// The copy of the pair style
PairStyle c;
+ typename AT::t_f_array f;
+ typename AT::t_efloat_1d d_eatom;
+ typename AT::t_virial_array d_vatom;
// The force array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,
- device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > f;
+ //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,
+ // device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,device_type,Kokkos::Experimental::ScatterSum,NeedDup<NEIGHFLAG,device_type>::value > dup_f;
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,
- device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > eatom;
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,
- device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > vatom;
+ //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,
+ // device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > eatom;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,device_type,Kokkos::Experimental::ScatterSum,NeedDup<NEIGHFLAG,device_type>::value > dup_eatom;
+
+ //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,
+ // device_type,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,device_type,Kokkos::Experimental::ScatterSum,NeedDup<NEIGHFLAG,device_type>::value > dup_vatom;
+
+
NeighListKokkos<device_type> list;
PairComputeFunctor(PairStyle* c_ptr,
NeighListKokkos<device_type>* list_ptr):
- c(*c_ptr),f(c.f),eatom(c.d_eatom),
- vatom(c.d_vatom),list(*list_ptr) {};
+ c(*c_ptr),list(*list_ptr) {
+ // allocate duplicated memory
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.d_vatom);
+ };
// Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;};
@@ -175,12 +98,25 @@ struct PairComputeFunctor {
return j >> SBBITS & 3;
}
+ void contribute() {
+ Kokkos::Experimental::contribute(c.f, dup_f);
+
+ if (c.eflag_atom)
+ Kokkos::Experimental::contribute(c.d_eatom, dup_eatom);
+
+ if (c.vflag_atom)
+ Kokkos::Experimental::contribute(c.d_vatom, dup_vatom);
+ }
+
// Loop over neighbors of one atom without coulomb interaction
// This function is called in parallel
template<int EVFLAG, int NEWTON_PAIR>
KOKKOS_FUNCTION
EV_FLOAT compute_item(const int& ii,
const NeighListKokkos<device_type> &list, const NoCoulTag&) const {
+
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,device_type>::value>();
+
EV_FLOAT ev;
const int i = list.d_ilist[ii];
const X_FLOAT xtmp = c.x(i,0);
@@ -214,9 +150,9 @@ struct PairComputeFunctor {
fztmp += delz*fpair;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) {
- f(j,0) -= delx*fpair;
- f(j,1) -= dely*fpair;
- f(j,2) -= delz*fpair;
+ a_f(j,0) -= delx*fpair;
+ a_f(j,1) -= dely*fpair;
+ a_f(j,2) -= delz*fpair;
}
if (EVFLAG) {
@@ -232,9 +168,9 @@ struct PairComputeFunctor {
}
- f(i,0) += fxtmp;
- f(i,1) += fytmp;
- f(i,2) += fztmp;
+ a_f(i,0) += fxtmp;
+ a_f(i,1) += fytmp;
+ a_f(i,2) += fztmp;
return ev;
}
@@ -245,6 +181,9 @@ struct PairComputeFunctor {
KOKKOS_FUNCTION
EV_FLOAT compute_item(const int& ii,
const NeighListKokkos<device_type> &list, const CoulTag& ) const {
+
+ auto a_f = dup_f.template access<AtomicDup<NEIGHFLAG,device_type>::value>();
+
EV_FLOAT ev;
const int i = list.d_ilist[ii];
const X_FLOAT xtmp = c.x(i,0);
@@ -285,9 +224,9 @@ struct PairComputeFunctor {
fztmp += delz*fpair;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) {
- f(j,0) -= delx*fpair;
- f(j,1) -= dely*fpair;
- f(j,2) -= delz*fpair;
+ a_f(j,0) -= delx*fpair;
+ a_f(j,1) -= dely*fpair;
+ a_f(j,2) -= delz*fpair;
}
if (EVFLAG) {
@@ -309,9 +248,9 @@ struct PairComputeFunctor {
}
}
- f(i,0) += fxtmp;
- f(i,1) += fytmp;
- f(i,2) += fztmp;
+ a_f(i,0) += fxtmp;
+ a_f(i,1) += fytmp;
+ a_f(i,2) += fztmp;
return ev;
}
@@ -321,6 +260,9 @@ struct PairComputeFunctor {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const
{
+ auto a_eatom = dup_eatom.template access<AtomicDup<NEIGHFLAG,device_type>::value>();
+ auto a_vatom = dup_vatom.template access<AtomicDup<NEIGHFLAG,device_type>::value>();
+
const int EFLAG = c.eflag;
const int NEWTON_PAIR = c.newton_pair;
const int VFLAG = c.vflag_either;
@@ -328,8 +270,8 @@ struct PairComputeFunctor {
if (EFLAG) {
if (c.eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
- if (NEWTON_PAIR || i < c.nlocal) eatom[i] += epairhalf;
- if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) eatom[j] += epairhalf;
+ if (NEWTON_PAIR || i < c.nlocal) a_eatom[i] += epairhalf;
+ if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) a_eatom[j] += epairhalf;
}
}
@@ -380,20 +322,20 @@ struct PairComputeFunctor {
if (c.vflag_atom) {
if (NEWTON_PAIR || i < c.nlocal) {
- vatom(i,0) += 0.5*v0;
- vatom(i,1) += 0.5*v1;
- vatom(i,2) += 0.5*v2;
- vatom(i,3) += 0.5*v3;
- vatom(i,4) += 0.5*v4;
- vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
if ((NEWTON_PAIR || j < c.nlocal) && NEIGHFLAG != FULL) {
- vatom(j,0) += 0.5*v0;
- vatom(j,1) += 0.5*v1;
- vatom(j,2) += 0.5*v2;
- vatom(j,3) += 0.5*v3;
- vatom(j,4) += 0.5*v4;
- vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
}
@@ -432,6 +374,9 @@ struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
return j >> SBBITS & 3;
}
+
+ void contribute() {}
+
template<int EVFLAG, int NEWTON_PAIR>
KOKKOS_FUNCTION
EV_FLOAT compute_item(const int& ii,
@@ -570,10 +515,12 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename Kokkos::Impl::enable
PairComputeFunctor<PairStyle,NEIGHFLAG,false,Specialisation > ff(fpair,list);
if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
else Kokkos::parallel_for(list->inum,ff);
+ ff.contribute();
} else {
PairComputeFunctor<PairStyle,NEIGHFLAG,true,Specialisation > ff(fpair,list);
if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
else Kokkos::parallel_for(list->inum,ff);
+ ff.contribute();
}
return ev;
}
--
GitLab
From 28b894a1d76ce7b4038d2a8bd0e4d00aa3cbb40e Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 22 Mar 2018 12:09:04 -0600
Subject: [PATCH 015/332] Remove unnecessary semicolon
---
src/KOKKOS/kokkos.h | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h
index 6ecb27eb32..c955bec600 100644
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@@ -50,7 +50,7 @@ class KokkosLMP : protected Pointers {
value = NeedDup<HALFTHREAD,DeviceType>::value;
return value;
- };
+ }
private:
static void my_signal_handler(int);
--
GitLab
From 385e1e5adf38668ddb4077a42eec22ada11576b7 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Thu, 22 Mar 2018 12:28:21 -0600
Subject: [PATCH 016/332] Fix compile error with CUDA
---
src/KOKKOS/kokkos_type.h | 2 +-
src/KOKKOS/neigh_list_kokkos.h | 2 --
2 files changed, 1 insertion(+), 3 deletions(-)
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index 21430455ba..665e53ac34 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -22,7 +22,7 @@
#include <Kokkos_Vectorization.hpp>
#include <Kokkos_ScatterView.hpp>
-enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in neigh_list_kokkos.h
+enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u};
#if defined(KOKKOS_HAVE_CXX11)
#undef ISFINITE
diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h
index 993543157b..585422c54f 100644
--- a/src/KOKKOS/neigh_list_kokkos.h
+++ b/src/KOKKOS/neigh_list_kokkos.h
@@ -20,8 +20,6 @@
namespace LAMMPS_NS {
-enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; // same as in kokkos_type.h
-
class AtomNeighbors
{
public:
--
GitLab
From 52254fe155e7cd5e4678c0b729305ba12850c8b4 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 2 Apr 2018 12:10:30 -0600
Subject: [PATCH 017/332] Fix issue in fix_qeq_reax_kokkos
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 36 +++++++++++++++++++++++-------
1 file changed, 28 insertions(+), 8 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 4d2ff8b1e5..b9fd49dd4e 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -487,8 +487,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse12_functor);
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
- FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
- Kokkos::parallel_for(inum,sparse13_functor);
+ if (neighflag == HALF) {
+ FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
+ Kokkos::parallel_for(inum,sparse13_functor);
+ } else if (neighflag == HALFTHREAD) {
+ FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
+ Kokkos::parallel_for(inum,sparse13_functor);
+ }
if (need_dup)
if (need_dup)
Kokkos::Experimental::contribute(d_o, dup_o);
@@ -541,8 +546,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
if (need_dup)
dup_o.reset_except(d_o);
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
+ if (neighflag == HALF) {
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ } else if (neighflag == HALFTHREAD) {
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ }
if (need_dup)
if (need_dup)
Kokkos::Experimental::contribute(d_o, dup_o);
@@ -616,8 +626,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
if (need_dup)
dup_o.reset_except(d_o);
- FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
- Kokkos::parallel_for(inum,sparse33_functor);
+ if (neighflag == HALF) {
+ FixQEqReaxKokkosSparse33Functor<DeviceType,HALF> sparse33_functor(this);
+ Kokkos::parallel_for(inum,sparse33_functor);
+ } else if (neighflag == HALFTHREAD) {
+ FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
+ Kokkos::parallel_for(inum,sparse33_functor);
+ }
if (need_dup)
if (need_dup)
Kokkos::Experimental::contribute(d_o, dup_o);
@@ -670,8 +685,13 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
if (need_dup)
dup_o.reset_except(d_o);
- FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
- Kokkos::parallel_for(inum,sparse23_functor);
+ if (neighflag == HALF) {
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ } else if (neighflag == HALFTHREAD) {
+ FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
+ Kokkos::parallel_for(inum,sparse23_functor);
+ }
if (need_dup)
if (need_dup)
Kokkos::Experimental::contribute(d_o, dup_o);
--
GitLab
From 7260bb58e18f968d0f4aae9a0a668b591cbc82a1 Mon Sep 17 00:00:00 2001
From: Sergey Lishchuk <svl@debian>
Date: Wed, 4 Jul 2018 11:03:30 +0100
Subject: [PATCH 018/332] Added Axilrod-Teller manybody potential
---
doc/src/Eqs/pair_atm.jpg | Bin 0 -> 5474 bytes
doc/src/Eqs/pair_atm.tex | 9 ++
doc/src/pair_atm.txt | 85 ++++++++++
examples/in.atm | 29 ++++
src/MANYBODY/pair_atm.cpp | 317 ++++++++++++++++++++++++++++++++++++++
src/MANYBODY/pair_atm.h | 76 +++++++++
6 files changed, 516 insertions(+)
create mode 100644 doc/src/Eqs/pair_atm.jpg
create mode 100644 doc/src/Eqs/pair_atm.tex
create mode 100644 doc/src/pair_atm.txt
create mode 100644 examples/in.atm
create mode 100644 src/MANYBODY/pair_atm.cpp
create mode 100644 src/MANYBODY/pair_atm.h
diff --git a/doc/src/Eqs/pair_atm.jpg b/doc/src/Eqs/pair_atm.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..d2e6d704e930c2def4801301c928998f7542f54b
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diff --git a/doc/src/Eqs/pair_atm.tex b/doc/src/Eqs/pair_atm.tex
new file mode 100644
index 0000000000..0e05370faf
--- /dev/null
+++ b/doc/src/Eqs/pair_atm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
+\end{equation}
+
+\end{document}
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
new file mode 100644
index 0000000000..48260c161a
--- /dev/null
+++ b/doc/src/pair_atm.txt
@@ -0,0 +1,85 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style atm command :h3
+
+[Syntax:]
+
+pair_style atm args = cutoff :pre
+
+[Examples:]
+
+pair_style 2.5
+pair_coeff * * * 0.072 :pre
+
+pair_style hybrid/overlay lj/cut 6.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072 :pre
+
+[Description:]
+
+The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod
+potential for the energy E of a system of atoms as
+
+:c,image(Eqs/pair_atm.jpg)
+
+where r12, r23 and r31 are the distances between the atoms,
+gamma1 is included by the sides r12 and r31
+with similar definitions for gamma2 and gamma3,
+nu is the three-body interaction strength (energy times distance^9 units).
+
+The {atm} is typically used in compination with some two-body potential
+using "hybrid/overlay"_pair_hybrid.html style as in an example above.
+
+The calculations are not undertaken if the distances between atoms satisfy
+r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
+tolerance tol is not used.
+
+The Axilrod-Teller-Muto potential file must contain entries for all the
+elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. 1 1 1). For a two-element simulation, the file must contain 4
+entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
+specify ATM parameters for all combinations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 10
+entries would be required, etc.
+
+:line
+
+[Shift, table, tail correction, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package. See
+the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Axilrod)
+[(Axilrod)]
+Axilrod and Teller, J Chem Phys, 11, 299 (1943);
+Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
diff --git a/examples/in.atm b/examples/in.atm
new file mode 100644
index 0000000000..0f3760baf9
--- /dev/null
+++ b/examples/in.atm
@@ -0,0 +1,29 @@
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable yy equal 10*$y
+variable zz equal 10*$z
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box 1 box
+create_atoms 1 box
+
+pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 1
+
+run 50
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
new file mode 100644
index 0000000000..0286c3ed1e
--- /dev/null
+++ b/src/MANYBODY/pair_atm.cpp
@@ -0,0 +1,317 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Sergey Lishchuk
+------------------------------------------------------------------------- */
+
+#include "pair_atm.h"
+
+#include <math.h>
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_atm_package[] =
+ "ATM package:\n\n"
+ "@Article{Lishchuk:2012:164501,\n"
+ " author = {S. V. Lishchuk},\n"
+ " title = {Role of three-body interactions in formation of bulk viscosity in liquid argon},\n"
+ " journal = {J.~Chem.~Phys.},\n"
+ " year = 2012,\n"
+ " volume = 136,\n"
+ " pages = {164501}\n"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_atm_package);
+
+ single_enable = 0;
+ restartinfo = 0;
+ one_coeff = 1;
+ manybody_flag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairATM::~PairATM()
+{
+ if (copymode) return;
+ if (allocated) {
+ memory->destroy(nu);
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ workhorse routine that computes pairwise interactions
+------------------------------------------------------------------------- */
+
+void PairATM::compute(int eflag, int vflag)
+{
+ int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
+ double xi,yi,zi,evdwl;
+ double rij2,rik2,rjk2,r6;
+ double rij[3],rik[3],rjk[3],fj[3],fk[3];
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xi = x[i][0];
+ yi = x[i][1];
+ zi = x[i][2];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ jnumm1 = jnum - 1;
+
+ for (jj = 0; jj < jnumm1; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ rij[0] = x[j][0] - xi;
+ rij[1] = x[j][1] - yi;
+ rij[2] = x[j][2] - zi;
+ rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+
+ for (kk = jj+1; kk < jnum; kk++) {
+ k = jlist[kk];
+ k &= NEIGHMASK;
+
+ rik[0] = x[k][0] - xi;
+ rik[1] = x[k][1] - yi;
+ rik[2] = x[k][2] - zi;
+ rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
+
+ rjk[0] = x[k][0] - x[j][0];
+ rjk[1] = x[k][1] - x[j][1];
+ rjk[2] = x[k][2] - x[j][2];
+ rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+
+ r6 = rij2*rik2*rjk2;
+ if (r6 > cut_sixth) continue;
+
+ interaction_ddd(nu[type[i]][type[j]][type[k]],
+ r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+
+ f[i][0] -= fj[0] + fk[0];
+ f[i][1] -= fj[1] + fk[1];
+ f[i][2] -= fj[2] + fk[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,rij,rik);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ reads the input script line with arguments you define
+------------------------------------------------------------------------- */
+
+void PairATM::settings(int narg, char **arg)
+{
+ if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+ cut_global = force->numeric(FLERR,arg[0]);
+}
+
+/* ----------------------------------------------------------------------
+ set coefficients for one i,j,k type triplet
+------------------------------------------------------------------------- */
+
+void PairATM::coeff(int narg, char **arg)
+{
+ if (narg != 4)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi,klo,khi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+ force->bounds(FLERR,arg[2],atom->ntypes,klo,khi);
+
+ double nu_one = force->numeric(FLERR,arg[3]);
+
+ cut_sixth = cut_global*cut_global;
+ cut_sixth = cut_sixth*cut_sixth*cut_sixth;
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j<=jhi; j++) {
+ for (int k = MAX(klo,j); k<=khi; k++) {
+ nu[i][j][k] = nu[i][k][j] =
+ nu[j][i][k] = nu[j][k][i] =
+ nu[k][i][j] = nu[k][j][i] = nu_one;
+ count++;
+ }
+ setflag[i][j] = 1;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairATM::init_style()
+{
+ // need a full neighbor list
+ int irequest = neighbor->request(this,instance_me);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+}
+
+/* ----------------------------------------------------------------------
+ perform initialization for one i,j type pair
+------------------------------------------------------------------------- */
+
+double PairATM::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ return cut_global;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j,k;
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j,k;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) {
+ if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
+ MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart_settings(FILE *fp)
+{
+ fwrite(&cut_global,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart_settings(FILE *fp)
+{
+ int me = comm->me;
+ if (me == 0) fread(&cut_global,sizeof(double),1,fp);
+ MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairATM::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+ memory->create(nu,n+1,n+1,n+1,"pair:a");
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+}
+
+/* ----------------------------------------------------------------------
+ Axilrod-Teller-Muto (dipole-dipole-dipole) potential
+------------------------------------------------------------------------- */
+
+void PairATM::interaction_ddd(double nu,
+ double r6, double rij2, double rik2, double rjk2,
+ double *rij, double *rik, double *rjk,
+ double *fj, double *fk, int eflag, double &eng)
+{
+ double r5inv,rri,rrj,rrk,rrr;
+ r5inv = nu / (r6*r6*sqrt(r6));
+ rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
+ rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
+ rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
+ rrr = 5.0*rri*rrj*rrk;
+ for (int i=0; i<3; i++) {
+ fj[i] = rrj*(rrk - rri)*rik[i]
+ - (rrk*rri - rjk2*rik2 + rrr/rij2)*rij[i]
+ + (rrk*rri - rik2*rij2 + rrr/rjk2)*rjk[i];
+ fj[i] *= 3.0*r5inv;
+ fk[i] = rrk*(rri + rrj)*rij[i]
+ + (rri*rrj + rik2*rij2 - rrr/rjk2)*rjk[i]
+ + (rri*rrj + rij2*rjk2 - rrr/rik2)*rik[i];
+ fk[i] *= 3.0*r5inv;
+ }
+ if (eflag) eng = (r6 - 0.6*rrr)*r5inv;
+}
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
new file mode 100644
index 0000000000..b5bfc64010
--- /dev/null
+++ b/src/MANYBODY/pair_atm.h
@@ -0,0 +1,76 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Sergey Lishchuk
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(atm,PairATM)
+
+#else
+
+#ifndef LMP_PAIR_ATM_H
+#define LMP_PAIR_ATM_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairATM : public Pair {
+ public:
+ PairATM(class LAMMPS *);
+ virtual ~PairATM();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ virtual void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+
+ protected:
+ double cut_global, cut_sixth;
+ double ***nu;
+
+ protected:
+ virtual void allocate();
+ void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal pair_style command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/
--
GitLab
From b259de95d27d1b5828379351a995bfb77aa098b5 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 13:00:52 -0600
Subject: [PATCH 019/332] fix for ScaFaCoS library
---
cmake/CMakeLists.txt | 13 +-
examples/scafacos/data.NaCl | 25 ++
examples/scafacos/in.scafacos | 22 ++
src/SCAFACOS/Install.sh | 67 +++++
src/SCAFACOS/fix_scafacos.cpp | 488 ++++++++++++++++++++++++++++++++++
src/SCAFACOS/fix_scafacos.h | 164 ++++++++++++
6 files changed, 776 insertions(+), 3 deletions(-)
create mode 100644 examples/scafacos/data.NaCl
create mode 100644 examples/scafacos/in.scafacos
create mode 100755 src/SCAFACOS/Install.sh
create mode 100644 src/SCAFACOS/fix_scafacos.cpp
create mode 100644 src/SCAFACOS/fix_scafacos.h
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 8bc079fd85..a335a441da 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -119,7 +119,7 @@ option(ENABLE_ALL "Build all default packages" OFF)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
REAX REPLICA RIGID SHOCK SNAP SRD)
-set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
+set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE SCAFACOS
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -150,11 +150,11 @@ pkg_depends(CORESHELL KSPACE)
######################################################
# packages with special compiler needs or external libs
######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_SCAFACOS)
enable_language(Fortran)
endif()
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_SCAFACOS)
enable_language(C)
endif()
@@ -313,6 +313,13 @@ if(PKG_LATTE)
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
+if(PKG_SCAFACOS)
+ FIND_PACKAGE(PkgConfig)
+ PKG_CHECK_MODULES(SCAFACOS scafacos)
+ include_directories(${SCAFACOS_INCLUDE_DIRS})
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+endif()
+
if(PKG_USER-MOLFILE)
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
diff --git a/examples/scafacos/data.NaCl b/examples/scafacos/data.NaCl
new file mode 100644
index 0000000000..1a599b957d
--- /dev/null
+++ b/examples/scafacos/data.NaCl
@@ -0,0 +1,25 @@
+ LAMMPS Description
+
+ 8 atoms
+
+ 2 atom types
+
+ 0.0000000000000000 2.000000000000000 xlo xhi
+ 0.0000000000000000 2.000000000000000 ylo yhi
+ 0.0000000000000000 2.000000000000000 zlo zhi
+
+ Masses
+
+ 1 22.98976928
+ 2 35.45
+
+ Atoms
+
+ 1 1 1 1.0 0.0 0.0 0.0
+ 2 1 2 -1.0 1.0 0.0 0.0
+ 3 1 2 -1.0 0.0 1.0 0.0
+ 4 1 1 1.0 1.0 1.0 0.0
+ 5 1 2 -1.0 0.0 0.0 1.0
+ 6 1 1 1.0 1.0 0.0 1.0
+ 7 1 1 1.0 0.0 1.0 1.0
+ 8 1 2 -1.0 1.0 1.0 1.0
diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos
new file mode 100644
index 0000000000..a2849583f5
--- /dev/null
+++ b/examples/scafacos/in.scafacos
@@ -0,0 +1,22 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style full
+
+read_data data.NaCl
+
+# need both mass settings due to hybrid atom style
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all scafacos fmm
+
+timestep 0.005
+
+run 100
diff --git a/src/SCAFACOS/Install.sh b/src/SCAFACOS/Install.sh
new file mode 100755
index 0000000000..ace610050b
--- /dev/null
+++ b/src/SCAFACOS/Install.sh
@@ -0,0 +1,67 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+ if (test $mode = 0) then
+ rm -f ../$1
+ elif (! cmp -s $1 ../$1) then
+ if (test -z "$2" || test -e ../$2) then
+ cp $1 ..
+ if (test $mode = 2) then
+ echo " updating src/$1"
+ fi
+ fi
+ elif (test -n "$2") then
+ if (test ! -e ../$2) then
+ rm -f ../$1
+ fi
+ fi
+}
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+ test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package
+ #sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
+ # multiline form needed for BSD sed on Macs
+ sed -i -e '4 i \
+include ..\/..\/lib\/scafacos\/Makefile.lammps
+' ../Makefile.package.settings
+ fi
+
+elif (test $1 = 0) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
+ fi
+
+fi
diff --git a/src/SCAFACOS/fix_scafacos.cpp b/src/SCAFACOS/fix_scafacos.cpp
new file mode 100644
index 0000000000..f888747047
--- /dev/null
+++ b/src/SCAFACOS/fix_scafacos.cpp
@@ -0,0 +1,488 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Rene Halver (JSC)
+------------------------------------------------------------------------- */
+
+#include <cstdio>
+#include <cstring>
+#include "fix_scafacos.h"
+#include "atom.h"
+#include "comm.h"
+#include "update.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "force.h"
+#include "pair.h"
+#include "modify.h"
+#include "compute.h"
+#include "memory.h"
+#include "error.h"
+
+// ScaFaCoS library
+#include <iostream>
+#include <sstream>
+#include <string>
+#include "fcs.h"
+#include "universe.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+#define INVOKED_PERATOM 8
+
+/* ---------------------------------------------------------------------- */
+
+FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ // form of fix string:
+ // fix <#> <group> scafacos <method> [ tolerance <type> <value> ]
+
+
+ if (narg < 4) error->all(FLERR,"Illegal fix scafacos command");
+
+ // read method from fix input
+ method = arg[3];
+ // check if fmm method was chosen
+ fmm_chosen = !strcmp(method.c_str(),"fmm");
+
+ int arg_index = 4;
+
+ tolerance_set = false;
+
+ while(arg_index < narg)
+ {
+ // check if tolerance option is set
+ if (strcmp(arg[arg_index],"tolerance") == 0)
+ {
+ tolerance_set = true;
+ ++arg_index;
+ if (strcmp(arg[arg_index],"energy") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ else if (strcmp(arg[arg_index],"energy_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
+ else if (strcmp(arg[arg_index],"field") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ else if (strcmp(arg[arg_index],"field_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
+ else if (strcmp(arg[arg_index],"potential") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
+ else if (strcmp(arg[arg_index],"potential_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
+ else
+ error->all(FLERR,"Illegal fix scafacos command");
+ ++arg_index;
+ tolerance_value = atof(arg[arg_index]);
+ ++arg_index;
+ }
+ else
+ error->all(FLERR,"Illegal fix scafacos command");
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixScafacos::~FixScafacos()
+{
+ memory->destroy(pot);
+ memory->destroy(field);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixScafacos::setmask()
+{
+ int mask = 0;
+ //mask |= INITIAL_INTEGRATE;
+ //mask |= FINAL_INTEGRATE;
+ mask |= PRE_REVERSE;
+ mask |= POST_FORCE;
+ mask |= MIN_POST_FORCE;
+ mask |= THERMO_ENERGY;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::init()
+{
+ // error checks
+
+ if (domain->dimension == 2)
+ error->all(FLERR,"Fix scafacos requires 3d problem");
+
+ rank = comm->me;
+
+ int nlocal = 0;
+ int proc_grid[3] = {comm->procgrid[0], comm->procgrid[1], comm->procgrid[2]};
+ int myloc[3] = {comm->myloc[0], comm->myloc[1], comm->myloc[2]};
+
+ // call ScaFaCoS init
+ // TODO: check if universe->uworld is a good idea for computations
+ result = fcs_init(&fcs,method.c_str(),universe->uworld);
+ if (!check_result(result, rank)) return;
+
+ setup_handle();
+
+ nlocal = atom -> nlocal;
+ // get particle data
+ x = &atom->x[0][0];
+ q = atom->q;
+
+ if (tolerance_set)
+ {
+ result = fcs_set_tolerance(fcs,tolerance_type,tolerance_value);
+ if (!check_result(result, rank)) return;
+ }
+
+ // print out parameters within handle
+ if (rank == 0) fcs_print_parameters(fcs);
+
+ // call the tuning routine (needs to be redone, if critical system parameters should change)
+ result = fcs_tune(fcs,nlocal,x,q);
+ if (!check_result(result, rank)) return;
+
+ // allocate arrays larger in order to avoid fast reallocation due to fluctuations
+ local_array_size = (int)(1.25 * (double)nlocal);
+
+ // allocate new result arrays
+ memory->create(pot,local_array_size,"scafacos:potential");
+ memory->create(field,local_array_size*3,"scafacos:field");
+
+ // set result vectors to zero
+ for ( int i = 0; i < local_array_size; ++i)
+ {
+ pot[i] = 0.0;
+ field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::init_list(int id, NeighList *ptr)
+{
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::setup(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::min_setup(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::setup_pre_reverse(int eflag, int vflag)
+{
+ pre_reverse(eflag,vflag);
+}
+
+/* ----------------------------------------------------------------------
+ integrate electronic degrees of freedom
+------------------------------------------------------------------------- */
+
+void FixScafacos::initial_integrate(int vflag) {}
+
+/* ----------------------------------------------------------------------
+ store eflag, so can use it in post_force to tally per-atom energies
+------------------------------------------------------------------------- */
+
+void FixScafacos::pre_reverse(int eflag, int vflag)
+{
+ int eflag_caller = eflag;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::post_force(int vflag)
+{
+
+ int nlocal;
+
+ nlocal = atom->nlocal;
+ x = &atom->x[0][0];
+ q = atom->q;
+
+ // check if box has changed since the last call of fcs_tune, if yes, call fcs_tune
+ if (box_has_changed())
+ {
+ setup_handle();
+ // print out parameters within handle
+ if (rank == 0)
+ {
+ std::cout << " updated ScaFaCoS handle: " << std::endl;
+ fcs_print_parameters(fcs);
+ }
+ // call the tuning routine (needs to be redone, if critical system parameters should change)
+ result = fcs_tune(fcs,nlocal,x,q);
+ if (!check_result(result, rank)) return;
+ }
+
+ /*
+ if (fmm_chosen && phantom_particle)
+ for (int i = 0; i < nlocal; ++i)
+ {
+ std::cout << rank << " " << i << " " << x[3*i] << " " << x[3*i+1] << " " << x[3*i+2] << " " << q[i] << std::endl;
+ }
+ */
+
+ // check if arrays for potentials and field are still large enough for the number of particles on process
+ if (nlocal > local_array_size)
+ {
+ // allocate arrays larger in order to avoid fast reallocation due to fluctuations
+ local_array_size = (int)(1.25 * (double)nlocal);
+
+ // destroy old result arrays
+ memory->destroy(pot);
+ memory->destroy(field);
+
+ // allocate result arrays
+ memory->create(pot,local_array_size,"scafacos:potential");
+ memory->create(field,3*local_array_size,"scafacos:field");
+
+ }
+
+ // set result vectors to zero
+ for ( int i = 0; i < nlocal; ++i)
+ {
+ pot[i] = 0.0;
+ field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
+ }
+
+ // compute Coulomb
+ fcs_run(fcs, nlocal, x, q, field, pot);
+ if(!check_result(result,rank)) return;
+
+ double E_coul_loc = 0.0;
+ // no reduction required (?)
+ //double E_coul = 0.0;
+
+ for (int i = 0; i < atom->nlocal; ++i)
+ {
+ //std::cout << atom->f[i][0] << " " << field[3*i] << " " << q[i] << std::endl;
+ atom->f[i][0] += field[3*i] * q[i];
+ atom->f[i][1] += field[3*i+1] * q[i];
+ atom->f[i][2] += field[3*i+2] * q[i];
+ E_coul_loc += 0.5 * q[i] * pot[i];
+ }
+
+ // not required (?)
+ // MPI_ALLREDUCE(&E_coul_loc, &E_coul, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
+
+ force->pair->eng_coul += E_coul_loc;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::min_post_force(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ integrate electronic degrees of freedom
+------------------------------------------------------------------------- */
+
+void FixScafacos::final_integrate() {}
+
+/* ---------------------------------------------------------------------- */
+
+void FixScafacos::reset_dt()
+{
+ //dtv = update->dt;
+ //dtf = 0.5 * update->dt * force->ftm2v;
+}
+
+/* ----------------------------------------------------------------------
+ DFTB energy from LATTE
+------------------------------------------------------------------------- */
+
+double FixScafacos::compute_scalar()
+{
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local arrays
+------------------------------------------------------------------------- */
+
+double FixScafacos::memory_usage()
+{
+ double bytes = 0.0;
+ bytes += local_array_size * sizeof(double);
+ bytes += local_array_size * 3 * sizeof(double);
+ return bytes;
+}
+
+/* ----------------------------------------------------------------------
+ setup of ScaFaCoS handle with common parameters
+------------------------------------------------------------------------- */
+void FixScafacos::setup_handle()
+{
+ // store periodicity
+ periodicity[0] = domain->xperiodic;
+ periodicity[1] = domain->yperiodic;
+ periodicity[2] = domain->zperiodic;
+
+ // store offset of the system
+ offset[0] = domain->boundary[0][0];
+ offset[1] = domain->boundary[1][0];
+ offset[2] = domain->boundary[2][0];
+
+ // calculate box vectors
+ box_x[0] = domain->prd[0];
+ box_x[1] = box_x[2] = 0.0;
+
+ box_y[1] = domain->prd[1];
+ box_y[0] = box_y[2] = 0.0;
+
+ box_z[2] = domain->prd[2];
+ box_z[1] = box_z[0] = 0.0;
+
+ total_particles = atom->natoms;
+
+ // TODO: for now disable short-range calculations within LAMMPS
+ near_field_flag = 0;
+
+ // enter all parameters required to ScaFaCoS handle
+ result = fcs_set_box_a(fcs, box_x);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_box_b(fcs, box_y);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_box_c(fcs, box_z);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_box_origin(fcs, offset);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_periodicity(fcs, periodicity);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_near_field_flag(fcs, near_field_flag);
+ if (!check_result(result, rank)) return;
+
+ result = fcs_set_total_particles(fcs, atom->natoms);
+ if (!check_result(result, rank)) return;
+}
+
+/* ----------------------------------------------------------------------
+ check if box parameters changed, requiring a new call to fcs_tune
+------------------------------------------------------------------------- */
+bool FixScafacos::box_has_changed()
+{
+ bool changed = false;
+
+ double n_periodicity[3];
+ double n_offset[3];
+ double n_box_x[3];
+ double n_box_y[3];
+ double n_box_z[3];
+
+ int n_total_particles;
+
+ // store periodicity
+ n_periodicity[0] = domain->xperiodic;
+ n_periodicity[1] = domain->yperiodic;
+ n_periodicity[2] = domain->zperiodic;
+
+ // store offset of the system
+ n_offset[0] = domain->boundary[0][0];
+ n_offset[1] = domain->boundary[1][0];
+ n_offset[2] = domain->boundary[2][0];
+
+ // calculate box vectors
+ n_box_x[0] = domain->prd[0];
+ n_box_x[1] = n_box_x[2] = 0.0;
+
+ n_box_y[1] = domain->prd[1];
+ n_box_y[0] = n_box_y[2] = 0.0;
+
+ n_box_z[2] = domain->prd[2];
+ n_box_z[1] = n_box_z[0] = 0.0;
+
+ n_total_particles = atom->natoms;
+
+ changed = changed ||
+ ( n_periodicity[0] != periodicity[0] ) ||
+ ( n_periodicity[1] != periodicity[1] ) ||
+ ( n_periodicity[2] != periodicity[2] ) ||
+ ( n_offset[0] != offset[0] ) ||
+ ( n_offset[1] != offset[1] ) ||
+ ( n_offset[2] != offset[2] ) ||
+ ( n_box_x[0] != box_x[0] ) ||
+ ( n_box_x[1] != box_x[1] ) ||
+ ( n_box_x[2] != box_x[2] ) ||
+ ( n_box_y[0] != box_y[0] ) ||
+ ( n_box_y[1] != box_y[1] ) ||
+ ( n_box_y[2] != box_y[2] ) ||
+ ( n_box_z[0] != box_z[0] ) ||
+ ( n_box_z[1] != box_z[1] ) ||
+ ( n_box_z[2] != box_z[2] ) ||
+ ( n_total_particles != total_particles );
+/*
+ if (changed)
+ {
+ std::cout << rank << " " << "n_per_x : per_x" << n_periodicity[0] << " " << periodicity[0] << std::endl;
+ std::cout << rank << " " << "n_per_y : per_y" << n_periodicity[1] << " " << periodicity[1] << std::endl;
+ std::cout << rank << " " << "n_per_z : per_z" << n_periodicity[2] << " " << periodicity[2] << std::endl;
+ std::cout << rank << " " << "n_off_x : off_x" << n_offset[0] << " " << offset[0] << std::endl;
+ std::cout << rank << " " << "n_off_y : off_y" << n_offset[1] << " " << offset[1] << std::endl;
+ std::cout << rank << " " << "n_off_z : off_z" << n_offset[2] << " " << offset[2] << std::endl;
+ std::cout << rank << " " << "n_bx_x : bx_x" << n_box_x[0] << " " << box_x[0] << std::endl;
+ std::cout << rank << " " << "n_bx_y : bx_y" << n_box_x[1] << " " << box_x[1] << std::endl;
+ std::cout << rank << " " << "n_bx_z : bx_z" << n_box_x[2] << " " << box_x[2] << std::endl;
+ std::cout << rank << " " << "n_by_x : by_x" << n_box_y[0] << " " << box_y[0] << std::endl;
+ std::cout << rank << " " << "n_by_y : by_y" << n_box_y[1] << " " << box_y[1] << std::endl;
+ std::cout << rank << " " << "n_by_z : by_z" << n_box_y[2] << " " << box_y[2] << std::endl;
+ std::cout << rank << " " << "n_bz_x : bz_x" << n_box_z[0] << " " << box_z[0] << std::endl;
+ std::cout << rank << " " << "n_bz_y : bz_y" << n_box_z[1] << " " << box_z[1] << std::endl;
+ std::cout << rank << " " << "n_bz_z : bz_z" << n_box_z[2] << " " << box_z[2] << std::endl;
+ std::cout << rank << " " << "n_total : total" << n_total_particles << " " << total_particles << std::endl;
+ }
+*/
+ return changed;
+}
+
+
+
+/* ----------------------------------------------------------------------
+ check of ScaFaCoS result
+------------------------------------------------------------------------- */
+bool FixScafacos::check_result(FCSResult result, int comm_rank)
+{
+ if (result)
+ {
+ std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl;
+ std::string err_msg;
+ std::stringstream ss;
+
+ ss << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n";
+ err_msg = ss.str();
+
+ error -> all(FLERR, err_msg.c_str());
+ fcs_result_destroy(result);
+ }
+ return true;
+}
+
diff --git a/src/SCAFACOS/fix_scafacos.h b/src/SCAFACOS/fix_scafacos.h
new file mode 100644
index 0000000000..ffd4a94d32
--- /dev/null
+++ b/src/SCAFACOS/fix_scafacos.h
@@ -0,0 +1,164 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(scafacos,FixScafacos)
+
+#else
+
+#ifndef LMP_FIX_SCAFACOS_H
+#define LMP_FIX_SCAFACOS_H
+
+#include "fix.h"
+#include "fcs.h"
+#include <string>
+
+namespace LAMMPS_NS {
+
+class FixScafacos : public Fix {
+ public:
+ FixScafacos(class LAMMPS *, int, char **);
+ virtual ~FixScafacos();
+ int setmask();
+ void init();
+ void init_list(int, NeighList*);
+ void setup(int);
+ void min_setup(int);
+ void setup_pre_reverse(int, int);
+ void initial_integrate(int);
+ void pre_reverse(int, int);
+ void post_force(int);
+ void min_post_force(int);
+ void final_integrate();
+ void reset_dt();
+ double compute_scalar();
+ double memory_usage();
+
+ protected:
+ std::string method;
+
+ // MPI rank
+ int rank;
+
+ // source arrays for positions and charges
+ double *x, *q;
+ // result arrays for potentials and field
+ double *pot, *field;
+
+ // box vectors for each dimension
+ fcs_float box_x[3], box_y[3], box_z[3];
+ // offset of the box from the origin
+ fcs_float offset[3];
+
+ // periodicity of the system
+ fcs_int periodicity[3];
+
+ // ScaFaCoS handle
+ FCS fcs;
+
+ // ScaFaCoS result variable
+ FCSResult result;
+
+ // function to check results
+ bool check_result(FCSResult, int);
+
+ // function to set up handle with common parameters
+ void setup_handle();
+
+ // function to check if the box parameters changed, so that a new tuning step is required
+ bool box_has_changed();
+
+ // store total number of particles (to check if tune needs to be called again)
+ fcs_int total_particles;
+
+ // store number of local particles (to be able to readjust the size of result arrays, when needed)
+ int local_array_size;
+
+ // should the near field calculations be computed by LAMMPS?
+ fcs_int near_field_flag;
+
+ // type of accuracy chosen (if customized)
+ fcs_int tolerance_type;
+
+ // value of tolerance
+ fcs_float tolerance_value;
+
+ // is tolerance set?
+ bool tolerance_set;
+
+ // check if fmm is chosen (ghost particles, since the implementation needs at least 1 particle on each process!)
+ bool fmm_chosen;
+
+ // FMM: fmm particle array size
+ int fmm_array_size;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Must use units metal with fix latte command
+
+UNDOCUMENTED
+
+E: Fix latte currently runs only in serial
+
+UNDOCUMENTED
+
+E: LAMMPS is linked against incompatible LATTE library
+
+UNDOCUMENTED
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
+
+UNDOCUMENTED
+
+E: Could not find fix latte compute ID
+
+UNDOCUMENTED
+
+E: Fix latte compute ID does not compute pe/atom
+
+UNDOCUMENTED
+
+E: Fix latte requires 3d problem
+
+UNDOCUMENTED
+
+E: Fix latte cannot compute Coulomb potential
+
+UNDOCUMENTED
+
+E: Fix latte requires 3d simulation
+
+UNDOCUMENTED
+
+W: Fix latte should come after all other integration fixes
+
+UNDOCUMENTED
+
+E: Internal LATTE problem
+
+UNDOCUMENTED
+
+*/
--
GitLab
From 400ae7226765d17234fb2e2c57191e2fc5b21fb8 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 13:18:28 -0600
Subject: [PATCH 020/332] added tolerance to the example
---
examples/scafacos/in.scafacos | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos
index a2849583f5..2a7e830110 100644
--- a/examples/scafacos/in.scafacos
+++ b/examples/scafacos/in.scafacos
@@ -5,8 +5,6 @@ atom_style full
read_data data.NaCl
-# need both mass settings due to hybrid atom style
-
velocity all set 0.0 0.0 0.0 mom no
pair_style zero 1.0
@@ -15,7 +13,8 @@ pair_coeff * *
neighbor 1.0 bin
neigh_modify delay 0
-fix 1 all scafacos fmm
+# using the fmm solver with a tolerance in energy of 10^-3
+fix 1 all scafacos fmm energy 0.001
timestep 0.005
--
GitLab
From 4743bb3c30c207b1a9b51ed821e5b96ceb9c4080 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 13:35:46 -0600
Subject: [PATCH 021/332] rename of the ScaFaCoS package
---
cmake/CMakeLists.txt | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index a335a441da..de3f54b9e1 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -119,7 +119,7 @@ option(ENABLE_ALL "Build all default packages" OFF)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
REAX REPLICA RIGID SHOCK SNAP SRD)
-set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE SCAFACOS
+set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-SCAFACOS
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -150,11 +150,11 @@ pkg_depends(CORESHELL KSPACE)
######################################################
# packages with special compiler needs or external libs
######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_SCAFACOS)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
enable_language(Fortran)
endif()
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_SCAFACOS)
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
enable_language(C)
endif()
--
GitLab
From dbfea0e6170c4a894fa65a086503b33c9944cc4c Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 13:53:31 -0600
Subject: [PATCH 022/332] update folder structure to comply to LAMMPS
contribution rules
---
cmake/CMakeLists.txt | 2 +-
src/{SCAFACOS => USER-SCAFACOS}/Install.sh | 0
src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.cpp | 0
src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.h | 0
4 files changed, 1 insertion(+), 1 deletion(-)
rename src/{SCAFACOS => USER-SCAFACOS}/Install.sh (100%)
rename src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.cpp (100%)
rename src/{SCAFACOS => USER-SCAFACOS}/fix_scafacos.h (100%)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 05e4964e0b..afb93b9d1b 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -348,7 +348,7 @@ if(PKG_LATTE)
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
-if(PKG_SCAFACOS)
+if(PKG_USER-SCAFACOS)
FIND_PACKAGE(PkgConfig)
PKG_CHECK_MODULES(SCAFACOS scafacos)
include_directories(${SCAFACOS_INCLUDE_DIRS})
diff --git a/src/SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh
similarity index 100%
rename from src/SCAFACOS/Install.sh
rename to src/USER-SCAFACOS/Install.sh
diff --git a/src/SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
similarity index 100%
rename from src/SCAFACOS/fix_scafacos.cpp
rename to src/USER-SCAFACOS/fix_scafacos.cpp
diff --git a/src/SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h
similarity index 100%
rename from src/SCAFACOS/fix_scafacos.h
rename to src/USER-SCAFACOS/fix_scafacos.h
--
GitLab
From 4c4d8372e45ca2ca16dab99b32a34fd8e8e94ecf Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 14:01:06 -0600
Subject: [PATCH 023/332] removed C++ std::cout I/O and replaced it with printf
---
src/USER-SCAFACOS/fix_scafacos.cpp | 52 ++++++++++++++++--------------
1 file changed, 27 insertions(+), 25 deletions(-)
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
index f888747047..40d2556cdd 100644
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ b/src/USER-SCAFACOS/fix_scafacos.cpp
@@ -31,7 +31,6 @@
#include "error.h"
// ScaFaCoS library
-#include <iostream>
#include <sstream>
#include <string>
#include "fcs.h"
@@ -67,28 +66,28 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
// check if tolerance option is set
if (strcmp(arg[arg_index],"tolerance") == 0)
{
- tolerance_set = true;
- ++arg_index;
- if (strcmp(arg[arg_index],"energy") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
- else if (strcmp(arg[arg_index],"energy_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
- else if (strcmp(arg[arg_index],"field") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
- else if (strcmp(arg[arg_index],"field_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
- else if (strcmp(arg[arg_index],"potential") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
- else if (strcmp(arg[arg_index],"potential_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
- else
- error->all(FLERR,"Illegal fix scafacos command");
- ++arg_index;
- tolerance_value = atof(arg[arg_index]);
- ++arg_index;
+ tolerance_set = true;
+ ++arg_index;
+ if (strcmp(arg[arg_index],"energy") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ else if (strcmp(arg[arg_index],"energy_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
+ else if (strcmp(arg[arg_index],"field") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ else if (strcmp(arg[arg_index],"field_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
+ else if (strcmp(arg[arg_index],"potential") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
+ else if (strcmp(arg[arg_index],"potential_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
+ else
+ error->all(FLERR,"Illegal fix scafacos command");
+ ++arg_index;
+ tolerance_value = atof(arg[arg_index]);
+ ++arg_index;
}
else
- error->all(FLERR,"Illegal fix scafacos command");
+ error->all(FLERR,"Illegal fix scafacos command");
}
}
@@ -226,12 +225,14 @@ void FixScafacos::post_force(int vflag)
if (box_has_changed())
{
setup_handle();
- // print out parameters within handle
+ // print out parameters within handle TODO: should be done in C style
+ /*
if (rank == 0)
{
- std::cout << " updated ScaFaCoS handle: " << std::endl;
- fcs_print_parameters(fcs);
+ std::cout << " updated ScaFaCoS handle: " << std::endl;
+ fcs_print_parameters(fcs);
}
+ */
// call the tuning routine (needs to be redone, if critical system parameters should change)
result = fcs_tune(fcs,nlocal,x,q);
if (!check_result(result, rank)) return;
@@ -473,7 +474,8 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
{
if (result)
{
- std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl;
+ printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
+ //std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl;
std::string err_msg;
std::stringstream ss;
--
GitLab
From dd38318f5f01e7efe1aeee229b89f0b113508f50 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 14:12:06 -0600
Subject: [PATCH 024/332] adjustments to indention and line lengths (<=80 now)
---
src/USER-SCAFACOS/fix_scafacos.cpp | 118 ++++++++++-------------------
1 file changed, 41 insertions(+), 77 deletions(-)
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
index 40d2556cdd..6b89348a16 100644
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ b/src/USER-SCAFACOS/fix_scafacos.cpp
@@ -54,8 +54,6 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
// read method from fix input
method = arg[3];
- // check if fmm method was chosen
- fmm_chosen = !strcmp(method.c_str(),"fmm");
int arg_index = 4;
@@ -149,23 +147,18 @@ void FixScafacos::init()
// print out parameters within handle
if (rank == 0) fcs_print_parameters(fcs);
- // call the tuning routine (needs to be redone, if critical system parameters should change)
+ // call the tuning routine (needs to be redone, if critical system
+ // parameters should change)
result = fcs_tune(fcs,nlocal,x,q);
if (!check_result(result, rank)) return;
- // allocate arrays larger in order to avoid fast reallocation due to fluctuations
+ // allocate arrays larger in order to avoid fast
+ // reallocation due to fluctuations
local_array_size = (int)(1.25 * (double)nlocal);
// allocate new result arrays
memory->create(pot,local_array_size,"scafacos:potential");
memory->create(field,local_array_size*3,"scafacos:field");
-
- // set result vectors to zero
- for ( int i = 0; i < local_array_size; ++i)
- {
- pot[i] = 0.0;
- field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
- }
}
/* ---------------------------------------------------------------------- */
@@ -221,10 +214,12 @@ void FixScafacos::post_force(int vflag)
x = &atom->x[0][0];
q = atom->q;
- // check if box has changed since the last call of fcs_tune, if yes, call fcs_tune
+ // check if box has changed since the last call of fcs_tune,
+ // if it has, call fcs_tune
if (box_has_changed())
{
setup_handle();
+
// print out parameters within handle TODO: should be done in C style
/*
if (rank == 0)
@@ -233,23 +228,19 @@ void FixScafacos::post_force(int vflag)
fcs_print_parameters(fcs);
}
*/
- // call the tuning routine (needs to be redone, if critical system parameters should change)
+
+ // call the tuning routine (needs to be redone, if critical
+ // system parameters should change)
result = fcs_tune(fcs,nlocal,x,q);
if (!check_result(result, rank)) return;
}
- /*
- if (fmm_chosen && phantom_particle)
- for (int i = 0; i < nlocal; ++i)
- {
- std::cout << rank << " " << i << " " << x[3*i] << " " << x[3*i+1] << " " << x[3*i+2] << " " << q[i] << std::endl;
- }
- */
-
- // check if arrays for potentials and field are still large enough for the number of particles on process
+ // check if arrays for potentials and field are still large enough
+ // for the number of particles on process
if (nlocal > local_array_size)
{
- // allocate arrays larger in order to avoid fast reallocation due to fluctuations
+ // allocate arrays larger in order to avoid fast
+ // reallocation due to fluctuations
local_array_size = (int)(1.25 * (double)nlocal);
// destroy old result arrays
@@ -274,8 +265,6 @@ void FixScafacos::post_force(int vflag)
if(!check_result(result,rank)) return;
double E_coul_loc = 0.0;
- // no reduction required (?)
- //double E_coul = 0.0;
for (int i = 0; i < atom->nlocal; ++i)
{
@@ -286,9 +275,6 @@ void FixScafacos::post_force(int vflag)
E_coul_loc += 0.5 * q[i] * pot[i];
}
- // not required (?)
- // MPI_ALLREDUCE(&E_coul_loc, &E_coul, 1, MPI_DOUBLE, MPI_SUM, universe->uworld);
-
force->pair->eng_coul += E_coul_loc;
}
@@ -392,39 +378,39 @@ void FixScafacos::setup_handle()
------------------------------------------------------------------------- */
bool FixScafacos::box_has_changed()
{
- bool changed = false;
+ bool changed = false;
- double n_periodicity[3];
- double n_offset[3];
- double n_box_x[3];
- double n_box_y[3];
- double n_box_z[3];
+ double n_periodicity[3];
+ double n_offset[3];
+ double n_box_x[3];
+ double n_box_y[3];
+ double n_box_z[3];
- int n_total_particles;
+ int n_total_particles;
- // store periodicity
- n_periodicity[0] = domain->xperiodic;
- n_periodicity[1] = domain->yperiodic;
- n_periodicity[2] = domain->zperiodic;
+ // store periodicity
+ n_periodicity[0] = domain->xperiodic;
+ n_periodicity[1] = domain->yperiodic;
+ n_periodicity[2] = domain->zperiodic;
- // store offset of the system
- n_offset[0] = domain->boundary[0][0];
- n_offset[1] = domain->boundary[1][0];
- n_offset[2] = domain->boundary[2][0];
+ // store offset of the system
+ n_offset[0] = domain->boundary[0][0];
+ n_offset[1] = domain->boundary[1][0];
+ n_offset[2] = domain->boundary[2][0];
- // calculate box vectors
- n_box_x[0] = domain->prd[0];
- n_box_x[1] = n_box_x[2] = 0.0;
+ // calculate box vectors
+ n_box_x[0] = domain->prd[0];
+ n_box_x[1] = n_box_x[2] = 0.0;
- n_box_y[1] = domain->prd[1];
- n_box_y[0] = n_box_y[2] = 0.0;
+ n_box_y[1] = domain->prd[1];
+ n_box_y[0] = n_box_y[2] = 0.0;
- n_box_z[2] = domain->prd[2];
- n_box_z[1] = n_box_z[0] = 0.0;
+ n_box_z[2] = domain->prd[2];
+ n_box_z[1] = n_box_z[0] = 0.0;
- n_total_particles = atom->natoms;
+ n_total_particles = atom->natoms;
- changed = changed ||
+ changed = changed ||
( n_periodicity[0] != periodicity[0] ) ||
( n_periodicity[1] != periodicity[1] ) ||
( n_periodicity[2] != periodicity[2] ) ||
@@ -441,28 +427,7 @@ bool FixScafacos::box_has_changed()
( n_box_z[1] != box_z[1] ) ||
( n_box_z[2] != box_z[2] ) ||
( n_total_particles != total_particles );
-/*
- if (changed)
- {
- std::cout << rank << " " << "n_per_x : per_x" << n_periodicity[0] << " " << periodicity[0] << std::endl;
- std::cout << rank << " " << "n_per_y : per_y" << n_periodicity[1] << " " << periodicity[1] << std::endl;
- std::cout << rank << " " << "n_per_z : per_z" << n_periodicity[2] << " " << periodicity[2] << std::endl;
- std::cout << rank << " " << "n_off_x : off_x" << n_offset[0] << " " << offset[0] << std::endl;
- std::cout << rank << " " << "n_off_y : off_y" << n_offset[1] << " " << offset[1] << std::endl;
- std::cout << rank << " " << "n_off_z : off_z" << n_offset[2] << " " << offset[2] << std::endl;
- std::cout << rank << " " << "n_bx_x : bx_x" << n_box_x[0] << " " << box_x[0] << std::endl;
- std::cout << rank << " " << "n_bx_y : bx_y" << n_box_x[1] << " " << box_x[1] << std::endl;
- std::cout << rank << " " << "n_bx_z : bx_z" << n_box_x[2] << " " << box_x[2] << std::endl;
- std::cout << rank << " " << "n_by_x : by_x" << n_box_y[0] << " " << box_y[0] << std::endl;
- std::cout << rank << " " << "n_by_y : by_y" << n_box_y[1] << " " << box_y[1] << std::endl;
- std::cout << rank << " " << "n_by_z : by_z" << n_box_y[2] << " " << box_y[2] << std::endl;
- std::cout << rank << " " << "n_bz_x : bz_x" << n_box_z[0] << " " << box_z[0] << std::endl;
- std::cout << rank << " " << "n_bz_y : bz_y" << n_box_z[1] << " " << box_z[1] << std::endl;
- std::cout << rank << " " << "n_bz_z : bz_z" << n_box_z[2] << " " << box_z[2] << std::endl;
- std::cout << rank << " " << "n_total : total" << n_total_particles << " " << total_particles << std::endl;
- }
-*/
- return changed;
+ return changed;
}
@@ -475,11 +440,11 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
if (result)
{
printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
- //std::cout << "ScaFaCoS ERROR: Caught error on task " << comm_rank << "!" << std::endl;
std::string err_msg;
std::stringstream ss;
- ss << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n";
+ ss << fcs_result_get_function(result) << "\n"
+ << fcs_result_get_message(result) << "\n";
err_msg = ss.str();
error -> all(FLERR, err_msg.c_str());
@@ -487,4 +452,3 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
}
return true;
}
-
--
GitLab
From 3a824b3a4b402f5b3d48f334111e1f66bd2e9415 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 9 Jul 2018 14:16:46 -0600
Subject: [PATCH 025/332] mods to Sergey's files
---
doc/src/pair_atm.html | 91 +++++++++++++++++++++++++++
doc/src/pair_atm.txt | 95 +++++++++++++++++++++++-----
examples/README | 1 +
examples/{ => atm}/in.atm | 6 +-
examples/atm/log.9Jul18.atm.g++.1 | 100 ++++++++++++++++++++++++++++++
examples/atm/log.9Jul18.atm.g++.4 | 100 ++++++++++++++++++++++++++++++
src/MANYBODY/pair_atm.cpp | 10 +--
src/MANYBODY/pair_atm.h | 10 +--
8 files changed, 383 insertions(+), 30 deletions(-)
create mode 100644 doc/src/pair_atm.html
rename examples/{ => atm}/in.atm (88%)
create mode 100644 examples/atm/log.9Jul18.atm.g++.1
create mode 100644 examples/atm/log.9Jul18.atm.g++.4
diff --git a/doc/src/pair_atm.html b/doc/src/pair_atm.html
new file mode 100644
index 0000000000..df8e6099cf
--- /dev/null
+++ b/doc/src/pair_atm.html
@@ -0,0 +1,91 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style atm command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style atm args = cutoff
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style 2.5
+pair_coeff * * * 0.072
+</PRE>
+<PRE>pair_style hybrid/overlay lj/cut 6.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>atm</I> style computes a 3-body <A HREF = "#Axilrod">Axilrod-Teller-Muto</A>
+potential for the energy E of a system of atoms as
+</P>
+<CENTER><IMG SRC = "Eqs/pair_atm.jpg">
+</CENTER>
+<P>where r12, r23 and r31 are the distances between the atoms,
+gamma1 is included by the sides r12 and r31
+with similar definitions for gamma2 and gamma3,
+nu is the three-body interaction strength (energy times distance^9 units).
+</P>
+<P>The <I>atm</I> is typically used in compination with some two-body potential
+using <A HREF = "pair_hybrid.html">hybrid/overlay</A> style as in an example above.
+</P>
+<P>The calculations are not undertaken if the distances between atoms satisfy
+r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
+tolerance tol is not used.
+</P>
+<P>The Axilrod-Teller-Muto potential file must contain entries for all the
+elements listed in the pair_coeff command. It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+</P>
+<P>For a single-element simulation, only a single entry is required
+(e.g. 1 1 1). For a two-element simulation, the file must contain 4
+entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
+specify ATM parameters for all combinations of the two elements
+interacting in three-body configurations. Thus for 3 elements, 10
+entries would be required, etc.
+</P>
+<HR>
+
+<P><B>Shift, table, tail correction, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This pair style can only be used via the <I>pair</I> keyword of the
+<A HREF = "run_style.html">run_style respa</A> command. It does not support the
+<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package. See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Axilrod"></A>
+
+<P><B>(Axilrod)</B>
+Axilrod and Teller, J Chem Phys, 11, 299 (1943);
+Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
+</P>
+</HTML>
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index 48260c161a..786400b626 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -10,16 +10,18 @@ pair_style atm command :h3
[Syntax:]
-pair_style atm args = cutoff :pre
+pair_style atm cutoff :pre
+
+cutoff = global cutoff for 3-body interactions (distance units) :ul
[Examples:]
pair_style 2.5
pair_coeff * * * 0.072 :pre
-pair_style hybrid/overlay lj/cut 6.5 atm 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * atm * 0.072 :pre
+pair_style hybrid/overlay lj/cut 6.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072 :pre
[Description:]
@@ -28,18 +30,60 @@ potential for the energy E of a system of atoms as
:c,image(Eqs/pair_atm.jpg)
-where r12, r23 and r31 are the distances between the atoms,
-gamma1 is included by the sides r12 and r31
-with similar definitions for gamma2 and gamma3,
-nu is the three-body interaction strength (energy times distance^9 units).
+where r12, r23 and r31 are the distances between pairs of atoms,
+gamma1 is the angle ???, gamma2 is the angle ???, gamma3 is the angle
+???, and nu is the three-body interaction strength.
+A diagram of the 3 atoms might help here.
+
+The {atm} potential is typically used in combination with a two-body
+potential using the "pair_style hybrid/overlay"_pair_hybrid.html
+command as in the example above.
+
+--------------------
-The {atm} is typically used in compination with some two-body potential
-using "hybrid/overlay"_pair_hybrid.html style as in an example above.
+The rest of this section needs some work to make things more clear.
+You need to explain exactly how the cutoff is used.
+
+I don't think this is true:
The calculations are not undertaken if the distances between atoms satisfy
-r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
+r12 r23 r31 > cutoff^3.
+
+If r12 > cutoff+skin, then that pair of atoms is not in
+the neighbor list, regardless of what r23 and r31 are,
+so how can it be computed?
+
+What does this line mean?
+Virtual cutoff distance based on a user defined
tolerance tol is not used.
+You must explain exactly what the user needs to put
+in the input script to model single element and multi-element
+systems.
+
+You refer to an ATM potential file, but I don't think there is
+such a thing. There is no code in pair_atm.cpp that reads
+a file. Isn't it all pair_coeff commands? In LAMMPS lingo,
+potential files are the files in the potentials dir.
+There is no such thing for ATM, right?
+
+What is the geometry of i,j,k interactions - you don't explain it.
+Which one is the central atom?
+
+You say all the K values for a particular I,J must be specified.
+I don't see where the code checks for this.
+
+This is the way to word the explation of the per-pair values required:
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the restart files read by the
+"read_restart"_read_restart.html commands:
+
+?? explain what K is and what are the allowed values
+nu (energy/distance^9 units) :ul
+
+Again: what file are you talking about?
The Axilrod-Teller-Muto potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
@@ -52,12 +96,29 @@ specify ATM parameters for all combinations of the two elements
interacting in three-body configurations. Thus for 3 elements, 10
entries would be required, etc.
+I think a better syntax for the pair coeff command might be this:
+
+pair_coeff I J v1 v2 ... vN
+
+when 1,2,...N are the number of atom types defined.
+Then there be one pair_coeff command for each type pair,
+the same syntax as all other potentials in LAMMPS use.
+
+Note that you refer to "elements", but the pair coeff command
+knows nothing about elements. Only atom types. There
+could be 10 atom types that all map to the same chemical
+element.
+
:line
-[Shift, table, tail correction, rRESPA info]:
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair styles do not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
-This pair style does not support the "pair_modify"_pair_modify.html
-shift, table, and tail options.
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
@@ -68,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
@@ -82,4 +143,4 @@ the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Axilrod)
[(Axilrod)]
Axilrod and Teller, J Chem Phys, 11, 299 (1943);
-Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
+Muto, Nippon, Sugaku, Butsuri, Gakkwaishi 17, 629 (1943).
diff --git a/examples/README b/examples/README
index a8dfe63d92..d6c946725f 100644
--- a/examples/README
+++ b/examples/README
@@ -59,6 +59,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
airebo: polyethylene with AIREBO potential
+atm: Axilrod-Teller-Muto potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
diff --git a/examples/in.atm b/examples/atm/in.atm
similarity index 88%
rename from examples/in.atm
rename to examples/atm/in.atm
index 0f3760baf9..52576c04c9 100644
--- a/examples/in.atm
+++ b/examples/atm/in.atm
@@ -1,3 +1,5 @@
+# Axilrod-Teller-Muto potential example
+
variable x index 1
variable y index 1
variable z index 1
@@ -24,6 +26,6 @@ velocity all create 1.033 12345678 loop geom
fix 1 all nvt temp 1.033 1.033 0.05
timestep 0.002
-thermo 1
+thermo 5
-run 50
+run 25
diff --git a/examples/atm/log.9Jul18.atm.g++.1 b/examples/atm/log.9Jul18.atm.g++.1
new file mode 100644
index 0000000000..27ba23e3a9
--- /dev/null
+++ b/examples/atm/log.9Jul18.atm.g++.1
@@ -0,0 +1,100 @@
+LAMMPS (29 Jun 2018)
+# Axilrod-Teller-Muto potential example
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable xx equal 10*1
+variable yy equal 10*$y
+variable yy equal 10*1
+variable zz equal 10*$z
+variable zz equal 10*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+Lattice spacing in x,y,z = 1.83252 1.83252 1.83252
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 10 0 ${yy} 0 ${zz}
+region box block 0 10 0 10 0 ${zz}
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+ Time spent = 0.00120211 secs
+
+pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 5
+
+run 25
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4, bins = 8 8 8
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair atm, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.033 -4.5929584 0 -3.0438458 -3.6506231
+ 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
+ 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
+ 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
+ 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
+ 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
+Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms
+
+Performance: 124.999 tau/day, 0.723 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 34.556 | 34.556 | 34.556 | 0.0 | 99.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.001323 | 0.001323 | 0.001323 | 0.0 | 0.00
+Output | 0.00018287 | 0.00018287 | 0.00018287 | 0.0 | 0.00
+Modify | 0.0016184 | 0.0016184 | 0.0016184 | 0.0 | 0.00
+Other | | 0.0006311 | | | 0.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10895 ave 10895 max 10895 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 640000 ave 640000 max 640000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.28e+06 ave 1.28e+06 max 1.28e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1280000
+Ave neighs/atom = 320
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:36
diff --git a/examples/atm/log.9Jul18.atm.g++.4 b/examples/atm/log.9Jul18.atm.g++.4
new file mode 100644
index 0000000000..300f82d581
--- /dev/null
+++ b/examples/atm/log.9Jul18.atm.g++.4
@@ -0,0 +1,100 @@
+LAMMPS (29 Jun 2018)
+# Axilrod-Teller-Muto potential example
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable xx equal 10*1
+variable yy equal 10*$y
+variable yy equal 10*1
+variable zz equal 10*$z
+variable zz equal 10*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+Lattice spacing in x,y,z = 1.83252 1.83252 1.83252
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 10 0 ${yy} 0 ${zz}
+region box block 0 10 0 10 0 ${zz}
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+ Time spent = 0.000735998 secs
+
+pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 5
+
+run 25
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4, bins = 8 8 8
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair atm, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.033 -4.5929584 0 -3.0438458 -3.6506231
+ 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
+ 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
+ 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
+ 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
+ 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
+Loop time of 10.061 on 4 procs for 25 steps with 4000 atoms
+
+Performance: 429.382 tau/day, 2.485 timesteps/s
+100.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15
+Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00
+Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01
+Other | | 0.0002971 | | | 0.00
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5835 ave 5835 max 5835 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 160000 ave 160000 max 160000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 320000 ave 320000 max 320000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1280000
+Ave neighs/atom = 320
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 0286c3ed1e..03c523eefe 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -49,8 +49,8 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
if (lmp->citeme) lmp->citeme->add(cite_atm_package);
single_enable = 0;
- restartinfo = 0;
- one_coeff = 1;
+ //restartinfo = 1; // it does save restart info, correct?
+ //one_coeff = 0; // it does not only use * *, correct?
manybody_flag = 1;
}
@@ -129,7 +129,7 @@ void PairATM::compute(int eflag, int vflag)
if (r6 > cut_sixth) continue;
interaction_ddd(nu[type[i]][type[j]][type[k]],
- r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+ r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
@@ -229,7 +229,9 @@ void PairATM::write_restart(FILE *fp)
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
- if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp);
+ if (setflag[i][j])
+ for (k = i; k <= atom->ntypes; k++)
+ fwrite(&nu[i][j][k],sizeof(double),1,fp);
}
}
}
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index b5bfc64010..45a6cda344 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -11,10 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ----------------------------------------------------------------------
- Contributing author: Sergey Lishchuk
-------------------------------------------------------------------------- */
-
#ifdef PAIR_CLASS
PairStyle(atm,PairATM)
@@ -46,9 +42,9 @@ class PairATM : public Pair {
double cut_global, cut_sixth;
double ***nu;
- protected:
- virtual void allocate();
- void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &);
+ void allocate();
+ void interaction_ddd(double, double, double, double, double, double *,
+ double *, double *, double *, double *, int, double &);
};
}
--
GitLab
From 75ec0a6a990ae6eec59ca7fa80c8cff14d561495 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 9 Jul 2018 14:17:21 -0600
Subject: [PATCH 026/332] remove HTML file
---
doc/src/pair_atm.html | 91 -------------------------------------------
1 file changed, 91 deletions(-)
delete mode 100644 doc/src/pair_atm.html
diff --git a/doc/src/pair_atm.html b/doc/src/pair_atm.html
deleted file mode 100644
index df8e6099cf..0000000000
--- a/doc/src/pair_atm.html
+++ /dev/null
@@ -1,91 +0,0 @@
-<HTML>
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
-</CENTER>
-
-
-
-
-
-
-<HR>
-
-<H3>pair_style atm command
-</H3>
-<P><B>Syntax:</B>
-</P>
-<PRE>pair_style atm args = cutoff
-</PRE>
-<P><B>Examples:</B>
-</P>
-<PRE>pair_style 2.5
-pair_coeff * * * 0.072
-</PRE>
-<PRE>pair_style hybrid/overlay lj/cut 6.5 atm 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * atm * 0.072
-</PRE>
-<P><B>Description:</B>
-</P>
-<P>The <I>atm</I> style computes a 3-body <A HREF = "#Axilrod">Axilrod-Teller-Muto</A>
-potential for the energy E of a system of atoms as
-</P>
-<CENTER><IMG SRC = "Eqs/pair_atm.jpg">
-</CENTER>
-<P>where r12, r23 and r31 are the distances between the atoms,
-gamma1 is included by the sides r12 and r31
-with similar definitions for gamma2 and gamma3,
-nu is the three-body interaction strength (energy times distance^9 units).
-</P>
-<P>The <I>atm</I> is typically used in compination with some two-body potential
-using <A HREF = "pair_hybrid.html">hybrid/overlay</A> style as in an example above.
-</P>
-<P>The calculations are not undertaken if the distances between atoms satisfy
-r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
-tolerance tol is not used.
-</P>
-<P>The Axilrod-Teller-Muto potential file must contain entries for all the
-elements listed in the pair_coeff command. It can also contain
-entries for additional elements not being used in a particular
-simulation; LAMMPS ignores those entries.
-</P>
-<P>For a single-element simulation, only a single entry is required
-(e.g. 1 1 1). For a two-element simulation, the file must contain 4
-entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
-specify ATM parameters for all combinations of the two elements
-interacting in three-body configurations. Thus for 3 elements, 10
-entries would be required, etc.
-</P>
-<HR>
-
-<P><B>Shift, table, tail correction, rRESPA info</B>:
-</P>
-<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
-shift, table, and tail options.
-</P>
-<P>This pair style can only be used via the <I>pair</I> keyword of the
-<A HREF = "run_style.html">run_style respa</A> command. It does not support the
-<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
-</P>
-<HR>
-
-<P><B>Restrictions:</B>
-</P>
-<P>This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
-</P>
-<P><B>Related commands:</B>
-</P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>
-</P>
-<P><B>Default:</B> none
-</P>
-<HR>
-
-<A NAME = "Axilrod"></A>
-
-<P><B>(Axilrod)</B>
-Axilrod and Teller, J Chem Phys, 11, 299 (1943);
-Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
-</P>
-</HTML>
--
GitLab
From ee98d026dcbf8b0884b012b06a744b4a807777e9 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 9 Jul 2018 14:28:25 -0600
Subject: [PATCH 027/332] preliminary documentation added (to be improved)
---
doc/src/fix_scafacos.txt | 44 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
create mode 100644 doc/src/fix_scafacos.txt
diff --git a/doc/src/fix_scafacos.txt b/doc/src/fix_scafacos.txt
new file mode 100644
index 0000000000..1a65ed0c5e
--- /dev/null
+++ b/doc/src/fix_scafacos.txt
@@ -0,0 +1,44 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix scafacos command :h3
+
+[Syntax:]
+
+fix ID group-ID scafacos solver tol_type tolerance :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+scafacos = style name of this fix command
+solver = NULL or name of solver for electro-statics computation :ul
+tol_type = NULL or one of (energy, energy_rel, field, field_rel, potential, potential_rel)
+tolerance = only of tol_type is given, value of tolerance
+
+[Examples:]
+
+fix 1 all scafacos fmm
+fix 1 all scafacos p3m field 0.001
+
+[Description:]
+
+This fix style is a wrapper for the Coulomb solver library ScaFaCoS,
+which provides a selection of different solvers for the compuation
+of electro-static interaction. If you download and build ScaFaCoS,
+it can be called as libray by LAMMPS via this fix, which allows the
+selection of a solver as well as setting the tolerance of a chosen
+parameter (if compatible with the chosen solver).
+
+ScaFaCoS was developed by a consortium of German research facilities
+with a BMBF (German Ministry of Science and Education) funded project
+in 2009-2012. Participants of the consortium were the Universities of
+Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
+Forschungszentrum Juelich.
+
+The library is available at "http://scafacos.de" or can be cloned
+from the git-repository "git://github.com/scafacos/scafacos.git".
+
+:line
--
GitLab
From 88d3233b66e68f54ac91cf4e3b3d4905d84d55e8 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 11 Jul 2018 14:02:30 -0600
Subject: [PATCH 028/332] replaced printf with fprintf as requested
---
src/USER-SCAFACOS/fix_scafacos.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
index 6b89348a16..9446e3b60c 100644
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ b/src/USER-SCAFACOS/fix_scafacos.cpp
@@ -439,7 +439,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
{
if (result)
{
- printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
+ fprintf(stdout,"ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
std::string err_msg;
std::stringstream ss;
@@ -447,7 +447,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
<< fcs_result_get_message(result) << "\n";
err_msg = ss.str();
- error -> all(FLERR, err_msg.c_str());
+ error -> one(FLERR, err_msg.c_str());
fcs_result_destroy(result);
}
return true;
--
GitLab
From 8cca44ae4541568df4a3dda4da902eabcb4a6138 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 11 Jul 2018 14:02:51 -0600
Subject: [PATCH 029/332] removed wrong error messages
---
src/USER-SCAFACOS/fix_scafacos.h | 50 --------------------------------
1 file changed, 50 deletions(-)
diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h
index ffd4a94d32..c48f4d8388 100644
--- a/src/USER-SCAFACOS/fix_scafacos.h
+++ b/src/USER-SCAFACOS/fix_scafacos.h
@@ -111,54 +111,4 @@ class FixScafacos : public Fix {
/* ERROR/WARNING messages:
-E: Must use units metal with fix latte command
-
-UNDOCUMENTED
-
-E: Fix latte currently runs only in serial
-
-UNDOCUMENTED
-
-E: LAMMPS is linked against incompatible LATTE library
-
-UNDOCUMENTED
-
-E: Illegal ... command
-
-Self-explanatory. Check the input script syntax and compare to the
-documentation for the command. You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
-
-UNDOCUMENTED
-
-E: Could not find fix latte compute ID
-
-UNDOCUMENTED
-
-E: Fix latte compute ID does not compute pe/atom
-
-UNDOCUMENTED
-
-E: Fix latte requires 3d problem
-
-UNDOCUMENTED
-
-E: Fix latte cannot compute Coulomb potential
-
-UNDOCUMENTED
-
-E: Fix latte requires 3d simulation
-
-UNDOCUMENTED
-
-W: Fix latte should come after all other integration fixes
-
-UNDOCUMENTED
-
-E: Internal LATTE problem
-
-UNDOCUMENTED
-
*/
--
GitLab
From cdf091f228651c291aa02e9a585d708073c47756 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 13 Jul 2018 08:37:29 -0600
Subject: [PATCH 030/332] fixed an error in the scafacos example (added missing
keyword tolerance)
---
examples/scafacos/in.scafacos | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos
index 2a7e830110..ae6b8e0193 100644
--- a/examples/scafacos/in.scafacos
+++ b/examples/scafacos/in.scafacos
@@ -14,7 +14,7 @@ neighbor 1.0 bin
neigh_modify delay 0
# using the fmm solver with a tolerance in energy of 10^-3
-fix 1 all scafacos fmm energy 0.001
+fix 1 all scafacos fmm tolerance energy 0.001
timestep 0.005
--
GitLab
From 6cfdcd1000360cbd1e53f319e9b51e2040505e4f Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 13 Jul 2018 08:49:47 -0600
Subject: [PATCH 031/332] removed custom error message, information is added to
error->one() call
---
src/USER-SCAFACOS/fix_scafacos.cpp | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
index 9446e3b60c..f82b80dd5f 100644
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ b/src/USER-SCAFACOS/fix_scafacos.cpp
@@ -439,7 +439,6 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
{
if (result)
{
- fprintf(stdout,"ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
std::string err_msg;
std::stringstream ss;
@@ -447,7 +446,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
<< fcs_result_get_message(result) << "\n";
err_msg = ss.str();
- error -> one(FLERR, err_msg.c_str());
+ error->one(FLERR, err_msg.c_str());
fcs_result_destroy(result);
}
return true;
--
GitLab
From bf5fbc92dfb2178ef620bb03876817da43a2be4d Mon Sep 17 00:00:00 2001
From: Sergey Lishchuk <svl@debian>
Date: Fri, 13 Jul 2018 20:18:53 +0100
Subject: [PATCH 032/332] Updated documentation and source
---
doc/src/JPG/pair_atm_dia.jpg | Bin 0 -> 31541 bytes
doc/src/angle_dipole.txt | 17 ++--
doc/src/fix_langevin_spin.txt | 4 +-
doc/src/fix_nve_spin.txt | 2 +-
doc/src/pair_atm.txt | 131 +++++++++++++++++++++++-------
doc/src/pair_spin_dmi.txt | 2 +-
doc/src/pair_spin_exchange.txt | 2 +-
doc/src/pair_spin_magelec.txt | 2 +-
doc/src/pair_spin_neel.txt | 2 +-
doc/src/run_style.txt | 77 +++++++++++++-----
doc/src/set.txt | 17 ++++
examples/SPIN/README | 20 +++++
lib/gpu/Nvidia.makefile_multi | 46 ++++++++++-
src/MAKE/MACHINES/Makefile.theta | 133 +++++++++++++++++++++++++++++++
src/MANYBODY/pair_atm.cpp | 21 +++--
src/MANYBODY/pair_atm.h | 10 +--
src/SPIN/atom_vec_spin.cpp | 10 +--
src/SPIN/compute_spin.cpp | 4 +-
src/SPIN/fix_langevin_spin.cpp | 8 +-
src/SPIN/fix_nve_spin.cpp | 13 +--
src/SPIN/fix_precession_spin.cpp | 10 +--
src/SPIN/pair_spin.cpp | 8 +-
src/SPIN/pair_spin_dmi.cpp | 8 +-
src/SPIN/pair_spin_exchange.cpp | 8 +-
src/SPIN/pair_spin_magelec.cpp | 14 ++--
src/SPIN/pair_spin_neel.cpp | 8 +-
src/balance.cpp | 6 +-
src/fix_balance.cpp | 13 ++-
src/fix_store.cpp | 2 -
src/reset_ids.cpp | 16 +++-
30 files changed, 480 insertions(+), 134 deletions(-)
create mode 100644 doc/src/JPG/pair_atm_dia.jpg
create mode 100644 examples/SPIN/README
create mode 100644 src/MAKE/MACHINES/Makefile.theta
diff --git a/doc/src/JPG/pair_atm_dia.jpg b/doc/src/JPG/pair_atm_dia.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..fd8edc5e676ee9973dd4ca1aced98b641c4157c7
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diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index d91f260d51..34cc8c153c 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -96,16 +96,17 @@ USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
section for more info on packages.
NOTE: In the "Angles" section of the data file, the atom ID 'j'
-corresponding to the dipole to restrain must come before the atom ID
-of the reference atom 'i'. A third atom ID 'k' must also be provided,
-although 'k' is just a 'dummy' atom which can be any atom; it may be
-useful to choose a convention (e.g., 'k'='i') and adhere to it. For
-example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
-reference atom, the corresponding line in the "Angles" section of the
-data file would read: X X 1 2 2
+defining the direction of the dipole vector to restrain must come
+before the atom ID of the reference atom 'i'. A third atom ID 'k' must
+also be provided to comply with the requirement of a valid angle
+definition. This atom ID k should be chosen to be that of an atom
+bonded to atom 'i' to avoid errors with "lost angle atoms" when running
+in parallel. Since the LAMMPS code checks for valid angle definitions,
+cannot use the same atom ID of either 'i' or 'j' (this was allowed
+and recommended with older LAMMPS versions).
The "newton" command for intramolecular interactions must be "on"
-(which is the default).
+(which is the default except when using some accelerator packages).
This angle style should not be used with SHAKE.
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 51f085ebdc..b089cd7f58 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -98,5 +98,5 @@ integration fix (e.g. {fix nve/spin}).
[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
:link(Tranchida2)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, (2018).
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index 6ccebcebf6..f4b38c270b 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -73,4 +73,4 @@ instead of "array" is also valid.
:link(Tranchida1)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index 48260c161a..01bbfa7a78 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -10,16 +10,21 @@ pair_style atm command :h3
[Syntax:]
-pair_style atm args = cutoff :pre
+pair_style atm cutoff :pre
+
+cutoff = global cutoff for 3-body interactions (distance units) :ul
[Examples:]
pair_style 2.5
pair_coeff * * * 0.072 :pre
-pair_style hybrid/overlay lj/cut 6.5 atm 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * atm * 0.072 :pre
+pair_style hybrid/overlay lj/cut 6.5 atm 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 1 1 atm 1 0.064
+pair_coeff 1 1 atm 2 0.080
+pair_coeff 1 2 atm 2 0.100
+pair_coeff 2 2 atm 2 0.125 :pre
[Description:]
@@ -28,36 +33,104 @@ potential for the energy E of a system of atoms as
:c,image(Eqs/pair_atm.jpg)
-where r12, r23 and r31 are the distances between the atoms,
-gamma1 is included by the sides r12 and r31
-with similar definitions for gamma2 and gamma3,
-nu is the three-body interaction strength (energy times distance^9 units).
+where nu is the three-body interaction strength,
+and the distances between pairs of atoms r12, r23 and r31
+and the angles gamma1, gamma2 and gamma3
+are shown at the diagram:
+
+:c,image(JPG/pair_atm_dia.jpg)
+
+There is no \"central\" atom, the interaction is symmetric with respect
+to permutation of atom types.
+
+The {atm} potential is typically used in combination with a two-body
+potential using the "pair_style hybrid/overlay"_pair_hybrid.html
+command as in the example above.
+
+The potential is calculated if all three atoms are in the
+"neighbor list"_neighbor.html
+and the distances between atoms satisfy r12 r23 r31 > cutoff^3.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the restart files read by the
+"read_restart"_read_restart.html commands:
+
+K - the type of the third atom
+nu (energy/distance^9 units) :ul
+
+For a single-atom type simulation, only a single entry is required, eg
+
+pair_coeff 1 1 1 nu :pre
+
+where all three atoms are of type 1.
+For a two-atom type simulation, more pair_coeff commands can be used.
+ATM interaction is symmetric with respect to permutation of atoms,
+it is necessary to provide pair_coeff command for one permutation.
+For example, the command
+
+pair_coeff 1 1 2 nu :pre
-The {atm} is typically used in compination with some two-body potential
-using "hybrid/overlay"_pair_hybrid.html style as in an example above.
+also implies
-The calculations are not undertaken if the distances between atoms satisfy
-r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
-tolerance tol is not used.
+pair_coeff 1 2 1 nu
+pair_coeff 2 1 1 nu :pre
-The Axilrod-Teller-Muto potential file must contain entries for all the
-elements listed in the pair_coeff command. It can also contain
-entries for additional elements not being used in a particular
-simulation; LAMMPS ignores those entries.
+Thus, to specify all ATM interactions between two atom types (eg 1 and 2)
+it is sufficient to provide four pair_coeff commands, eg:
-For a single-element simulation, only a single entry is required
-(e.g. 1 1 1). For a two-element simulation, the file must contain 4
-entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
-specify ATM parameters for all combinations of the two elements
-interacting in three-body configurations. Thus for 3 elements, 10
-entries would be required, etc.
+pair_coeff 1 1 1 nu1
+pair_coeff 1 1 2 nu2
+pair_coeff 1 2 2 nu3
+pair_coeff 2 2 2 nu4 :pre
+
+For 3 atom types, 10 pair_coeff commands
+(eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333)
+will describe all possible ATM interactions, etc.
+It is not necessary to provide the pair_coeff commands for interactions
+of all combinations of atom types: if some combination is not defined then
+there is no ATM interaction for this combination and all its permutations.
+
+--------------------
+
+[Steve:]
+
+I think a better syntax for the pair coeff command might be this:
+
+pair_coeff I J v1 v2 ... vN
+
+when 1,2,...N are the number of atom types defined.
+Then there be one pair_coeff command for each type pair,
+the same syntax as all other potentials in LAMMPS use.
+
+[Sergey:]
+
+The reason for my original pair_coeff command syntax is that
+I would like to reserve further arguments for possible extension of
+ATM potential in LAMMPS to further terms in the multipole expansion of
+many-body dispersion interaction.
+For example, the next term would be dipole-dipole-quadrupole, it may be
+activated if the next argument of pair_coeff is present
+without breaking backward compatibility.
+
+Also, the command you propose
+(i) will not account that the value of nu for different permutations
+of atom types is the same, and
+(ii) will make the numbering of atom types messy since there is
+no requirement to supply the values of nu for all triplets.
+
+--------------------
:line
-[Shift, table, tail correction, rRESPA info]:
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair styles do not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
-This pair style does not support the "pair_modify"_pair_modify.html
-shift, table, and tail options.
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
@@ -68,8 +141,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
@@ -82,4 +155,4 @@ the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Axilrod)
[(Axilrod)]
Axilrod and Teller, J Chem Phys, 11, 299 (1943);
-Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).
+Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 9fe53df18a..24877906f3 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -63,4 +63,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Tranchida5)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 97b6d0b34f..ad3357cb5e 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -79,4 +79,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Tranchida3)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index 0185a5abb2..8ba24c46af 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -70,4 +70,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Tranchida4)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index f7c9608a93..8551f8d636 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -78,4 +78,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:link(Tranchida6)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index ba836a07dd..7717ede86f 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the
iterations of level 2 per iteration of level 3, etc. N-1 looping
parameters must be specified.
-The "timestep"_timestep.html command sets the timestep for the
-outermost rRESPA level. Thus if the example command above for a
-4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
-would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that
-specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html
-parameters, "dump"_dump.html every N timesteps, etc) refer to the
-outermost timesteps.
+Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
+you could choose to have bond interactions computed 8x per large
+timestep, angle interactions computed 4x, pair interactions computed
+2x, and long-range interactions once per large timestep.
+
+The "timestep"_timestep.html command sets the large timestep for the
+outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for
+4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
+inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS
+commands that specify number of timesteps (e.g. "thermo"_thermo.html
+for thermo output every N steps, "neigh_modify
+delay/every"_neigh_modify.html parameters, "dump"_dump.html every N
+steps, etc) refer to the outermost timesteps.
The rRESPA keywords enable you to specify at what level of the
hierarchy various forces will be computed. If not specified, the
@@ -167,11 +173,17 @@ have their force go ramped to 0.0 so the overlap with the next regime
compute forces for all pairs from 5.0 outward, with those from 5.0 to
6.0 having their value ramped in an inverse manner.
-Only some pair potentials support the use of the {inner} and {middle}
-and {outer} keywords. If not, only the {pair} keyword can be used
-with that pair style, meaning all pairwise forces are computed at the
-same rRESPA level. See the doc pages for individual pair styles for
-details.i
+Note that you can use {inner} and {outer} without using {middle} to
+split the pairwise computations into two portions instead of three.
+Unless you are using a very long pairwise cutoff, a 2-way split is
+often faster than a 3-way split, since it avoids too much duplicate
+computation of pairwise interactions near the intermediate cutoffs.
+
+Also note that only a few pair potentials support the use of the
+{inner} and {middle} and {outer} keywords. If not, only the {pair}
+keyword can be used with that pair style, meaning all pairwise forces
+are computed at the same rRESPA level. See the doc pages for
+individual pair styles for details.
Another option for using pair potentials with rRESPA is with the
{hybrid} keyword, which requires the use of the "pair_style hybrid or
@@ -238,12 +250,24 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a
For non-biomolecular simulations, the {respa} style can be
advantageous if there is a clear separation of time scales - fast and
-slow modes in the simulation. Even a LJ system can benefit from
-rRESPA if the interactions are divided by the inner, middle and outer
-keywords. A 2-fold or more speedup can be obtained while maintaining
-good energy conservation. In real units, for a pure LJ fluid at
-liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
-Kcal/mol, the following settings seem to work well:
+slow modes in the simulation. For example, a system of slowly-moving
+charged polymer chains could be setup as follows:
+
+timestep 4.0
+run_style respa 2 8 :pre
+
+This is two-level rRESPA with an 8x difference between the short and
+long timesteps. The bonds, angles, dihedrals will be computed every
+0.5 fs (assuming real units), while the pair and kspace interactions
+will be computed once every 4 fs. These are the default settings for
+each kind of interaction, so no additional keywords are necessary.
+
+Even a LJ system can benefit from rRESPA if the interactions are
+divided by the inner, middle and outer keywords. A 2-fold or more
+speedup can be obtained while maintaining good energy conservation.
+In real units, for a pure LJ fluid at liquid density, with a sigma of
+3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings
+seem to work well:
timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
@@ -271,9 +295,9 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
The {verlet/split} style can only be used if LAMMPS was built with the
-REPLICA package. Correspondingly the {respa/omp} style is available only
-if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+REPLICA package. Correspondingly the {respa/omp} style is available
+only if the USER-OMP package was included. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are
@@ -287,6 +311,17 @@ conserving energy to adequate precision.
run_style verlet :pre
+For run_style respa, the default assignment of interactions
+to rRESPA levels is as follows:
+
+bond forces = level 1 (innermost loop)
+angle forces = same level as bond forces
+dihedral forces = same level as angle forces
+improper forces = same level as dihedral forces
+pair forces = leven N (outermost level)
+kspace forces = same level as pair forces
+inner, middle, outer forces = no default :ul
+
:line
:link(Tuckerman3)
diff --git a/doc/src/set.txt b/doc/src/set.txt
index 4757d1c575..d05660dc42 100644
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@@ -17,6 +17,7 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat} or \
+ {spin} or {spin/random} or {quat} or \
{quat/random} or {diameter} or {shape} or \
{length} or {tri} or {theta} or {theta/random} or \
{angmom} or {omega} or \
@@ -43,6 +44,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{dipole/random} value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
+ {spin} values = g x y z
+ g = magnitude of magnetic spin vector (in Bohr magneton's unit)
+ x,y,z = orientation of magnetic spin vector
+ any of x,y,z can be an atom-style variable (see below)
+ {spin/random} value = seed Dlen
+ seed = random # seed (positive integer) for magnetic spin orientations
+ Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
{quat} values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle (degrees)
@@ -232,6 +240,15 @@ the orientation of a particular atom is the same, regardless of how
many processors are being used. This keyword does not allow use of an
atom-style variable.
+Keyword {spin} uses the specified g value to set the magnitude of the
+magnetic spin vectors, and the x,y,z values as components of a vector
+to set as the orientation of the magnetic spin vectors of the selected
+atoms.
+
+Keyword {spin/random} randomizes the orientation of the magnetic spin
+vectors for the selected atoms and sets the magnitude of each to the
+specified {Dlen} value.
+
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The
particles must define a quaternion for their orientation
diff --git a/examples/SPIN/README b/examples/SPIN/README
new file mode 100644
index 0000000000..5ad252e7f2
--- /dev/null
+++ b/examples/SPIN/README
@@ -0,0 +1,20 @@
+This directory contains examples and applications of the SPIN package
+=====================================================================
+
+- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide
+examples of spin-lattice calculations.
+
+- the bfo repository provides an example of spin dynamics calculation
+performed on a fixed lattice, and applied to the multiferroic
+material bismuth-oxide.
+
+- the read_restart directory provides examples allowing to write or
+read data files, and restart magneto-mechanical simulations.
+
+- vizualization of the dump files can be achieved using Ovito or
+VMD. See the vmd repository for help vizualizing results with VMD.
+
+** Note, the aim of this repository is mainly to provide users with
+examples. Better values and tuning of the magnetic and mechanical
+interactions can be achieved for more accurate materials
+simulations. **
diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi
index 5fb35cce3c..94cfd4af6b 100644
--- a/lib/gpu/Nvidia.makefile_multi
+++ b/lib/gpu/Nvidia.makefile_multi
@@ -79,7 +79,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
$(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
$(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
$(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
- $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o
+ $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
+ $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
+ $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
+ $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o
CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
$(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
@@ -137,7 +140,10 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
$(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \
$(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \
$(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \
- $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h
+ $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
+ $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
+ $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
+ $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
@@ -837,6 +843,42 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_
$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
$(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)
+$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h
+ $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu
+
+$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin
+ $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h
+
+$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o
+ $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h
+ $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h
+ $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu
+
+$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin
+ $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h
+
+$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o
+ $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h
+ $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h
+ $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu
+
+$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin
+ $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
+
+$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o
+ $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h
+ $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR)
+
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
diff --git a/src/MAKE/MACHINES/Makefile.theta b/src/MAKE/MACHINES/Makefile.theta
new file mode 100644
index 0000000000..cad5a03b42
--- /dev/null
+++ b/src/MAKE/MACHINES/Makefile.theta
@@ -0,0 +1,133 @@
+# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
+# module load perftools-base perftools
+# make theta -j 8
+# pat_build -g mpi -u ./lmp_theta
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC = CC -mkl
+#OPTFLAGS = -O0
+OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
+ -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+#CCFLAGS += -DLMP_INTEL_NO_TBB
+#CCFLAGS += -DLAMMPS_BIGBIG
+#CCFLAGS += -D_USE_PAPI
+#CCFLAGS += -D_USE_CRAYPAT_API
+SHFLAGS = -fPIC
+DEPFLAGS = -M
+
+LINK = $(CC)
+LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+LINKFLAGS += -dynamic
+LIB =
+#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
+LIB += -ltbbmalloc
+#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
+SIZE = size
+
+ARCHIVE = ar
+ARFLAGS = -rc
+SHLIBFLAGS = -shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 2.2 (step 4) of manual
+
+LMP_INC = -DLAMMPS_GZIP #-DLAMMPS_JPEG
+
+# MPI library
+# see discussion in Section 2.2 (step 5) of manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
+MPI_PATH =
+MPI_LIB =
+
+# FFT library
+# see discussion in Section 2.2 (step 6) of manaul
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC = -DFFT_MKL -DFFT_SINGLE
+FFT_PATH =
+FFT_LIB = -L$(MKLROOT)/lib/intel64/ -Wl,--start-group -lmkl_intel_ilp64 \
+ -lmkl_intel_thread -lmkl_core -Wl,--end-group
+
+# JPEG and/or PNG library
+# see discussion in Section 2.2 (step 7) of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =
+JPG_PATH =
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include Makefile.package.settings
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE): $(OBJ)
+ $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+ $(SIZE) $(EXE)
+
+# Library targets
+
+lib: $(OBJ)
+ $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib: $(OBJ)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+ $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+ $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+ @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+ icc -O -o $@ $<
+
+sinclude .depend
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 0286c3ed1e..0db076acd0 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -49,8 +49,8 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
if (lmp->citeme) lmp->citeme->add(cite_atm_package);
single_enable = 0;
- restartinfo = 0;
- one_coeff = 1;
+ restartinfo = 1;
+ one_coeff = 0;
manybody_flag = 1;
}
@@ -78,6 +78,7 @@ void PairATM::compute(int eflag, int vflag)
double xi,yi,zi,evdwl;
double rij2,rik2,rjk2,r6;
double rij[3],rik[3],rjk[3],fj[3],fk[3];
+ double nu_local;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@@ -128,8 +129,10 @@ void PairATM::compute(int eflag, int vflag)
r6 = rij2*rik2*rjk2;
if (r6 > cut_sixth) continue;
- interaction_ddd(nu[type[i]][type[j]][type[k]],
- r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+ nu_local = nu[type[i]][type[j]][type[k]];
+ if (nu_local == 0.0) continue;
+ interaction_ddd(nu_local,
+ r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
@@ -169,6 +172,12 @@ void PairATM::coeff(int narg, char **arg)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
+ int n = atom->ntypes;
+ for (int i = 0; i <= n; i++)
+ for (int j = 0; j <= n; j++)
+ for (int k = 0; k <= n; k++)
+ nu[i][j][k] = 0.0;
+
int ilo,ihi,jlo,jhi,klo,khi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
@@ -229,7 +238,9 @@ void PairATM::write_restart(FILE *fp)
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
- if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp);
+ if (setflag[i][j])
+ for (k = i; k <= atom->ntypes; k++)
+ fwrite(&nu[i][j][k],sizeof(double),1,fp);
}
}
}
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index b5bfc64010..45a6cda344 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -11,10 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ----------------------------------------------------------------------
- Contributing author: Sergey Lishchuk
-------------------------------------------------------------------------- */
-
#ifdef PAIR_CLASS
PairStyle(atm,PairATM)
@@ -46,9 +42,9 @@ class PairATM : public Pair {
double cut_global, cut_sixth;
double ***nu;
- protected:
- virtual void allocate();
- void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &);
+ void allocate();
+ void interaction_ddd(double, double, double, double, double, double *,
+ double *, double *, double *, double *, int, double &);
};
}
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 4871fe0c40..8b47eff624 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -20,12 +20,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "atom_vec_spin.h"
#include "comm.h"
@@ -54,7 +54,7 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
size_data_atom = 9;
size_data_vel = 4;
xcol_data = 4;
-
+
atom->sp_flag = 1;
}
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index 54818a9b70..b67f62d53d 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -18,11 +18,11 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "atom.h"
#include "compute_spin.h"
#include "domain.h"
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index 97b33197ce..cb34465482 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -18,13 +18,13 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "atom.h"
#include "atom_vec_ellipsoid.h"
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index d91636af58..b75f03212a 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "atom.h"
#include "atom_vec.h"
@@ -59,8 +59,9 @@ static const char cite_fix_nve_spin[] =
"title={Massively parallel symplectic algorithm for coupled magnetic spin "
"dynamics and molecular dynamics},\n"
"author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n"
- "journal={arXiv preprint arXiv:1801.10233},\n"
- "year={2018}\n"
+ "journal={Journal of Computational Physics},\n"
+ "year={2018},\n"
+ "publisher={Elsevier}\n"
"}\n\n";
enum{NONE};
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index eedf0becb7..b908478952 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -18,13 +18,13 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "domain.h"
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index acb7ffe548..398206b26e 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "comm.h"
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index 07ae684939..b792969c5d 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "comm.h"
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 7b05d7337e..1b7b36b6db 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "comm.h"
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index e9e7c1fb3f..315b691d17 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "comm.h"
@@ -436,9 +436,9 @@ void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double sp
meiy *= ME_mech[itype][jtype];
meiz *= ME_mech[itype][jtype];
- fi[0] = meiy*vz - meiz*vy;
- fi[1] = meiz*vx - meix*vz;
- fi[2] = meix*vy - meiy*vx;
+ fi[0] += meiy*vz - meiz*vy;
+ fi[1] += meiz*vx - meix*vz;
+ fi[2] += meix*vy - meiy*vx;
}
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index d74db638bd..0daafad756 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -18,12 +18,12 @@
Please cite the related publication:
Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
Massively parallel symplectic algorithm for coupled magnetic spin dynamics
- and molecular dynamics. arXiv preprint arXiv:1801.10233.
+ and molecular dynamics. Journal of Computational Physics.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "comm.h"
diff --git a/src/balance.cpp b/src/balance.cpp
index 86deb55b47..7dd13e8766 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -350,13 +350,13 @@ void Balance::command(int narg, char **arg)
domain->set_local_box();
// move particles to new processors via irregular()
+ // set disable = 0, so weights migrate with atoms for imbfinal calculation
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
if (wtflag) fixstore->disable = 0;
if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc);
else irregular->migrate_atoms(1);
- if (wtflag) fixstore->disable = 1;
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
@@ -377,9 +377,11 @@ void Balance::command(int narg, char **arg)
}
// imbfinal = final imbalance
+ // set disable = 1, so weights no longer migrate with atoms
double maxfinal;
double imbfinal = imbalance_factor(maxfinal);
+ if (wtflag) fixstore->disable = 1;
// stats output
@@ -540,6 +542,8 @@ void Balance::weight_storage(char *prefix)
fixstore = (FixStore *) modify->fix[modify->nfix-1];
} else fixstore = (FixStore *) modify->fix[ifix];
+ // do not carry weights with atoms during normal atom migration
+
fixstore->disable = 1;
if (prefix) delete [] fixargs[0];
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index b2f545c73f..e748e0ae31 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -114,6 +114,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
if (nevery) force_reneighbor = 1;
lastbalance = -1;
+ next_reneighbor = -1;
// compute initial outputs
@@ -248,6 +249,10 @@ void FixBalance::pre_neighbor()
if (!pending) return;
imbfinal = balance->imbalance_factor(maxloadperproc);
pending = 0;
+
+ // set disable = 1, so weights no longer migrate with atoms
+
+ if (wtflag) balance->fixstore->disable = 1;
}
/* ----------------------------------------------------------------------
@@ -275,21 +280,23 @@ void FixBalance::rebalance()
// reset proc sub-domains
// check and warn if any proc's subbox is smaller than neigh skin
- // since may lead to lost atoms in exchange()
+ // since may lead to lost atoms in comm->exchange()
if (domain->triclinic) domain->set_lamda_box();
domain->set_local_box();
domain->subbox_too_small_check(neighbor->skin);
// move atoms to new processors via irregular()
- // only needed if migrate_check() says an atom moves to far
+ // for non-RCB only needed if migrate_check() says an atom moves too far
// else allow caller's comm->exchange() to do it
+ // set disable = 0, so weights migrate with atoms
+ // important to delay disable = 1 until after pre_neighbor imbfinal calc
+ // b/c atoms may migrate again in comm->exchange()
if (domain->triclinic) domain->x2lamda(atom->nlocal);
if (wtflag) balance->fixstore->disable = 0;
if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc);
else if (irregular->migrate_check()) irregular->migrate_atoms();
- if (wtflag) balance->fixstore->disable = 1;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// invoke KSpace setup_grid() to adjust to new proc sub-domains
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 3b1f3dca77..350e120972 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -154,8 +154,6 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
-
- // printf("AAA HOW GET HERE\n");
}
/* ----------------------------------------------------------------------
diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp
index 8a33cd535b..fd898bd3ab 100644
--- a/src/reset_ids.cpp
+++ b/src/reset_ids.cpp
@@ -16,6 +16,7 @@
#include "atom_vec.h"
#include "domain.h"
#include "comm.h"
+#include "special.h"
#include "memory.h"
#include "error.h"
@@ -44,7 +45,7 @@ void ResetIDs::command(int narg, char **arg)
}
// create an atom map if one doesn't exist already
-
+
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
@@ -93,7 +94,7 @@ void ResetIDs::command(int narg, char **arg)
// forward_comm_array acquires new IDs for ghost atoms
double **newIDs;
- memory->create(newIDs,nall,1,"reset_ids:newIDs");
+ memory->create(newIDs,nall,1,"reset_ids:newIDs");
for (int i = 0; i < nlocal; i++) {
newIDs[i][0] = tag[i];
@@ -105,7 +106,7 @@ void ResetIDs::command(int narg, char **arg)
// loop over bonds, angles, etc and reset IDs in stored topology arrays
// only necessary for molecular = 1, not molecular = 2
// badcount = atom IDs that could not be found
-
+
int badcount = 0;
if (atom->molecular == 1) {
@@ -232,8 +233,15 @@ void ResetIDs::command(int narg, char **arg)
atom->map_init();
atom->map_set();
+ // need to update exclusions with new atom IDs
+
+ if (atom->molecular == 1) {
+ Special special(lmp);
+ special.build();
+ }
+
// delete temporary atom map
-
+
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
--
GitLab
From eeaf90722775d57e12a5505d84bd27358c902918 Mon Sep 17 00:00:00 2001
From: sergeylishchuk <sergey.lishchuk@gmail.com>
Date: Fri, 13 Jul 2018 21:36:40 +0100
Subject: [PATCH 033/332] Resolved merge conflict.
---
doc/src/pair_atm.txt | 67 ---------------------------------------
src/MANYBODY/pair_atm.cpp | 9 ------
2 files changed, 76 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index a79641c6c2..96e002f2f8 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -21,14 +21,10 @@ pair_coeff * * * 0.072 :pre
pair_style hybrid/overlay lj/cut 6.5 atm 2.5
pair_coeff * * lj/cut 1.0 1.0
-<<<<<<< HEAD
pair_coeff 1 1 atm 1 0.064
pair_coeff 1 1 atm 2 0.080
pair_coeff 1 2 atm 2 0.100
pair_coeff 2 2 atm 2 0.125 :pre
-=======
-pair_coeff * * atm * 0.072 :pre
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
[Description:]
@@ -37,7 +33,6 @@ potential for the energy E of a system of atoms as
:c,image(Eqs/pair_atm.jpg)
-<<<<<<< HEAD
where nu is the three-body interaction strength,
and the distances between pairs of atoms r12, r23 and r31
and the angles gamma1, gamma2 and gamma3
@@ -47,18 +42,11 @@ are shown at the diagram:
There is no \"central\" atom, the interaction is symmetric with respect
to permutation of atom types.
-=======
-where r12, r23 and r31 are the distances between pairs of atoms,
-gamma1 is the angle ???, gamma2 is the angle ???, gamma3 is the angle
-???, and nu is the three-body interaction strength.
-A diagram of the 3 atoms might help here.
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-<<<<<<< HEAD
The potential is calculated if all three atoms are in the
"neighbor list"_neighbor.html
and the distances between atoms satisfy r12 r23 r31 > cutoff^3.
@@ -90,57 +78,6 @@ pair_coeff 2 1 1 nu :pre
Thus, to specify all ATM interactions between two atom types (eg 1 and 2)
it is sufficient to provide four pair_coeff commands, eg:
-=======
---------------------
-
-The rest of this section needs some work to make things more clear.
-
-You need to explain exactly how the cutoff is used.
-
-I don't think this is true:
-The calculations are not undertaken if the distances between atoms satisfy
-r12 r23 r31 > cutoff^3.
-
-If r12 > cutoff+skin, then that pair of atoms is not in
-the neighbor list, regardless of what r23 and r31 are,
-so how can it be computed?
-
-What does this line mean?
-Virtual cutoff distance based on a user defined
-tolerance tol is not used.
-
-You must explain exactly what the user needs to put
-in the input script to model single element and multi-element
-systems.
-
-You refer to an ATM potential file, but I don't think there is
-such a thing. There is no code in pair_atm.cpp that reads
-a file. Isn't it all pair_coeff commands? In LAMMPS lingo,
-potential files are the files in the potentials dir.
-There is no such thing for ATM, right?
-
-What is the geometry of i,j,k interactions - you don't explain it.
-Which one is the central atom?
-
-You say all the K values for a particular I,J must be specified.
-I don't see where the code checks for this.
-
-This is the way to word the explation of the per-pair values required:
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the restart files read by the
-"read_restart"_read_restart.html commands:
-
-?? explain what K is and what are the allowed values
-nu (energy/distance^9 units) :ul
-
-Again: what file are you talking about?
-The Axilrod-Teller-Muto potential file must contain entries for all the
-elements listed in the pair_coeff command. It can also contain
-entries for additional elements not being used in a particular
-simulation; LAMMPS ignores those entries.
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
pair_coeff 1 1 1 nu1
pair_coeff 1 1 2 nu2
@@ -231,8 +168,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:link(Axilrod)
[(Axilrod)]
Axilrod and Teller, J Chem Phys, 11, 299 (1943);
-<<<<<<< HEAD
Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
-=======
-Muto, Nippon, Sugaku, Butsuri, Gakkwaishi 17, 629 (1943).
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index a9731a46d8..0db076acd0 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -49,13 +49,8 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
if (lmp->citeme) lmp->citeme->add(cite_atm_package);
single_enable = 0;
-<<<<<<< HEAD
restartinfo = 1;
one_coeff = 0;
-=======
- //restartinfo = 1; // it does save restart info, correct?
- //one_coeff = 0; // it does not only use * *, correct?
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
manybody_flag = 1;
}
@@ -134,13 +129,9 @@ void PairATM::compute(int eflag, int vflag)
r6 = rij2*rik2*rjk2;
if (r6 > cut_sixth) continue;
-<<<<<<< HEAD
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
interaction_ddd(nu_local,
-=======
- interaction_ddd(nu[type[i]][type[j]][type[k]],
->>>>>>> 75ec0a6a990ae6eec59ca7fa80c8cff14d561495
r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
--
GitLab
From e7f4e059cf1d552d9d809f48d26ff7ee4778f996 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 13 Jul 2018 16:46:06 -0600
Subject: [PATCH 034/332] convert to KSspace style rather than fix
---
examples/scafacos/in.scafacos | 25 ++-
lib/scafacos/Install.py | 168 ++++++++++++++++
src/Makefile | 4 +-
src/USER-SCAFACOS/Install.sh | 21 +-
src/USER-SCAFACOS/fix_scafacos.cpp | 7 +-
src/USER-SCAFACOS/fix_scafacos.h | 50 +++++
src/USER-SCAFACOS/scafacos.cpp | 308 +++++++++++++++++++++++++++++
src/USER-SCAFACOS/scafacos.h | 69 +++++++
8 files changed, 626 insertions(+), 26 deletions(-)
create mode 100644 lib/scafacos/Install.py
create mode 100644 src/USER-SCAFACOS/scafacos.cpp
create mode 100644 src/USER-SCAFACOS/scafacos.h
diff --git a/examples/scafacos/in.scafacos b/examples/scafacos/in.scafacos
index ae6b8e0193..f9b6733eef 100644
--- a/examples/scafacos/in.scafacos
+++ b/examples/scafacos/in.scafacos
@@ -5,17 +5,32 @@ atom_style full
read_data data.NaCl
-velocity all set 0.0 0.0 0.0 mom no
+replicate 8 8 8
-pair_style zero 1.0
-pair_coeff * *
+velocity all create 1.5 49893
neighbor 1.0 bin
neigh_modify delay 0
-# using the fmm solver with a tolerance in energy of 10^-3
-fix 1 all scafacos fmm tolerance energy 0.001
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p3m tolerance field 0.001
timestep 0.005
+thermo 10
run 100
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
new file mode 100644
index 0000000000..5d4ca7e96a
--- /dev/null
+++ b/lib/scafacos/Install.py
@@ -0,0 +1,168 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, build, and link to the Scafacos library
+# used to automate the steps described in the README file in this dir
+
+from __future__ import print_function
+import sys,os,re,subprocess
+
+# help message
+
+help = """
+Syntax from src dir: make lib-scafacos args="-b"
+ or: make lib-scafacos args="-p /usr/local/scafacos"
+Syntax from lib dir: python Install.py -b
+ or: python Install.py -p /usr/local/scafacos
+
+specify zero or more options, order does not matter
+
+ -b = download and build the Scafacos library
+ -p = specify folder of existing Scafacos installation
+
+ always creates includelink, liblink to Scafacos dirs
+
+Example:
+
+make lib-scafacos args="-b" # download/build in lib/scafacos/scafacos
+make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation in $HOME
+"""
+
+# settings
+
+#version = "voro++-0.4.6"
+#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
+
+# print error message or help
+
+def error(str=None):
+ if not str: print(help)
+ else: print("ERROR",str)
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
+def geturl(url,fname):
+ success = False
+
+ if which('curl') != None:
+ cmd = 'curl -L -o "%s" %s' % (fname,url)
+ try:
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ success = True
+ except subprocess.CalledProcessError as e:
+ print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+ if not success and which('wget') != None:
+ cmd = 'wget -O "%s" %s' % (fname,url)
+ try:
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ success = True
+ except subprocess.CalledProcessError as e:
+ print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+ if not success:
+ error("Failed to download source code with 'curl' or 'wget'")
+ return
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+#if nargs == 0: error()
+
+homepath = "."
+
+buildflag = False
+pathflag = False
+linkflag = True
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-v":
+ if iarg+2 > nargs: error()
+ version = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-p":
+ if iarg+2 > nargs: error()
+ scafacospath = fullpath(args[iarg+1])
+ pathflag = True
+ iarg += 2
+ elif args[iarg] == "-b":
+ buildflag = True
+ iarg += 1
+ else: error()
+
+homepath = fullpath(homepath)
+#homedir = "%s/%s" % (homepath,version)
+homedir = homepath
+
+if (pathflag):
+ if not os.path.isdir(scafacospath): error("Scafacos path does not exist")
+ homedir =scafacospath
+
+if (buildflag and pathflag):
+ error("Cannot use -b and -p flag at the same time")
+
+#if (not buildflag and not pathflag):
+# error("Have to use either -b or -p flag")
+
+# download and unpack Scafacos tarball
+
+if buildflag:
+ print("Downloading Scafacos ...")
+ geturl(url,"%s/%s.tar.gz" % (homepath,version))
+
+ print("Unpacking Voro++ tarball ...")
+ if os.path.exists("%s/%s" % (homepath,version)):
+ cmd = 'rm -rf "%s/%s"' % (homepath,version)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ os.remove("%s/%s.tar.gz" % (homepath,version))
+ if os.path.basename(homedir) != version:
+ if os.path.exists(homedir):
+ cmd = 'rm -rf "%s"' % homedir
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ os.rename("%s/%s" % (homepath,version),homedir)
+
+# build Scafacos
+
+if buildflag:
+ print("Building Scafacos ...")
+ cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ print(txt.decode('UTF-8'))
+
+# create 2 links in lib/scafacos to Scafacos include/lib dirs
+
+if linkflag:
+ print("Creating links to Scafacos include and lib files")
+ if os.path.isfile("includelink") or os.path.islink("includelink"):
+ os.remove("includelink")
+ if os.path.isfile("liblink") or os.path.islink("liblink"):
+ os.remove("liblink")
+ cmd = 'ln -s "scafacos/include" includelink'
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ cmd = 'ln -s "scafacos/lib" liblink'
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe..5ca5e7ddc6 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -62,8 +62,8 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-intel user-lb user-manifold user-meamc user-meso \
user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
- user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
- user-uef user-vtk
+ user-quip user-reaxc user-scafacos user-smd user-smtbq \
+ user-sph user-tally user-uef user-vtk
PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
python reax voronoi \
diff --git a/src/USER-SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh
index ace610050b..964212fc51 100755
--- a/src/USER-SCAFACOS/Install.sh
+++ b/src/USER-SCAFACOS/Install.sh
@@ -37,31 +37,18 @@ done
if (test $1 = 1) then
if (test -e ../Makefile.package) then
+ sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/scafacos/includelink |' ../Makefile.package
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/scafacos/liblink |' ../Makefile.package
- #sed -i -e 's|^PKG_LIB =[ \t]*|&-lscafacos |' ../Makefile.package
- sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(scafacos_SYSINC) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(scafacos_SYSLIB) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(scafacos_SYSPATH) |' ../Makefile.package
- fi
-
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
- # multiline form needed for BSD sed on Macs
- sed -i -e '4 i \
-include ..\/..\/lib\/scafacos\/Makefile.lammps
-' ../Makefile.package.settings
+ sed -i -e 's%^PKG_LIB =[ \t]*%&`grep Libs: ../../lib/scafacos/liblink/pkgconfig/scafacos.pc | cut -d " " -f 2-` %' ../Makefile.package
fi
elif (test $1 = 0) then
- if (test -e ../Makefile.package) then
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
fi
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*scafacos.*$/d' ../Makefile.package.settings
- fi
-
fi
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
index f82b80dd5f..08aebb9f22 100644
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ b/src/USER-SCAFACOS/fix_scafacos.cpp
@@ -17,6 +17,7 @@
#include <cstdio>
#include <cstring>
+#include <cstdlib>
#include "fix_scafacos.h"
#include "atom.h"
#include "comm.h"
@@ -81,7 +82,7 @@ FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
else
error->all(FLERR,"Illegal fix scafacos command");
++arg_index;
- tolerance_value = atof(arg[arg_index]);
+ tolerance_value = atof(arg[arg_index]);
++arg_index;
}
else
@@ -439,6 +440,7 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
{
if (result)
{
+ printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
std::string err_msg;
std::stringstream ss;
@@ -446,8 +448,9 @@ bool FixScafacos::check_result(FCSResult result, int comm_rank)
<< fcs_result_get_message(result) << "\n";
err_msg = ss.str();
- error->one(FLERR, err_msg.c_str());
+ error -> all(FLERR, err_msg.c_str());
fcs_result_destroy(result);
}
return true;
}
+
diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h
index c48f4d8388..ffd4a94d32 100644
--- a/src/USER-SCAFACOS/fix_scafacos.h
+++ b/src/USER-SCAFACOS/fix_scafacos.h
@@ -111,4 +111,54 @@ class FixScafacos : public Fix {
/* ERROR/WARNING messages:
+E: Must use units metal with fix latte command
+
+UNDOCUMENTED
+
+E: Fix latte currently runs only in serial
+
+UNDOCUMENTED
+
+E: LAMMPS is linked against incompatible LATTE library
+
+UNDOCUMENTED
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
+
+UNDOCUMENTED
+
+E: Could not find fix latte compute ID
+
+UNDOCUMENTED
+
+E: Fix latte compute ID does not compute pe/atom
+
+UNDOCUMENTED
+
+E: Fix latte requires 3d problem
+
+UNDOCUMENTED
+
+E: Fix latte cannot compute Coulomb potential
+
+UNDOCUMENTED
+
+E: Fix latte requires 3d simulation
+
+UNDOCUMENTED
+
+W: Fix latte should come after all other integration fixes
+
+UNDOCUMENTED
+
+E: Internal LATTE problem
+
+UNDOCUMENTED
+
*/
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
new file mode 100644
index 0000000000..89c67b828b
--- /dev/null
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -0,0 +1,308 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Rene Halver (JSC)
+------------------------------------------------------------------------- */
+
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
+#include "scafacos.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+// ScaFaCoS library
+
+#include <string>
+#include <sstream>
+#include "fcs.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
+{
+ if (narg < 2) error->all(FLERR,"Illegal scafacos command");
+
+ int n = strlen(arg[0]) + 1;
+ method = new char[n];
+ strcpy(method,arg[0]);
+
+ // additional args
+
+ int tflag = 0;
+
+ int iarg = 1;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"tolerance") == 0) {
+ if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command");
+ tflag = 1;
+ if (strcmp(arg[iarg+1],"energy") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ else if (strcmp(arg[iarg+1],"energy_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
+ else if (strcmp(arg[iarg+1],"field") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ else if (strcmp(arg[iarg+1],"field_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
+ else if (strcmp(arg[iarg+1],"potential") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
+ else if (strcmp(arg[iarg+1],"potential_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
+ else error->all(FLERR,"Illegal scafacos command");
+ tolerance = force->numeric(FLERR,arg[iarg+2]);
+ iarg += 3;
+ } else error->all(FLERR,"Illegal scafacos command");
+ }
+
+ if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command");
+
+ // initializations
+
+ me = comm->me;
+ initialized = 0;
+
+ maxatom = 0;
+ epot = NULL;
+ efield = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+Scafacos::~Scafacos()
+{
+ delete [] method;
+
+ memory->destroy(epot);
+ memory->destroy(efield);
+
+ // NOTE: any clean-up call to ScaFaCoS needed?
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Scafacos::init()
+{
+ // error checks
+ // NOTE: allow triclinic at some point
+
+ if (domain->dimension == 2)
+ error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
+
+ if (domain->triclinic)
+ error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
+
+ // one-time initialization of ScaFaCoS
+
+ if (!initialized) {
+ result = fcs_init(&fcs,method,world);
+ check_result(result);
+
+ setup_handle();
+
+ result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
+ check_result(result);
+
+ if (me == 0) fcs_print_parameters(fcs);
+
+ double **x = atom->x;
+ double *q = atom->q;
+ int nlocal = atom->nlocal;
+
+ result = fcs_tune(fcs,nlocal,&x[0][0],q);
+ }
+
+ initialized = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Scafacos::setup() {}
+
+/* ---------------------------------------------------------------------- */
+
+void Scafacos::compute(int eflag, int vflag)
+{
+ double **x = atom->x;
+ double *q = atom->q;
+ int nlocal = atom->nlocal;
+
+ // if simluation box has changed, call fcs_tune()
+
+ if (box_has_changed()) {
+ printf("AAA\n");
+ setup_handle();
+ result = fcs_tune(fcs,nlocal,&x[0][0],q);
+ check_result(result);
+ }
+
+ // grow epot & efield if necessary
+
+ if (nlocal > maxatom) {
+ memory->destroy(epot);
+ memory->destroy(efield);
+ maxatom = atom->nmax;
+ memory->create(epot,maxatom,"scafacos:epot");
+ memory->create(efield,maxatom,3,"scafacos:efield");
+
+ }
+
+ // initialize epot & efield
+ // NOTE: is this necessary?
+
+ for (int i = 0; i < nlocal; i++) {
+ epot[i] = 0.0;
+ efield[i][0] = efield[i][1] = efield[i][2] = 0.0;
+ }
+
+ // ScaFaCoS calculation of full Coulombics
+
+ result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
+ check_result(result);
+
+ // apply Efield to each particle
+ // accumulate total energy
+
+ double **f = atom->f;
+
+ double qone;
+ double myeng = 0.0;
+
+ for (int i = 0; i < nlocal; i++) {
+ qone = q[i];
+ f[i][0] += qone * efield[i][0];
+ f[i][1] += qone * efield[i][1];
+ f[i][2] += qone * efield[i][2];
+ myeng += 0.5 * qone * epot[i];
+ }
+
+ MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local arrays
+------------------------------------------------------------------------- */
+
+double Scafacos::memory_usage()
+{
+ double bytes = 0.0;
+ bytes += maxatom * sizeof(double);
+ bytes += 3*maxatom * sizeof(double);
+ return bytes;
+}
+
+/* ----------------------------------------------------------------------
+ setup of ScaFaCoS handle with common parameters
+------------------------------------------------------------------------- */
+
+void Scafacos::setup_handle()
+{
+ // store simulation box params
+ // NOTE: this assumes orthogonal box
+ // NOTE: total particles may not be a 4-byte int
+ // NOTE: what does SCFCS mean by offset?
+ // it's an integer flag in LAMMPS
+
+ old_periodicity[0] = domain->xperiodic;
+ old_periodicity[1] = domain->yperiodic;
+ old_periodicity[2] = domain->zperiodic;
+
+ old_offset[0] = domain->boundary[0][0];
+ old_offset[1] = domain->boundary[1][0];
+ old_offset[2] = domain->boundary[2][0];
+
+ old_box_x[0] = domain->prd[0];
+ old_box_x[1] = old_box_x[2] = 0.0;
+ old_box_y[1] = domain->prd[1];
+ old_box_y[0] = old_box_y[2] = 0.0;
+ old_box_z[2] = domain->prd[2];
+ old_box_z[1] = old_box_z[0] = 0.0;
+
+ old_natoms = atom->natoms;
+
+ // set all required ScaFaCoS params
+
+ result = fcs_set_box_a(fcs,old_box_x);
+ check_result(result);
+
+ result = fcs_set_box_b(fcs,old_box_y);
+ check_result(result);
+
+ result = fcs_set_box_c(fcs,old_box_z);
+ check_result(result);
+
+ result = fcs_set_box_origin(fcs,old_offset);
+ check_result(result);
+
+ result = fcs_set_periodicity(fcs,old_periodicity);
+ check_result(result);
+
+ result = fcs_set_total_particles(fcs,old_natoms);
+ check_result(result);
+
+ // NOTE: for now disable short-range calculations within LAMMPS
+
+ int near_field_flag = 0;
+ result = fcs_set_near_field_flag(fcs,near_field_flag);
+ check_result(result);
+}
+
+/* ----------------------------------------------------------------------
+ check if box parameters changed, requiring a new call to fcs_tune
+------------------------------------------------------------------------- */
+
+bool Scafacos::box_has_changed()
+{
+ int *periodicity = domain->periodicity;
+ double *prd = domain->prd;
+
+ bool changed =
+ (periodicity[0] != old_periodicity[0]) ||
+ (periodicity[1] != old_periodicity[1]) ||
+ (periodicity[2] != old_periodicity[2]) ||
+ (domain->boundary[0][0] != old_offset[0]) ||
+ (domain->boundary[1][0] != old_offset[1]) ||
+ (domain->boundary[2][0] != old_offset[2]) ||
+ (prd[0] != old_box_x[0]) ||
+ (prd[1] != old_box_y[1]) ||
+ (prd[2] != old_box_z[2]) ||
+ (atom->natoms != old_natoms);
+
+ return changed;
+}
+
+/* ----------------------------------------------------------------------
+ check ScaFaCoS result for error condition
+ NOTE: will all procs have same error?
+------------------------------------------------------------------------- */
+
+void Scafacos::check_result(FCSResult result)
+{
+ if (!result) return;
+
+ std::stringstream ss;
+ ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
+ << fcs_result_get_message(result) << "\n";
+ fcs_result_destroy(result);
+ std::string err_msg = ss.str();
+ const char *str = err_msg.c_str();
+
+ error->one(FLERR,str);
+}
+
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
new file mode 100644
index 0000000000..33911ee9fd
--- /dev/null
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -0,0 +1,69 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef KSPACE_CLASS
+
+KSpaceStyle(scafacos,Scafacos)
+
+#else
+
+#ifndef LMP_SCAFACOS_H
+#define LMP_SCAFACOS_H
+
+#include "kspace.h"
+#include "fcs.h"
+
+namespace LAMMPS_NS {
+
+class Scafacos : public KSpace {
+ public:
+ Scafacos(class LAMMPS *, int, char **);
+ ~Scafacos();
+ void init();
+ void setup();
+ void compute(int, int);
+ double memory_usage();
+
+ private:
+ int me;
+
+ char *method;
+ double tolerance;
+ double *epot,**efield;
+ int tolerance_type;
+ int initialized,maxatom;
+
+ FCS fcs; // ScaFaCoS handle
+ FCSResult result; // result for each ScaFaCoS call
+
+ // simulation state: box, natoms
+ // so ScaFaCoS can detect if changes, e.g. for NPT
+
+ fcs_float old_box_x[3],old_box_y[3],old_box_z[3];
+ fcs_float old_offset[3];
+ fcs_int old_periodicity[3];
+ fcs_int old_natoms;
+
+ void check_result(FCSResult);
+ void setup_handle();
+ bool box_has_changed();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
--
GitLab
From d4385ade159f0a2d163ace5fb38328e2d7d8da8e Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 16 Jul 2018 11:22:22 -0600
Subject: [PATCH 035/332] more changes to ATM source and doc file
---
doc/src/Section_commands.txt | 3 +-
doc/src/pair_atm.txt | 132 +++++++++++++-----------------
doc/src/pair_style.txt | 1 +
examples/atm/log.9Jul18.atm.g++.1 | 30 +++----
examples/atm/log.9Jul18.atm.g++.4 | 30 +++----
src/MANYBODY/pair_atm.cpp | 101 +++++++++++++----------
6 files changed, 151 insertions(+), 146 deletions(-)
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index e44595455f..49ade2ca1b 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -582,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"ehex"_fix_ehex.html,
-"enforce2d"_fix_enforce2d.html,
+"enforce2d (k)"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze"_fix_freeze.html,
@@ -929,6 +929,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"adp (o)"_pair_adp.html,
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
+"atm"_pair_atm.html,
"beck (go)"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index 96e002f2f8..e442c32814 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -16,7 +16,7 @@ cutoff = global cutoff for 3-body interactions (distance units) :ul
[Examples:]
-pair_style 2.5
+pair_style atm 2.5
pair_coeff * * * 0.072 :pre
pair_style hybrid/overlay lj/cut 6.5 atm 2.5
@@ -33,106 +33,92 @@ potential for the energy E of a system of atoms as
:c,image(Eqs/pair_atm.jpg)
-where nu is the three-body interaction strength,
-and the distances between pairs of atoms r12, r23 and r31
-and the angles gamma1, gamma2 and gamma3
-are shown at the diagram:
+where nu is the three-body interaction strength. The distances
+between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2,
+gamma3 are as shown in this diagram:
:c,image(JPG/pair_atm_dia.jpg)
-There is no \"central\" atom, the interaction is symmetric with respect
-to permutation of atom types.
+Note that for the interaction between a triplet of atoms I,J,K, there
+is no "central" atom. The interaction is symmetric with respect to
+permutation of the three atoms. In fact, it is computed 3 times by
+the code with each of I,J,K being atom 1. Thus the nu value must be
+the same for all those permutations of the atom types of I,J,K as
+discussed below.
The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-The potential is calculated if all three atoms are in the
-"neighbor list"_neighbor.html
-and the distances between atoms satisfy r12 r23 r31 > cutoff^3.
+The potential for a triplet of atom is calculated only if all 3
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the restart files read by the
"read_restart"_read_restart.html commands:
-K - the type of the third atom
-nu (energy/distance^9 units) :ul
+K = atom type of the third atom (1 to Ntypes)
+nu = prefactor (energy/distance^9 units) :ul
-For a single-atom type simulation, only a single entry is required, eg
+K can be specified in one of two ways. An explicit numeric value can
+be used, as in the 2nd example above. J <= K is required. LAMMPS
+sets the coefficients for the other 5 symmetric interactions to the
+same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set
+to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This
+enforces the symmetry discussed above.
-pair_coeff 1 1 1 nu :pre
+A wildcard asterisk can be used for K to set the coefficients for
+multiple triplets of atom types. This takes the form "*" or "*n" or
+"n*" or "m*n". If N = the number of atom types, then an asterisk with
+no numeric values means all types from 1 to N. A leading asterisk
+means all types from 1 to n (inclusive). A trailing asterisk means
+all types from n to N (inclusive). A middle asterisk means all types
+from m to n (inclusive). Note that only type triplets with J <= K are
+considered; if asterisks imply type triplets where K < J, they are
+ignored.
-where all three atoms are of type 1.
-For a two-atom type simulation, more pair_coeff commands can be used.
-ATM interaction is symmetric with respect to permutation of atoms,
-it is necessary to provide pair_coeff command for one permutation.
-For example, the command
+Note that a pair_coeff command can override a previous setting for the
+same I,J,K triplet. For example, these commands set nu for all I,J.K
+triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet:
-pair_coeff 1 1 2 nu :pre
+pair_coeff * * * 0.25
+pair_coeff 2 3 4 0.1 :pre
-also implies
+Note that for a simulation with a single atom type, only a single
+entry is required, e.g.
-pair_coeff 1 2 1 nu
-pair_coeff 2 1 1 nu :pre
+pair_coeff 1 1 1 0.25 :per
-Thus, to specify all ATM interactions between two atom types (eg 1 and 2)
-it is sufficient to provide four pair_coeff commands, eg:
+For a simulation with two atom types, four pair_coeff commands will
+specify all possible nu values:
pair_coeff 1 1 1 nu1
pair_coeff 1 1 2 nu2
pair_coeff 1 2 2 nu3
pair_coeff 2 2 2 nu4 :pre
-For 3 atom types, 10 pair_coeff commands
-(eg 111, 112, 113, 122, 123, 133, 222, 223, 233, 333)
-will describe all possible ATM interactions, etc.
-It is not necessary to provide the pair_coeff commands for interactions
-of all combinations of atom types: if some combination is not defined then
-there is no ATM interaction for this combination and all its permutations.
+For a simulation with three atom types, ten pair_coeff commands will
+specify all possible nu values:
---------------------
-
-[Steve:]
-
-I think a better syntax for the pair coeff command might be this:
-
-pair_coeff I J v1 v2 ... vN
-
-when 1,2,...N are the number of atom types defined.
-Then there be one pair_coeff command for each type pair,
-the same syntax as all other potentials in LAMMPS use.
-
-[Sergey:]
-
-The reason for my original pair_coeff command syntax is that
-I would like to reserve further arguments for possible extension of
-ATM potential in LAMMPS to further terms in the multipole expansion of
-many-body dispersion interaction.
-For example, the next term would be dipole-dipole-quadrupole, it may be
-activated if the next argument of pair_coeff is present
-without breaking backward compatibility.
-
-Also, the command you propose
-(i) will not account that the value of nu for different permutations
-of atom types is the same, and
-(ii) will make the numbering of atom types messy since there is
-no requirement to supply the values of nu for all triplets.
-
---------------------
-
-I think a better syntax for the pair coeff command might be this:
-
-pair_coeff I J v1 v2 ... vN
-
-when 1,2,...N are the number of atom types defined.
-Then there be one pair_coeff command for each type pair,
-the same syntax as all other potentials in LAMMPS use.
-
-Note that you refer to "elements", but the pair coeff command
-knows nothing about elements. Only atom types. There
-could be 10 atom types that all map to the same chemical
-element.
+pair_coeff 1 1 1 nu1
+pair_coeff 1 1 2 nu2
+pair_coeff 1 1 3 nu3
+pair_coeff 1 2 2 nu4
+pair_coeff 1 2 3 nu5
+pair_coeff 1 3 3 nu6
+pair_coeff 2 2 2 nu7
+pair_coeff 2 2 3 nu8
+pair_coeff 2 3 3 nu9
+pair_coeff 3 3 3 nu10 :pre
+
+By default the nu value for all triplets is set to 0.0. Thus it is
+not required to provide pair_coeff commands that enumerate triplet
+interactions for all K types. If some I,J,K combination is not
+speficied, then there will be no 3-body ATM interactions for that
+combination and all its permutations. However, as with all pair
+styles, it is required to specify a pair_coeff command for all I,J
+combinations, else an error will result.
:line
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 475761add7..7e29544a70 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -103,6 +103,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
+"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
diff --git a/examples/atm/log.9Jul18.atm.g++.1 b/examples/atm/log.9Jul18.atm.g++.1
index 27ba23e3a9..0613533f33 100644
--- a/examples/atm/log.9Jul18.atm.g++.1
+++ b/examples/atm/log.9Jul18.atm.g++.1
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.00120211 secs
+ Time spent = 0.00125098 secs
pair_style hybrid/overlay lj/cut 4.5 atm 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.5929584 0 -3.0438458 -3.6506231
- 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
- 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
- 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
- 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
- 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
-Loop time of 34.5602 on 1 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.733482 0 -3.1843694 -3.924644
+ 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
+ 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
+ 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
+ 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
+ 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
+Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms
-Performance: 124.999 tau/day, 0.723 timesteps/s
+Performance: 155.167 tau/day, 0.898 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 34.556 | 34.556 | 34.556 | 0.0 | 99.99
+Pair | 27.837 | 27.837 | 27.837 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.001323 | 0.001323 | 0.001323 | 0.0 | 0.00
-Output | 0.00018287 | 0.00018287 | 0.00018287 | 0.0 | 0.00
-Modify | 0.0016184 | 0.0016184 | 0.0016184 | 0.0 | 0.00
-Other | | 0.0006311 | | | 0.00
+Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.01
+Output | 0.00016594 | 0.00016594 | 0.00016594 | 0.0 | 0.00
+Modify | 0.001785 | 0.001785 | 0.001785 | 0.0 | 0.01
+Other | | 0.0006731 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:36
+Total wall time: 0:00:29
diff --git a/examples/atm/log.9Jul18.atm.g++.4 b/examples/atm/log.9Jul18.atm.g++.4
index 300f82d581..5627348fab 100644
--- a/examples/atm/log.9Jul18.atm.g++.4
+++ b/examples/atm/log.9Jul18.atm.g++.4
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.000735998 secs
+ Time spent = 0.000769138 secs
pair_style hybrid/overlay lj/cut 4.5 atm 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.5929584 0 -3.0438458 -3.6506231
- 5 1.0335109 -4.5924034 0 -3.0425247 -3.6376817
- 10 1.0347484 -4.5941952 0 -3.0424606 -3.6032204
- 15 1.0357954 -4.5962409 0 -3.0429363 -3.5421887
- 20 1.0350606 -4.595891 0 -3.0436883 -3.4478779
- 25 1.0301813 -4.5896962 0 -3.0448107 -3.3111695
-Loop time of 10.061 on 4 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.733482 0 -3.1843694 -3.924644
+ 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
+ 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
+ 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
+ 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
+ 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
+Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms
-Performance: 429.382 tau/day, 2.485 timesteps/s
+Performance: 598.314 tau/day, 3.462 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 9.8393 | 9.9439 | 10.008 | 2.0 | 98.84
+Pair | 7.1346 | 7.1684 | 7.1863 | 0.8 | 99.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.052154 | 0.11613 | 0.22077 | 18.7 | 1.15
-Output | 7.2241e-05 | 8.2552e-05 | 0.00011158 | 0.0 | 0.00
-Modify | 0.00053763 | 0.00055265 | 0.00056624 | 0.0 | 0.01
-Other | | 0.0002971 | | | 0.00
+Comm | 0.032945 | 0.0509 | 0.084664 | 9.1 | 0.70
+Output | 0.00010133 | 0.00011051 | 0.00013804 | 0.0 | 0.00
+Modify | 0.00059557 | 0.00060683 | 0.00061274 | 0.0 | 0.01
+Other | | 0.000318 | | | 0.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:10
+Total wall time: 0:00:07
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 0db076acd0..2ba8912899 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -61,10 +61,12 @@ PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
PairATM::~PairATM()
{
if (copymode) return;
+
if (allocated) {
- memory->destroy(nu);
memory->destroy(setflag);
memory->destroy(cutsq);
+
+ memory->destroy(nu);
}
}
@@ -89,6 +91,8 @@ void PairATM::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
+ double cutoffsq = cut_global*cut_global;
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -127,10 +131,11 @@ void PairATM::compute(int eflag, int vflag)
rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
r6 = rij2*rik2*rjk2;
- if (r6 > cut_sixth) continue;
+ if (r6 > cutoffsq) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
+
interaction_ddd(nu_local,
r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
@@ -152,32 +157,50 @@ void PairATM::compute(int eflag, int vflag)
if (vflag_fdotr) virial_fdotr_compute();
}
+/* ---------------------------------------------------------------------- */
+
+void PairATM::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(nu,n+1,n+1,n+1,"pair:nu");
+
+ // initialize all nu values to 0.0
+
+ for (int i = 1; i <= n; i++)
+ for (int j = 1; j <= n; j++)
+ for (int k = 1; k <= n; k++)
+ nu[i][j][k] = 0.0;
+}
+
/* ----------------------------------------------------------------------
- reads the input script line with arguments you define
+ global settings
------------------------------------------------------------------------- */
void PairATM::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+
cut_global = force->numeric(FLERR,arg[0]);
}
/* ----------------------------------------------------------------------
- set coefficients for one i,j,k type triplet
+ set coefficients for one I,J,K type triplet
------------------------------------------------------------------------- */
void PairATM::coeff(int narg, char **arg)
{
- if (narg != 4)
- error->all(FLERR,"Incorrect args for pair coefficients");
+ if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
- int n = atom->ntypes;
- for (int i = 0; i <= n; i++)
- for (int j = 0; j <= n; j++)
- for (int k = 0; k <= n; k++)
- nu[i][j][k] = 0.0;
-
int ilo,ihi,jlo,jhi,klo,khi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
@@ -185,16 +208,11 @@ void PairATM::coeff(int narg, char **arg)
double nu_one = force->numeric(FLERR,arg[3]);
- cut_sixth = cut_global*cut_global;
- cut_sixth = cut_sixth*cut_sixth*cut_sixth;
-
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j<=jhi; j++) {
for (int k = MAX(klo,j); k<=khi; k++) {
- nu[i][j][k] = nu[i][k][j] =
- nu[j][i][k] = nu[j][k][i] =
- nu[k][i][j] = nu[k][j][i] = nu_one;
+ nu[i][j][k] = nu_one;
count++;
}
setflag[i][j] = 1;
@@ -211,18 +229,28 @@ void PairATM::coeff(int narg, char **arg)
void PairATM::init_style()
{
// need a full neighbor list
+
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
- perform initialization for one i,j type pair
+ init for one i,j type pair and corresponding j,i
+ also for all k type permutations
------------------------------------------------------------------------- */
double PairATM::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ // set all 6 symmetric permutations of I,J,K types to same nu value
+
+ int ntypes = atom->ntypes;
+ for (int k = j; k <= ntypes; k++)
+ nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] =
+ nu[i][j][k];
+
return cut_global;
}
@@ -239,7 +267,7 @@ void PairATM::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j])
- for (k = i; k <= atom->ntypes; k++)
+ for (k = j; k <= atom->ntypes; k++)
fwrite(&nu[i][j][k],sizeof(double),1,fp);
}
}
@@ -260,7 +288,7 @@ void PairATM::read_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
- if (setflag[i][j]) for (k = i; k <= atom->ntypes; k++) {
+ if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) {
if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
}
@@ -288,25 +316,14 @@ void PairATM::read_restart_settings(FILE *fp)
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
}
-/* ---------------------------------------------------------------------- */
-
-void PairATM::allocate()
-{
- allocated = 1;
- int n = atom->ntypes;
- memory->create(nu,n+1,n+1,n+1,"pair:a");
- memory->create(setflag,n+1,n+1,"pair:setflag");
- memory->create(cutsq,n+1,n+1,"pair:cutsq");
-}
-
/* ----------------------------------------------------------------------
Axilrod-Teller-Muto (dipole-dipole-dipole) potential
------------------------------------------------------------------------- */
void PairATM::interaction_ddd(double nu,
- double r6, double rij2, double rik2, double rjk2,
- double *rij, double *rik, double *rjk,
- double *fj, double *fk, int eflag, double &eng)
+ double r6, double rij2, double rik2, double rjk2,
+ double *rij, double *rik, double *rjk,
+ double *fj, double *fk, int eflag, double &eng)
{
double r5inv,rri,rrj,rrk,rrr;
r5inv = nu / (r6*r6*sqrt(r6));
@@ -314,14 +331,14 @@ void PairATM::interaction_ddd(double nu,
rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
rrr = 5.0*rri*rrj*rrk;
- for (int i=0; i<3; i++) {
- fj[i] = rrj*(rrk - rri)*rik[i]
- - (rrk*rri - rjk2*rik2 + rrr/rij2)*rij[i]
- + (rrk*rri - rik2*rij2 + rrr/rjk2)*rjk[i];
+ for (int i = 0; i < 3; i++) {
+ fj[i] = rrj*(rrk - rri)*rik[i] -
+ (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] +
+ (rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i];
fj[i] *= 3.0*r5inv;
- fk[i] = rrk*(rri + rrj)*rij[i]
- + (rri*rrj + rik2*rij2 - rrr/rjk2)*rjk[i]
- + (rri*rrj + rij2*rjk2 - rrr/rik2)*rik[i];
+ fk[i] = rrk*(rri + rrj)*rij[i] +
+ (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] +
+ (rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i];
fk[i] *= 3.0*r5inv;
}
if (eflag) eng = (r6 - 0.6*rrr)*r5inv;
--
GitLab
From eebd075a1523a6f5d49855d3f73f65651a69c558 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 18 Jul 2018 11:05:54 -0600
Subject: [PATCH 036/332] added scaling for different units (lj, metal, ...)
and storage of atom-wise potentials (eatom / eatom_flag)
---
src/USER-SCAFACOS/scafacos.cpp | 21 +++++++++++++++++++--
1 file changed, 19 insertions(+), 2 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 89c67b828b..c5efd6a191 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -110,6 +110,10 @@ void Scafacos::init()
// one-time initialization of ScaFaCoS
+ scale = 1.0;
+ qqrd2e = force->qqrd2e;
+ //qsum_qsq();
+
if (!initialized) {
result = fcs_init(&fcs,method,world);
check_result(result);
@@ -143,10 +147,15 @@ void Scafacos::compute(int eflag, int vflag)
double *q = atom->q;
int nlocal = atom->nlocal;
+ const double qscale = qqrd2e * scale;
+
// if simluation box has changed, call fcs_tune()
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else
+ eflag_atom = 0;
+
if (box_has_changed()) {
- printf("AAA\n");
setup_handle();
result = fcs_tune(fcs,nlocal,&x[0][0],q);
check_result(result);
@@ -185,13 +194,21 @@ void Scafacos::compute(int eflag, int vflag)
double myeng = 0.0;
for (int i = 0; i < nlocal; i++) {
- qone = q[i];
+ qone = q[i] * qscale;
f[i][0] += qone * efield[i][0];
f[i][1] += qone * efield[i][1];
f[i][2] += qone * efield[i][2];
myeng += 0.5 * qone * epot[i];
}
+ if (eflag_atom)
+ {
+ for (int i = 0; i < nlocal; i++)
+ {
+ eatom[i] = qscale * epot[i];
+ }
+ }
+
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
}
--
GitLab
From 1a959a5683accbf9ad8c36198de73b9557d2c5f0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 18 Jul 2018 13:26:45 -0400
Subject: [PATCH 037/332] must add USER-SCAFACOS to PACKLIB variable in
Makefile
We need "make no-lib" to be correct for automated testing to work, since only known packages with libraries can be successfully compiled through jenkins and other tools. Those scripts usually do "make yes-all no-lib" and then "make yes-XXX" for selected packages where it is known how to build the required libs.
---
src/Makefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/Makefile b/src/Makefile
index 5ca5e7ddc6..4e19f43afb 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -68,7 +68,7 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
- user-netcdf user-qmmm user-quip user-smd user-vtk
+ user-netcdf user-qmmm user-quip user-scafacos user-smd user-vtk
PACKSYS = compress mpiio python user-lb
--
GitLab
From b0c9fde1dd455194f4ef7767d5790ba022eaa7a9 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 18 Jul 2018 15:32:03 -0600
Subject: [PATCH 038/332] more changes from Steve
---
doc/src/Section_packages.txt | 55 +++
doc/src/fix_scafacos.txt | 44 ---
doc/src/kspace_modify.txt | 415 ++++++++++++---------
doc/src/kspace_style.txt | 91 ++++-
examples/USER/scafacos/README | 10 +
examples/{ => USER}/scafacos/data.NaCl | 0
examples/{ => USER}/scafacos/in.scafacos | 0
lib/scafacos/Install.py | 15 +-
src/USER-SCAFACOS/README | 5 +
src/USER-SCAFACOS/fix_scafacos.cpp | 456 -----------------------
src/USER-SCAFACOS/fix_scafacos.h | 164 --------
src/USER-SCAFACOS/scafacos.cpp | 103 ++---
src/USER-SCAFACOS/scafacos.h | 1 +
src/kspace.cpp | 6 +-
src/kspace.h | 2 +
15 files changed, 470 insertions(+), 897 deletions(-)
delete mode 100644 doc/src/fix_scafacos.txt
create mode 100644 examples/USER/scafacos/README
rename examples/{ => USER}/scafacos/data.NaCl (100%)
rename examples/{ => USER}/scafacos/in.scafacos (100%)
create mode 100644 src/USER-SCAFACOS/README
delete mode 100644 src/USER-SCAFACOS/fix_scafacos.cpp
delete mode 100644 src/USER-SCAFACOS/fix_scafacos.h
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 218866e271..ea03bdb74e 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -149,6 +149,7 @@ Package, Description, Doc page, Example, Library
"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-SCAFACOS"_#USER-SCAFACOS, ScaFaCoS long-range Coulombics,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
@@ -2730,6 +2731,60 @@ examples/reax :ul
:line
+RENE: check this section
+
+USER-SCAFACOS package :link(USER-SCAFACOS),h4
+
+[Contents:]
+
+A KSpace style which wraps the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de.
+
+To use this package you must have the ScaFaCoS library available on
+your system. It is available for download at "http://scafacos.de" or
+can be cloned from the git-repository
+"git://github.com/scafacos/scafacos.git".
+
+[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS was developed by a consortium of German research facilities
+with a BMBF (German Ministry of Science and Education) funded project
+in 2009-2012. Participants of the consortium were the Universities of
+Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
+Forschungszentrum Juelich.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first download and
+build the ScaFaCoS library. You can do this manually if you prefer;
+follow the instructions in lib/scafacos/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/scafacos/Install.py script with the specified
+args:
+
+make lib-scafacos # print help message
+make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
+make lib-voronoi args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-user-scafacos
+make machine :pre
+
+make no-user-scafacos
+make machine :pre
+
+[Supporting info:]
+
+src/USER-SCAFACOS: filenames -> commands
+src/USER-SCAFACOS/README
+"kspace_style scafacos"_kspace_style.html
+"kspace_modify"_kspace_modify.html
+examples/USER/scafacos :ul
+
+:line
+
USER-SMD package :link(USER-SMD),h4
[Contents:]
diff --git a/doc/src/fix_scafacos.txt b/doc/src/fix_scafacos.txt
deleted file mode 100644
index 1a65ed0c5e..0000000000
--- a/doc/src/fix_scafacos.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-fix scafacos command :h3
-
-[Syntax:]
-
-fix ID group-ID scafacos solver tol_type tolerance :pre
-
-ID, group-ID are documented in "fix"_fix.html command
-scafacos = style name of this fix command
-solver = NULL or name of solver for electro-statics computation :ul
-tol_type = NULL or one of (energy, energy_rel, field, field_rel, potential, potential_rel)
-tolerance = only of tol_type is given, value of tolerance
-
-[Examples:]
-
-fix 1 all scafacos fmm
-fix 1 all scafacos p3m field 0.001
-
-[Description:]
-
-This fix style is a wrapper for the Coulomb solver library ScaFaCoS,
-which provides a selection of different solvers for the compuation
-of electro-static interaction. If you download and build ScaFaCoS,
-it can be called as libray by LAMMPS via this fix, which allows the
-selection of a solver as well as setting the tolerance of a chosen
-parameter (if compatible with the chosen solver).
-
-ScaFaCoS was developed by a consortium of German research facilities
-with a BMBF (German Ministry of Science and Education) funded project
-in 2009-2012. Participants of the consortium were the Universities of
-Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
-Forschungszentrum Juelich.
-
-The library is available at "http://scafacos.de" or can be cloned
-from the git-repository "git://github.com/scafacos/scafacos.git".
-
-:line
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 6d27bb7076..fbc569306c 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -13,47 +13,51 @@ kspace_modify command :h3
kspace_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
-keyword = {mesh} or {order} or {order/disp} or {mix/disp} or {overlap} or {minorder} or {force} or {gewald} or {gewald/disp} or {slab} or (nozforce} or {compute} or {cutoff/adjust} or {fftbench} or {collective} or {diff} or {kmax/ewald} or {force/disp/real} or {force/disp/kspace} or {splittol} or {disp/auto}:l
+keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} or {fftbench} or {force/disp/kspace} or {force/disp/real} or {force} or {gewald/disp} or {gewald} or {kmax/ewald} or {mesh} or {minorder} or {mix/disp} or {order/disp} or {order} or {overlap} or {scafacos} or {slab} or {splittol} :l
+ {collective} value = {yes} or {no}
+ {compute} value = {yes} or {no}
+ {cutoff/adjust} value = {yes} or {no}
+ {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
+ {disp/auto} value = yes or no
+ {fftbench} value = {yes} or {no}
+ {force/disp/real} value = accuracy (force units)
+ {force/disp/kspace} value = accuracy (force units)
+ {force} value = accuracy (force units)
+ {gewald} value = rinv (1/distance units)
+ rinv = G-ewald parameter for Coulombics
+ {gewald/disp} value = rinv (1/distance units)
+ rinv = G-ewald parameter for dispersion
+ {kmax/ewald} value = kx ky kz
+ kx,ky,kz = number of Ewald sum kspace vectors in each dimension
{mesh} value = x y z
x,y,z = grid size in each dimension for long-range Coulombics
{mesh/disp} value = x y z
x,y,z = grid size in each dimension for 1/r^6 dispersion
+ {minorder} value = M
+ M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
+ {mix/disp} value = {pair} or {geom} or {none}
{order} value = N
N = extent of Gaussian for PPPM or MSM mapping of charge to grid
{order/disp} value = N
N = extent of Gaussian for PPPM mapping of dispersion term to grid
- {mix/disp} value = {pair} or {geom} or {none}
{overlap} = {yes} or {no} = whether the grid stencil for PPPM is allowed to overlap into more than the nearest-neighbor processor
- {minorder} value = M
- M = min allowed extent of Gaussian when auto-adjusting to minimize grid communication
- {force} value = accuracy (force units)
- {gewald} value = rinv (1/distance units)
- rinv = G-ewald parameter for Coulombics
- {gewald/disp} value = rinv (1/distance units)
- rinv = G-ewald parameter for dispersion
+ {pressure/scalar} value = {yes} or {no}
+ {scafacos} values = option value1 value2 ...
+ option = {tolerance}
+ value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel}
{slab} value = volfactor or {nozforce}
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
{nozforce} turns off kspace forces in the z direction
- {compute} value = {yes} or {no}
- {cutoff/adjust} value = {yes} or {no}
- {pressure/scalar} value = {yes} or {no}
- {fftbench} value = {yes} or {no}
- {collective} value = {yes} or {no}
- {diff} value = {ad} or {ik} = 2 or 4 FFTs for PPPM in smoothed or non-smoothed mode
- {kmax/ewald} value = kx ky kz
- kx,ky,kz = number of Ewald sum kspace vectors in each dimension
- {force/disp/real} value = accuracy (force units)
- {force/disp/kspace} value = accuracy (force units)
{splittol} value = tol
- tol = relative size of two eigenvalues (see discussion below)
- {disp/auto} value = yes or no :pre
+ tol = relative size of two eigenvalues (see discussion below) :pre
:ule
[Examples:]
kspace_modify mesh 24 24 30 order 6
-kspace_modify slab 3.0 :pre
+kspace_modify slab 3.0
+kspace_modify scafacos tolerance energy :pre
[Description:]
@@ -61,6 +65,132 @@ Set parameters used by the kspace solvers defined by the
"kspace_style"_kspace_style.html command. Not all parameters are
relevant to all kspace styles.
+:line
+
+The {collective} keyword applies only to PPPM. It is set to {no} by
+default, except on IBM BlueGene machines. If this option is set to
+{yes}, LAMMPS will use MPI collective operations to remap data for
+3d-FFT operations instead of the default point-to-point communication.
+This is faster on IBM BlueGene machines, and may also be faster on
+other machines if they have an efficient implementation of MPI
+collective operations and adequate hardware.
+
+:line
+
+The {compute} keyword allows Kspace computations to be turned off,
+even though a "kspace_style"_kspace_style.html is defined. This is
+not useful for running a real simulation, but can be useful for
+debugging purposes or for computing only partial forces that do not
+include the Kspace contribution. You can also do this by simply not
+defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
+"pair_style"_pair_style.html requires a kspace style to be defined.
+This keyword gives you that option.
+
+:line
+
+The {cutoff/adjust} keyword applies only to MSM. If this option is
+turned on, the Coulombic cutoff will be automatically adjusted at the
+beginning of the run to give the desired estimated error. Other
+cutoffs such as LJ will not be affected. If the grid is not set using
+the {mesh} command, this command will also attempt to use the optimal
+grid that minimizes cost using an estimate given by
+"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat
+experimental, and still may not yield the optimal parameters.
+
+:line
+
+The {diff} keyword specifies the differentiation scheme used by the
+PPPM method to compute forces on particles given electrostatic
+potentials on the PPPM mesh. The {ik} approach is the default for
+PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It
+performs differentiation in Kspace, and uses 3 FFTs to transfer each
+component of the computed fields back to real space for total of 4
+FFTs per timestep.
+
+The analytic differentiation {ad} approach uses only 1 FFT to transfer
+information back to real space for a total of 2 FFTs per timestep. It
+then performs analytic differentiation on the single quantity to
+generate the 3 components of the electric field at each grid point.
+This is sometimes referred to as "smoothed" PPPM. This approach
+requires a somewhat larger PPPM mesh to achieve the same accuracy as
+the {ik} method. Currently, only the {ik} method (default) can be
+used for a triclinic simulation cell with PPPM. The {ad} method is
+always used for MSM.
+
+NOTE: Currently, not all PPPM styles support the {ad} option. Support
+for those PPPM variants will be added later.
+
+:line
+
+The {disp/auto} option controls whether the pppm/disp is allowed to
+generate PPPM parameters automatically. If set to {no}, parameters have
+to be specified using the {gewald/disp}, {mesh/disp},
+{force/disp/real} or {force/disp/kspace} keywords, or
+the code will stop with an error message. When this option is set to
+{yes}, the error message will not appear and the simulation will start.
+For a typical application, using the automatic parameter generation
+will provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+
+:line
+
+The {fftbench} keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.
+
+:line
+
+The {force/disp/real} and {force/disp/kspace} keywords set the force
+accuracy for the real and space computations for the dispersion part
+of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal
+performance and accuracy in the results is obtained when these values
+are different.
+
+:line
+
+The {force} keyword overrides the relative accuracy parameter set by
+the "kspace_style"_kspace_style.html command with an absolute
+accuracy. The accuracy determines the RMS error in per-atom forces
+calculated by the long-range solver and is thus specified in force
+units. A negative value for the accuracy setting means to use the
+relative accuracy parameter. The accuracy setting is used in
+conjunction with the pairwise cutoff to determine the number of
+K-space vectors for style {ewald}, the FFT grid size for style
+{pppm}, or the real space grid size for style {msm}.
+
+:line
+
+The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
+parameter for charge as {rinv} in reciprocal distance units. Without
+this setting, LAMMPS chooses the parameter automatically as a function
+of cutoff, precision, grid spacing, etc. This means it can vary from
+one simulation to the next which may not be desirable for matching a
+KSpace solver to a pre-tabulated pairwise potential. This setting can
+also be useful if Ewald or PPPM fails to choose a good grid spacing
+and G-ewald parameter automatically. If the value is set to 0.0,
+LAMMPS will choose the G-ewald parameter automatically. MSM does not
+use the {gewald} parameter.
+
+:line
+
+The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
+parameter for dispersion as {rinv} in reciprocal distance units. It
+has the same meaning as the {gewald} setting for Coulombics.
+
+:line
+
+The {kmax/ewald} keyword sets the number of kspace vectors in each
+dimension for kspace style {ewald}. The three values must be positive
+integers, or else (0,0,0), which unsets the option. When this option
+is not set, the Ewald sum scheme chooses its own kspace vectors,
+consistent with the user-specified accuracy and pairwise cutoff. In
+any case, if kspace style {ewald} is invoked, the values used are
+printed to the screen and the log file at the start of the run.
+
+:line
+
The {mesh} keyword sets the grid size for kspace style {pppm} or
{msm}. In the case of PPPM, this is the FFT mesh, and each dimension
must be factorizable into powers of 2, 3, and 5. In the case of MSM,
@@ -70,6 +200,8 @@ or MSM solver chooses its own grid size, consistent with the
user-specified accuracy and pairwise cutoff. Values for x,y,z of
0,0,0 unset the option.
+:line
+
The {mesh/disp} keyword sets the grid size for kspace style
{pppm/disp}. This is the FFT mesh for long-range dispersion and ach
dimension must be factorizable into powers of 2, 3, and 5. When this
@@ -77,6 +209,45 @@ option is not set, the PPPM solver chooses its own grid size,
consistent with the user-specified accuracy and pairwise cutoff.
Values for x,y,z of 0,0,0 unset the option.
+:line
+
+The {minorder} keyword allows LAMMPS to reduce the {order} setting if
+necessary to keep the communication of ghost grid point limited to
+exchanges between nearest-neighbor processors. See the discussion of
+the {overlap} keyword for details. If the {overlap} keyword is set to
+{yes}, which is the default, this is never needed. If it set to {no}
+and overlap occurs, then LAMMPS will reduce the order setting, one
+step at a time, until the ghost grid overlap only extends to nearest
+neighbor processors. The {minorder} keyword limits how small the
+{order} setting can become. The minimum allowed value for PPPM is 2,
+which is the default. If {minorder} is set to the same value as
+{order} then no reduction is allowed, and LAMMPS will generate an
+error if the grid communication is non-nearest-neighbor and {overlap}
+is set to {no}. The {minorder} keyword is not currently supported in
+MSM.
+
+:line
+
+The {mix/disp} keyword selects the mixing rule for the dispersion
+coefficients. With {pair}, the dispersion coefficients of unlike
+types are computed as indicated with "pair_modify"_pair_modify.html.
+With {geom}, geometric mixing is enforced on the dispersion
+coefficients in the kspace coefficients. When using the arithmetic
+mixing rule, this will speed-up the simulations but introduces some
+error in the force computations, as shown in "(Wennberg)"_#Wennberg.
+With {none}, it is assumed that no mixing rule is
+applicable. Splitting of the dispersion coefficients will be performed
+as described in "(Isele-Holder)"_#Isele-Holder1.
+
+This splitting can be influenced with the {splittol} keywords. Only
+the eigenvalues that are larger than tol compared to the largest
+eigenvalues are included. Using this keywords the original matrix of
+dispersion coefficients is approximated. This leads to faster
+computations, but the accuracy in the reciprocal space computations of
+the dispersion part is decreased.
+
+:line
+
The {order} keyword determines how many grid spacings an atom's charge
extends when it is mapped to the grid in kspace style {pppm} or {msm}.
The default for this parameter is 5 for PPPM and 8 for MSM, which
@@ -91,11 +262,23 @@ inherent trade-off involved: a small grid will lower the cost of FFTs
or MSM direct sum, but a larger order parameter will increase the cost
of interpolating charge/fields to/from the grid.
+The PPPM order parameter may be reset by LAMMPS when it sets up the
+FFT grid if the implied grid stencil extends beyond the grid cells
+owned by neighboring processors. Typically this will only occur when
+small problems are run on large numbers of processors. A warning will
+be generated indicating the order parameter is being reduced to allow
+LAMMPS to run the problem. Automatic adjustment of the order parameter
+is not supported in MSM.
+
+:line
+
The {order/disp} keyword determines how many grid spacings an atom's
dispersion term extends when it is mapped to the grid in kspace style
{pppm/disp}. It has the same meaning as the {order} setting for
Coulombics.
+:line
+
The {overlap} keyword can be used in conjunction with the {minorder}
keyword with the PPPM styles to adjust the amount of communication
that occurs when values on the FFT grid are exchanged between
@@ -111,53 +294,42 @@ communication will be limited to nearest-neighbor processors and the
{minorder} keyword discussion. The {overlap} keyword is always set to
{yes} in MSM.
-The {minorder} keyword allows LAMMPS to reduce the {order} setting if
-necessary to keep the communication of ghost grid point limited to
-exchanges between nearest-neighbor processors. See the discussion of
-the {overlap} keyword for details. If the {overlap} keyword is set to
-{yes}, which is the default, this is never needed. If it set to {no}
-and overlap occurs, then LAMMPS will reduce the order setting, one
-step at a time, until the ghost grid overlap only extends to nearest
-neighbor processors. The {minorder} keyword limits how small the
-{order} setting can become. The minimum allowed value for PPPM is 2,
-which is the default. If {minorder} is set to the same value as
-{order} then no reduction is allowed, and LAMMPS will generate an
-error if the grid communication is non-nearest-neighbor and {overlap}
-is set to {no}. The {minorder} keyword is not currently supported in
-MSM.
+:line
-The PPPM order parameter may be reset by LAMMPS when it sets up the
-FFT grid if the implied grid stencil extends beyond the grid cells
-owned by neighboring processors. Typically this will only occur when
-small problems are run on large numbers of processors. A warning will
-be generated indicating the order parameter is being reduced to allow
-LAMMPS to run the problem. Automatic adjustment of the order parameter
-is not supported in MSM.
+The {pressure/scalar} keyword applies only to MSM. If this option is
+turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
+be computed, which can be used, for example, to run an isotropic barostat.
+Computing the full pressure tensor with MSM is expensive, and this option
+provides a faster alternative. The scalar pressure is computed using a
+relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer
+instead of using the virial equation. This option cannot be used to access
+individual components of the pressure tensor, to compute per-atom virial,
+or with suffix kspace/pair styles of MSM, like OMP or GPU.
-The {force} keyword overrides the relative accuracy parameter set by
-the "kspace_style"_kspace_style.html command with an absolute
-accuracy. The accuracy determines the RMS error in per-atom forces
-calculated by the long-range solver and is thus specified in force
-units. A negative value for the accuracy setting means to use the
-relative accuracy parameter. The accuracy setting is used in
-conjunction with the pairwise cutoff to determine the number of
-K-space vectors for style {ewald}, the FFT grid size for style
-{pppm}, or the real space grid size for style {msm}.
+:line
-The {gewald} keyword sets the value of the Ewald or PPPM G-ewald
-parameter for charge as {rinv} in reciprocal distance units. Without
-this setting, LAMMPS chooses the parameter automatically as a function
-of cutoff, precision, grid spacing, etc. This means it can vary from
-one simulation to the next which may not be desirable for matching a
-KSpace solver to a pre-tabulated pairwise potential. This setting can
-also be useful if Ewald or PPPM fails to choose a good grid spacing
-and G-ewald parameter automatically. If the value is set to 0.0,
-LAMMPS will choose the G-ewald parameter automatically. MSM does not
-use the {gewald} parameter.
+RENE: check this section
-The {gewald/disp} keyword sets the value of the Ewald or PPPM G-ewald
-parameter for dispersion as {rinv} in reciprocal distance units. It
-has the same meaning as the {gewald} setting for Coulombics.
+The {scafacos} keyword is used for settings that are passed to the
+ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html.
+
+The {tolerance} option affects how the {accuracy} specified with
+the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS.
+The following values may be used:
+
+energy = absolute accuracy in total Coulomic energy
+energy_rel = relative accuracy in total Coulomic energy
+field = absolute accuracy in electric field
+field_rel = relative accuracy in electric field
+potential = absolute accuracy in total Coulomic potential
+potential_rel = relative accuracy in total Coulomic potential
+
+RENE: which one is closest to what LAMMPS used (see kspace_style
+command) - is it "field"? That's why I set it as the default.
+
+RENE: How is potential different than energy for this ??
+
+:line
The {slab} keyword allows an Ewald or PPPM solver to be used for a
systems that are periodic in x,y but non-periodic in z - a
@@ -191,109 +363,11 @@ the "fix efield"_fix_efield.html command, it will not give the correct
dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction
not being compatible with how "fix efield"_fix_efield.html works.
-The {compute} keyword allows Kspace computations to be turned off,
-even though a "kspace_style"_kspace_style.html is defined. This is
-not useful for running a real simulation, but can be useful for
-debugging purposes or for computing only partial forces that do not
-include the Kspace contribution. You can also do this by simply not
-defining a "kspace_style"_kspace_style.html, but a Kspace-compatible
-"pair_style"_pair_style.html requires a kspace style to be defined.
-This keyword gives you that option.
-
-The {cutoff/adjust} keyword applies only to MSM. If this option is
-turned on, the Coulombic cutoff will be automatically adjusted at the
-beginning of the run to give the desired estimated error. Other
-cutoffs such as LJ will not be affected. If the grid is not set using
-the {mesh} command, this command will also attempt to use the optimal
-grid that minimizes cost using an estimate given by
-"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat
-experimental, and still may not yield the optimal parameters.
-
-The {pressure/scalar} keyword applies only to MSM. If this option is
-turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
-be computed, which can be used, for example, to run an isotropic barostat.
-Computing the full pressure tensor with MSM is expensive, and this option
-provides a faster alternative. The scalar pressure is computed using a
-relationship between the Coulombic energy and pressure "(Hummer)"_#Hummer
-instead of using the virial equation. This option cannot be used to access
-individual components of the pressure tensor, to compute per-atom virial,
-or with suffix kspace/pair styles of MSM, like OMP or GPU.
-
-The {fftbench} keyword applies only to PPPM. It is off by default. If
-this option is turned on, LAMMPS will perform a short FFT benchmark
-computation and report its timings, and will thus finish a some seconds
-later than it would if this option were off.
-
-The {collective} keyword applies only to PPPM. It is set to {no} by
-default, except on IBM BlueGene machines. If this option is set to
-{yes}, LAMMPS will use MPI collective operations to remap data for
-3d-FFT operations instead of the default point-to-point communication.
-This is faster on IBM BlueGene machines, and may also be faster on
-other machines if they have an efficient implementation of MPI
-collective operations and adequate hardware.
-
-The {diff} keyword specifies the differentiation scheme used by the
-PPPM method to compute forces on particles given electrostatic
-potentials on the PPPM mesh. The {ik} approach is the default for
-PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It
-performs differentiation in Kspace, and uses 3 FFTs to transfer each
-component of the computed fields back to real space for total of 4
-FFTs per timestep.
-
-The analytic differentiation {ad} approach uses only 1 FFT to transfer
-information back to real space for a total of 2 FFTs per timestep. It
-then performs analytic differentiation on the single quantity to
-generate the 3 components of the electric field at each grid point.
-This is sometimes referred to as "smoothed" PPPM. This approach
-requires a somewhat larger PPPM mesh to achieve the same accuracy as
-the {ik} method. Currently, only the {ik} method (default) can be
-used for a triclinic simulation cell with PPPM. The {ad} method is
-always used for MSM.
-
-NOTE: Currently, not all PPPM styles support the {ad} option. Support
-for those PPPM variants will be added later.
-
-The {kmax/ewald} keyword sets the number of kspace vectors in each
-dimension for kspace style {ewald}. The three values must be positive
-integers, or else (0,0,0), which unsets the option. When this option
-is not set, the Ewald sum scheme chooses its own kspace vectors,
-consistent with the user-specified accuracy and pairwise cutoff. In
-any case, if kspace style {ewald} is invoked, the values used are
-printed to the screen and the log file at the start of the run.
+:line
-With the {mix/disp} keyword one can select the mixing rule for the
-dispersion coefficients. With {pair}, the dispersion coefficients of
-unlike types are computed as indicated with
-"pair_modify"_pair_modify.html. With {geom}, geometric mixing is
-enforced on the dispersion coefficients in the kspace
-coefficients. When using the arithmetic mixing rule, this will
-speed-up the simulations but introduces some error in the force
-computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is
-assumed that no mixing rule is applicable. Splitting of the dispersion
-coefficients will be performed as described in
-"(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with
-the {splittol} keywords. Only the eigenvalues that are larger than tol
-compared to the largest eigenvalues are included. Using this keywords
-the original matrix of dispersion coefficients is approximated. This
-leads to faster computations, but the accuracy in the reciprocal space
-computations of the dispersion part is decreased.
+The {splittol} keyword is disussed above with the {mix/disp} keyword.
-The {force/disp/real} and {force/disp/kspace} keywords set the force
-accuracy for the real and space computations for the dispersion part
-of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal
-performance and accuracy in the results is obtained when these values
-are different.
-
-The {disp/auto} option controls whether the pppm/disp is allowed to
-generate PPPM parameters automatically. If set to {no}, parameters have
-to be specified using the {gewald/disp}, {mesh/disp},
-{force/disp/real} or {force/disp/kspace} keywords, or
-the code will stop with an error message. When this option is set to
-{yes}, the error message will not appear and the simulation will start.
-For a typical application, using the automatic parameter generation
-will provide simulations that are either inaccurate or slow. Using this
-option is thus not recommended. For guidelines on how to obtain good
-parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+:line
[Restrictions:] none
@@ -306,10 +380,11 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
-yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
-(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
-split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
-order/disp = 7.
+yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff =
+ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace
+= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel,
+order = order/disp = 7. For scafacos settings, scafacos tolerance
+field.
:line
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 4f27c9aa78..e5333489cc 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -12,7 +12,7 @@ kspace_style command :h3
kspace_style style value :pre
-style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} :ulb,l
+style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
{none} value = none
{ewald} value = accuracy
accuracy = desired relative error in forces
@@ -22,7 +22,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{pppm} value = accuracy
accuracy = desired relative error in forces
- {pppm/cg} value = accuracy (smallq)
+ {pppm/cg} values = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{pppm/disp} value = accuracy
@@ -56,7 +56,10 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
{msm/cg/omp} value = accuracy (smallq)
accuracy = desired relative error in forces
- smallq = cutoff for charges to be considered (optional) (charge units) :pre
+ smallq = cutoff for charges to be considered (optional) (charge units)
+ {scafacos} values = method accuracy
+ method = fmm or p3m or ... RENE
+ accuracy = desired relative error in forces :pre
:ule
[Examples:]
@@ -64,6 +67,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace style msm 1.0e-4
+kspace style scafacos fmm 1.0e-4
kspace_style none :pre
[Description:]
@@ -210,6 +214,63 @@ pressure simulation with MSM will cause the code to run slower.
:line
+RENE: edit this section
+
+The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de which provides a variety of solver
+methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012
+gives an overview of ScaFaCoS.
+
+ScaFaCoS was developed by a consortium of German research facilities
+with a BMBF (German Ministry of Science and Education) funded project
+in 2009-2012. Participants of the consortium were the Universities of
+Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
+Forschungszentrum Juelich.
+
+The library is available for download at "http://scafacos.de" or can
+be cloned from the git-repository
+"git://github.com/scafacos/scafacos.git".
+
+In order to use this KSpace style, you must download and build the
+ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
+installed package which links LAMMPS to the ScaFaCoS library.
+See details on "this page"_Section_packages.html#USER-SCAFACOS.
+
+NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
+Coulombic interactions, both short- and long-range. Thus you should
+NOT use a Coulmbic pair style when using kspace_style scafacos. Thus
+the total Coulombic energy (short- and long-range) will be tallied for
+"thermodynamic output"_thermo_style.html command as part of the
+{elong} keyword; the {ecoul} keyword will be zero.
+
+NOTE: See the restriction below about use of ScaFaCoS in LAMMPS with
+molecular charged systems or the TIP4P water model.
+
+Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
+Coulombic interactions, both short- and long-range. Thus you should
+NOT use a Coulmbic pair style when using kspace_style scafacos. Thus
+the total Coulombic energy (short- and long-range) will be tallied for
+"thermodynamic output"_thermo_style.html command as part of the
+{elong} keyword; the {ecoul} keyword will be zero.
+
+The specified {method} determines which ScaFaCoS algorithm is used.
+The list of methods shown above are the ScaFaCoS methods currently
+available from LAMMPS.
+
+RENE: explain this accuracy better compared to what
+it means for other LAMMPS methods?
+
+The specified {accuracy} is similar to the accuracy setting for other
+LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
+it in different ways for different methods it supports. See the
+"kspace_modify scafacos accuracy"_kspace_modify.html command for
+details.
+
+The "kspace_modify scafacos"_kspace_modify.html command also explains
+all the ScaFaCoS options currently exposed to LAMMPS.
+
+:line
+
The specified {accuracy} determines the relative RMS error in per-atom
forces calculated by the long-range solver. It is set as a
dimensionless number, relative to the force that two unit point
@@ -321,12 +382,24 @@ dimensions. The only exception is if the slab option is set with
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
+The scafacos KSpace style will only be enabled if LAMMPS is built with
+the USER-SCAFACOS package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+The use of ScaFaCos in LAMMPS does not yet support molecular charged
+systems where the short-range Coulombic interactions between atoms in
+the same bond/angle/dihedral are weighted by the
+"special_bonds"_special_bonds.html command. Likewise it does not
+support the "TIP4P water style" where a fictitious charge site is
+introduced in each water molecule.
+
[Related commands:]
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
-lj/long/coul/long"_pair_lj_long.html, "pair_style buck/coul/long"_pair_buck.html
+lj/long/coul/long"_pair_lj_long.html, "pair_style
+buck/coul/long"_pair_buck.html
[Default:]
@@ -384,5 +457,11 @@ Evaluation of Forces for the Simulation of Biomolecules, University of
Illinois at Urbana-Champaign, (2006).
:link(Hardy2009)
-[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009)
-164-177.
+[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
+(2009).
+
+RENE:
+
+:link(Who2012)
+[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
+(2012).
diff --git a/examples/USER/scafacos/README b/examples/USER/scafacos/README
new file mode 100644
index 0000000000..0ddd19d3ee
--- /dev/null
+++ b/examples/USER/scafacos/README
@@ -0,0 +1,10 @@
+RENE: this dir needs a few short-running examples,
+for both 1 and 4 procs, of using different Scafacos methods.
+with sample log file outputs - so users can verify
+they are running it correctly
+
+For each input script, there should be files like
+
+in.scafacos.fmm
+log.20Jul18.scafacos.fmm.g++.1
+log.20Jul18.scafacos.fmm.g++.4
diff --git a/examples/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl
similarity index 100%
rename from examples/scafacos/data.NaCl
rename to examples/USER/scafacos/data.NaCl
diff --git a/examples/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos
similarity index 100%
rename from examples/scafacos/in.scafacos
rename to examples/USER/scafacos/in.scafacos
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
index 5d4ca7e96a..1b39335511 100644
--- a/lib/scafacos/Install.py
+++ b/lib/scafacos/Install.py
@@ -29,7 +29,7 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation
# settings
-#version = "voro++-0.4.6"
+version = "scafacos-1.0"
#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
# print error message or help
@@ -89,7 +89,6 @@ def geturl(url,fname):
args = sys.argv[1:]
nargs = len(args)
-#if nargs == 0: error()
homepath = "."
@@ -114,8 +113,7 @@ while iarg < nargs:
else: error()
homepath = fullpath(homepath)
-#homedir = "%s/%s" % (homepath,version)
-homedir = homepath
+homedir = "%s/%s" % (homepath,version)
if (pathflag):
if not os.path.isdir(scafacospath): error("Scafacos path does not exist")
@@ -124,16 +122,13 @@ if (pathflag):
if (buildflag and pathflag):
error("Cannot use -b and -p flag at the same time")
-#if (not buildflag and not pathflag):
-# error("Have to use either -b or -p flag")
-
# download and unpack Scafacos tarball
if buildflag:
print("Downloading Scafacos ...")
geturl(url,"%s/%s.tar.gz" % (homepath,version))
- print("Unpacking Voro++ tarball ...")
+ print("Unpacking Scafacos tarball ...")
if os.path.exists("%s/%s" % (homepath,version)):
cmd = 'rm -rf "%s/%s"' % (homepath,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
@@ -162,7 +157,7 @@ if linkflag:
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
- cmd = 'ln -s "scafacos/include" includelink'
+ cmd = 'ln -s "%s/include" includelink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
- cmd = 'ln -s "scafacos/lib" liblink'
+ cmd = 'ln -s "%s/lib" liblink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
diff --git a/src/USER-SCAFACOS/README b/src/USER-SCAFACOS/README
new file mode 100644
index 0000000000..30534499e4
--- /dev/null
+++ b/src/USER-SCAFACOS/README
@@ -0,0 +1,5 @@
+RENE: need a short README file - see other examples in the
+USER package dirs within src
+
+give short background on ScaFaCos, authors, contact info
+for LAMMPS users to have if needed, citation
diff --git a/src/USER-SCAFACOS/fix_scafacos.cpp b/src/USER-SCAFACOS/fix_scafacos.cpp
deleted file mode 100644
index 08aebb9f22..0000000000
--- a/src/USER-SCAFACOS/fix_scafacos.cpp
+++ /dev/null
@@ -1,456 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Rene Halver (JSC)
-------------------------------------------------------------------------- */
-
-#include <cstdio>
-#include <cstring>
-#include <cstdlib>
-#include "fix_scafacos.h"
-#include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "neighbor.h"
-#include "domain.h"
-#include "force.h"
-#include "pair.h"
-#include "modify.h"
-#include "compute.h"
-#include "memory.h"
-#include "error.h"
-
-// ScaFaCoS library
-#include <sstream>
-#include <string>
-#include "fcs.h"
-#include "universe.h"
-
-using namespace LAMMPS_NS;
-using namespace FixConst;
-
-#define INVOKED_PERATOM 8
-
-/* ---------------------------------------------------------------------- */
-
-FixScafacos::FixScafacos(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
-{
- // form of fix string:
- // fix <#> <group> scafacos <method> [ tolerance <type> <value> ]
-
-
- if (narg < 4) error->all(FLERR,"Illegal fix scafacos command");
-
- // read method from fix input
- method = arg[3];
-
- int arg_index = 4;
-
- tolerance_set = false;
-
- while(arg_index < narg)
- {
- // check if tolerance option is set
- if (strcmp(arg[arg_index],"tolerance") == 0)
- {
- tolerance_set = true;
- ++arg_index;
- if (strcmp(arg[arg_index],"energy") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
- else if (strcmp(arg[arg_index],"energy_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
- else if (strcmp(arg[arg_index],"field") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
- else if (strcmp(arg[arg_index],"field_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
- else if (strcmp(arg[arg_index],"potential") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
- else if (strcmp(arg[arg_index],"potential_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
- else
- error->all(FLERR,"Illegal fix scafacos command");
- ++arg_index;
- tolerance_value = atof(arg[arg_index]);
- ++arg_index;
- }
- else
- error->all(FLERR,"Illegal fix scafacos command");
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-FixScafacos::~FixScafacos()
-{
- memory->destroy(pot);
- memory->destroy(field);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixScafacos::setmask()
-{
- int mask = 0;
- //mask |= INITIAL_INTEGRATE;
- //mask |= FINAL_INTEGRATE;
- mask |= PRE_REVERSE;
- mask |= POST_FORCE;
- mask |= MIN_POST_FORCE;
- mask |= THERMO_ENERGY;
- return mask;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::init()
-{
- // error checks
-
- if (domain->dimension == 2)
- error->all(FLERR,"Fix scafacos requires 3d problem");
-
- rank = comm->me;
-
- int nlocal = 0;
- int proc_grid[3] = {comm->procgrid[0], comm->procgrid[1], comm->procgrid[2]};
- int myloc[3] = {comm->myloc[0], comm->myloc[1], comm->myloc[2]};
-
- // call ScaFaCoS init
- // TODO: check if universe->uworld is a good idea for computations
- result = fcs_init(&fcs,method.c_str(),universe->uworld);
- if (!check_result(result, rank)) return;
-
- setup_handle();
-
- nlocal = atom -> nlocal;
- // get particle data
- x = &atom->x[0][0];
- q = atom->q;
-
- if (tolerance_set)
- {
- result = fcs_set_tolerance(fcs,tolerance_type,tolerance_value);
- if (!check_result(result, rank)) return;
- }
-
- // print out parameters within handle
- if (rank == 0) fcs_print_parameters(fcs);
-
- // call the tuning routine (needs to be redone, if critical system
- // parameters should change)
- result = fcs_tune(fcs,nlocal,x,q);
- if (!check_result(result, rank)) return;
-
- // allocate arrays larger in order to avoid fast
- // reallocation due to fluctuations
- local_array_size = (int)(1.25 * (double)nlocal);
-
- // allocate new result arrays
- memory->create(pot,local_array_size,"scafacos:potential");
- memory->create(field,local_array_size*3,"scafacos:field");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::init_list(int id, NeighList *ptr)
-{
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::setup(int vflag)
-{
- post_force(vflag);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::min_setup(int vflag)
-{
- post_force(vflag);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::setup_pre_reverse(int eflag, int vflag)
-{
- pre_reverse(eflag,vflag);
-}
-
-/* ----------------------------------------------------------------------
- integrate electronic degrees of freedom
-------------------------------------------------------------------------- */
-
-void FixScafacos::initial_integrate(int vflag) {}
-
-/* ----------------------------------------------------------------------
- store eflag, so can use it in post_force to tally per-atom energies
-------------------------------------------------------------------------- */
-
-void FixScafacos::pre_reverse(int eflag, int vflag)
-{
- int eflag_caller = eflag;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::post_force(int vflag)
-{
-
- int nlocal;
-
- nlocal = atom->nlocal;
- x = &atom->x[0][0];
- q = atom->q;
-
- // check if box has changed since the last call of fcs_tune,
- // if it has, call fcs_tune
- if (box_has_changed())
- {
- setup_handle();
-
- // print out parameters within handle TODO: should be done in C style
- /*
- if (rank == 0)
- {
- std::cout << " updated ScaFaCoS handle: " << std::endl;
- fcs_print_parameters(fcs);
- }
- */
-
- // call the tuning routine (needs to be redone, if critical
- // system parameters should change)
- result = fcs_tune(fcs,nlocal,x,q);
- if (!check_result(result, rank)) return;
- }
-
- // check if arrays for potentials and field are still large enough
- // for the number of particles on process
- if (nlocal > local_array_size)
- {
- // allocate arrays larger in order to avoid fast
- // reallocation due to fluctuations
- local_array_size = (int)(1.25 * (double)nlocal);
-
- // destroy old result arrays
- memory->destroy(pot);
- memory->destroy(field);
-
- // allocate result arrays
- memory->create(pot,local_array_size,"scafacos:potential");
- memory->create(field,3*local_array_size,"scafacos:field");
-
- }
-
- // set result vectors to zero
- for ( int i = 0; i < nlocal; ++i)
- {
- pot[i] = 0.0;
- field[3*i] = field[3*i+1] = field[3*i+2] = 0.0;
- }
-
- // compute Coulomb
- fcs_run(fcs, nlocal, x, q, field, pot);
- if(!check_result(result,rank)) return;
-
- double E_coul_loc = 0.0;
-
- for (int i = 0; i < atom->nlocal; ++i)
- {
- //std::cout << atom->f[i][0] << " " << field[3*i] << " " << q[i] << std::endl;
- atom->f[i][0] += field[3*i] * q[i];
- atom->f[i][1] += field[3*i+1] * q[i];
- atom->f[i][2] += field[3*i+2] * q[i];
- E_coul_loc += 0.5 * q[i] * pot[i];
- }
-
- force->pair->eng_coul += E_coul_loc;
-
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::min_post_force(int vflag)
-{
- post_force(vflag);
-}
-
-/* ----------------------------------------------------------------------
- integrate electronic degrees of freedom
-------------------------------------------------------------------------- */
-
-void FixScafacos::final_integrate() {}
-
-/* ---------------------------------------------------------------------- */
-
-void FixScafacos::reset_dt()
-{
- //dtv = update->dt;
- //dtf = 0.5 * update->dt * force->ftm2v;
-}
-
-/* ----------------------------------------------------------------------
- DFTB energy from LATTE
-------------------------------------------------------------------------- */
-
-double FixScafacos::compute_scalar()
-{
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local arrays
-------------------------------------------------------------------------- */
-
-double FixScafacos::memory_usage()
-{
- double bytes = 0.0;
- bytes += local_array_size * sizeof(double);
- bytes += local_array_size * 3 * sizeof(double);
- return bytes;
-}
-
-/* ----------------------------------------------------------------------
- setup of ScaFaCoS handle with common parameters
-------------------------------------------------------------------------- */
-void FixScafacos::setup_handle()
-{
- // store periodicity
- periodicity[0] = domain->xperiodic;
- periodicity[1] = domain->yperiodic;
- periodicity[2] = domain->zperiodic;
-
- // store offset of the system
- offset[0] = domain->boundary[0][0];
- offset[1] = domain->boundary[1][0];
- offset[2] = domain->boundary[2][0];
-
- // calculate box vectors
- box_x[0] = domain->prd[0];
- box_x[1] = box_x[2] = 0.0;
-
- box_y[1] = domain->prd[1];
- box_y[0] = box_y[2] = 0.0;
-
- box_z[2] = domain->prd[2];
- box_z[1] = box_z[0] = 0.0;
-
- total_particles = atom->natoms;
-
- // TODO: for now disable short-range calculations within LAMMPS
- near_field_flag = 0;
-
- // enter all parameters required to ScaFaCoS handle
- result = fcs_set_box_a(fcs, box_x);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_box_b(fcs, box_y);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_box_c(fcs, box_z);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_box_origin(fcs, offset);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_periodicity(fcs, periodicity);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_near_field_flag(fcs, near_field_flag);
- if (!check_result(result, rank)) return;
-
- result = fcs_set_total_particles(fcs, atom->natoms);
- if (!check_result(result, rank)) return;
-}
-
-/* ----------------------------------------------------------------------
- check if box parameters changed, requiring a new call to fcs_tune
-------------------------------------------------------------------------- */
-bool FixScafacos::box_has_changed()
-{
- bool changed = false;
-
- double n_periodicity[3];
- double n_offset[3];
- double n_box_x[3];
- double n_box_y[3];
- double n_box_z[3];
-
- int n_total_particles;
-
- // store periodicity
- n_periodicity[0] = domain->xperiodic;
- n_periodicity[1] = domain->yperiodic;
- n_periodicity[2] = domain->zperiodic;
-
- // store offset of the system
- n_offset[0] = domain->boundary[0][0];
- n_offset[1] = domain->boundary[1][0];
- n_offset[2] = domain->boundary[2][0];
-
- // calculate box vectors
- n_box_x[0] = domain->prd[0];
- n_box_x[1] = n_box_x[2] = 0.0;
-
- n_box_y[1] = domain->prd[1];
- n_box_y[0] = n_box_y[2] = 0.0;
-
- n_box_z[2] = domain->prd[2];
- n_box_z[1] = n_box_z[0] = 0.0;
-
- n_total_particles = atom->natoms;
-
- changed = changed ||
- ( n_periodicity[0] != periodicity[0] ) ||
- ( n_periodicity[1] != periodicity[1] ) ||
- ( n_periodicity[2] != periodicity[2] ) ||
- ( n_offset[0] != offset[0] ) ||
- ( n_offset[1] != offset[1] ) ||
- ( n_offset[2] != offset[2] ) ||
- ( n_box_x[0] != box_x[0] ) ||
- ( n_box_x[1] != box_x[1] ) ||
- ( n_box_x[2] != box_x[2] ) ||
- ( n_box_y[0] != box_y[0] ) ||
- ( n_box_y[1] != box_y[1] ) ||
- ( n_box_y[2] != box_y[2] ) ||
- ( n_box_z[0] != box_z[0] ) ||
- ( n_box_z[1] != box_z[1] ) ||
- ( n_box_z[2] != box_z[2] ) ||
- ( n_total_particles != total_particles );
- return changed;
-}
-
-
-
-/* ----------------------------------------------------------------------
- check of ScaFaCoS result
-------------------------------------------------------------------------- */
-bool FixScafacos::check_result(FCSResult result, int comm_rank)
-{
- if (result)
- {
- printf("ScaFaCoS Error: Caught error on task %d.\n", comm_rank);
- std::string err_msg;
- std::stringstream ss;
-
- ss << fcs_result_get_function(result) << "\n"
- << fcs_result_get_message(result) << "\n";
- err_msg = ss.str();
-
- error -> all(FLERR, err_msg.c_str());
- fcs_result_destroy(result);
- }
- return true;
-}
-
diff --git a/src/USER-SCAFACOS/fix_scafacos.h b/src/USER-SCAFACOS/fix_scafacos.h
deleted file mode 100644
index ffd4a94d32..0000000000
--- a/src/USER-SCAFACOS/fix_scafacos.h
+++ /dev/null
@@ -1,164 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef FIX_CLASS
-
-FixStyle(scafacos,FixScafacos)
-
-#else
-
-#ifndef LMP_FIX_SCAFACOS_H
-#define LMP_FIX_SCAFACOS_H
-
-#include "fix.h"
-#include "fcs.h"
-#include <string>
-
-namespace LAMMPS_NS {
-
-class FixScafacos : public Fix {
- public:
- FixScafacos(class LAMMPS *, int, char **);
- virtual ~FixScafacos();
- int setmask();
- void init();
- void init_list(int, NeighList*);
- void setup(int);
- void min_setup(int);
- void setup_pre_reverse(int, int);
- void initial_integrate(int);
- void pre_reverse(int, int);
- void post_force(int);
- void min_post_force(int);
- void final_integrate();
- void reset_dt();
- double compute_scalar();
- double memory_usage();
-
- protected:
- std::string method;
-
- // MPI rank
- int rank;
-
- // source arrays for positions and charges
- double *x, *q;
- // result arrays for potentials and field
- double *pot, *field;
-
- // box vectors for each dimension
- fcs_float box_x[3], box_y[3], box_z[3];
- // offset of the box from the origin
- fcs_float offset[3];
-
- // periodicity of the system
- fcs_int periodicity[3];
-
- // ScaFaCoS handle
- FCS fcs;
-
- // ScaFaCoS result variable
- FCSResult result;
-
- // function to check results
- bool check_result(FCSResult, int);
-
- // function to set up handle with common parameters
- void setup_handle();
-
- // function to check if the box parameters changed, so that a new tuning step is required
- bool box_has_changed();
-
- // store total number of particles (to check if tune needs to be called again)
- fcs_int total_particles;
-
- // store number of local particles (to be able to readjust the size of result arrays, when needed)
- int local_array_size;
-
- // should the near field calculations be computed by LAMMPS?
- fcs_int near_field_flag;
-
- // type of accuracy chosen (if customized)
- fcs_int tolerance_type;
-
- // value of tolerance
- fcs_float tolerance_value;
-
- // is tolerance set?
- bool tolerance_set;
-
- // check if fmm is chosen (ghost particles, since the implementation needs at least 1 particle on each process!)
- bool fmm_chosen;
-
- // FMM: fmm particle array size
- int fmm_array_size;
-};
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
-E: Must use units metal with fix latte command
-
-UNDOCUMENTED
-
-E: Fix latte currently runs only in serial
-
-UNDOCUMENTED
-
-E: LAMMPS is linked against incompatible LATTE library
-
-UNDOCUMENTED
-
-E: Illegal ... command
-
-Self-explanatory. Check the input script syntax and compare to the
-documentation for the command. You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
-
-UNDOCUMENTED
-
-E: Could not find fix latte compute ID
-
-UNDOCUMENTED
-
-E: Fix latte compute ID does not compute pe/atom
-
-UNDOCUMENTED
-
-E: Fix latte requires 3d problem
-
-UNDOCUMENTED
-
-E: Fix latte cannot compute Coulomb potential
-
-UNDOCUMENTED
-
-E: Fix latte requires 3d simulation
-
-UNDOCUMENTED
-
-W: Fix latte should come after all other integration fixes
-
-UNDOCUMENTED
-
-E: Internal LATTE problem
-
-UNDOCUMENTED
-
-*/
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index c5efd6a191..10721b33c8 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -38,40 +38,16 @@ using namespace LAMMPS_NS;
Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
- if (narg < 2) error->all(FLERR,"Illegal scafacos command");
+ if (narg != 2) error->all(FLERR,"Illegal scafacos command");
int n = strlen(arg[0]) + 1;
method = new char[n];
strcpy(method,arg[0]);
+ tolerance = force->numeric(FLERR,arg[1]);
- // additional args
-
- int tflag = 0;
-
- int iarg = 1;
- while (iarg < narg) {
- if (strcmp(arg[iarg],"tolerance") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command");
- tflag = 1;
- if (strcmp(arg[iarg+1],"energy") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
- else if (strcmp(arg[iarg+1],"energy_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
- else if (strcmp(arg[iarg+1],"field") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
- else if (strcmp(arg[iarg+1],"field_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
- else if (strcmp(arg[iarg+1],"potential") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
- else if (strcmp(arg[iarg+1],"potential_rel") == 0)
- tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
- else error->all(FLERR,"Illegal scafacos command");
- tolerance = force->numeric(FLERR,arg[iarg+2]);
- iarg += 3;
- } else error->all(FLERR,"Illegal scafacos command");
- }
+ // optional ScaFaCoS library setting defaults
- if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command");
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
// initializations
@@ -92,7 +68,7 @@ Scafacos::~Scafacos()
memory->destroy(epot);
memory->destroy(efield);
- // NOTE: any clean-up call to ScaFaCoS needed?
+ // RENE: any clean-up/shut-down call to ScaFaCoS needed?
}
/* ---------------------------------------------------------------------- */
@@ -100,7 +76,6 @@ Scafacos::~Scafacos()
void Scafacos::init()
{
// error checks
- // NOTE: allow triclinic at some point
if (domain->dimension == 2)
error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
@@ -108,11 +83,13 @@ void Scafacos::init()
if (domain->triclinic)
error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
+ if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8)
+ error->all(FLERR,"Scafacos atom count exceeds 2B");
+
// one-time initialization of ScaFaCoS
scale = 1.0;
qqrd2e = force->qqrd2e;
- //qsum_qsq();
if (!initialized) {
result = fcs_init(&fcs,method,world);
@@ -147,13 +124,14 @@ void Scafacos::compute(int eflag, int vflag)
double *q = atom->q;
int nlocal = atom->nlocal;
+ // RENE: why is scale needed?
+
const double qscale = qqrd2e * scale;
- // if simluation box has changed, call fcs_tune()
-
if (eflag || vflag) ev_setup(eflag,vflag);
- else
- eflag_atom = 0;
+ else eflag_atom = 0;
+
+ // if simulation box has changed, call fcs_tune()
if (box_has_changed()) {
setup_handle();
@@ -173,7 +151,7 @@ void Scafacos::compute(int eflag, int vflag)
}
// initialize epot & efield
- // NOTE: is this necessary?
+ // RENE: is this necessary? or does Scafacos just set them
for (int i = 0; i < nlocal; i++) {
epot[i] = 0.0;
@@ -201,17 +179,47 @@ void Scafacos::compute(int eflag, int vflag)
myeng += 0.5 * qone * epot[i];
}
- if (eflag_atom)
- {
+ if (eflag_atom) {
for (int i = 0; i < nlocal; i++)
- {
eatom[i] = qscale * epot[i];
- }
}
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
}
+/* ---------------------------------------------------------------------- */
+
+int Scafacos::modify_param(int narg, char **arg)
+{
+ // RENE: add any Scafacos options here you want to expose to LAMMPS
+ // syntax: kspace_modify scafacos keyword value1 value2 ...
+ // keyword = tolerance
+ // value1 = energy, energy_rel, etc
+ // everyone of these should have a default, so user doesn't need to set
+
+ if (strcmp(arg[0],"scafacos") != 0) return 0;
+
+ if (strcmp(arg[1],"tolerance") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal kspace_modify command");
+ if (strcmp(arg[2],"energy") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ else if (strcmp(arg[2],"energy_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
+ else if (strcmp(arg[2],"field") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ else if (strcmp(arg[2],"field_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
+ else if (strcmp(arg[2],"potential") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
+ else if (strcmp(arg[2],"potential_rel") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
+ else error->all(FLERR,"Illegal kspace_modify command");
+ return 3;
+ }
+
+ return 0;
+}
+
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
@@ -231,15 +239,14 @@ double Scafacos::memory_usage()
void Scafacos::setup_handle()
{
// store simulation box params
- // NOTE: this assumes orthogonal box
- // NOTE: total particles may not be a 4-byte int
- // NOTE: what does SCFCS mean by offset?
- // it's an integer flag in LAMMPS
old_periodicity[0] = domain->xperiodic;
old_periodicity[1] = domain->yperiodic;
old_periodicity[2] = domain->zperiodic;
+ // RENE: what does SCFCS mean by offset?
+ // it's an integer flag in LAMMPS, but being stored in a float?
+
old_offset[0] = domain->boundary[0][0];
old_offset[1] = domain->boundary[1][0];
old_offset[2] = domain->boundary[2][0];
@@ -273,7 +280,9 @@ void Scafacos::setup_handle()
result = fcs_set_total_particles(fcs,old_natoms);
check_result(result);
- // NOTE: for now disable short-range calculations within LAMMPS
+ // RENE: disable short-range calculations within LAMMPS
+ // not sure what this is doing
+ // is this the correct thing to do for now?
int near_field_flag = 0;
result = fcs_set_near_field_flag(fcs,near_field_flag);
@@ -306,7 +315,6 @@ bool Scafacos::box_has_changed()
/* ----------------------------------------------------------------------
check ScaFaCoS result for error condition
- NOTE: will all procs have same error?
------------------------------------------------------------------------- */
void Scafacos::check_result(FCSResult result)
@@ -320,6 +328,9 @@ void Scafacos::check_result(FCSResult result)
std::string err_msg = ss.str();
const char *str = err_msg.c_str();
+ // RENE: will all procs have same error?
+ // if so, then should call error->all(FLERR,str)
+
error->one(FLERR,str);
}
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index 33911ee9fd..f3708129f1 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -32,6 +32,7 @@ class Scafacos : public KSpace {
void init();
void setup();
void compute(int, int);
+ int modify_param(int, char **);
double memory_usage();
private:
diff --git a/src/kspace.cpp b/src/kspace.cpp
index fc8b12288b..de96bee8b8 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -580,7 +580,11 @@ void KSpace::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) auto_disp_flag = 0;
else error->all(FLERR,"Illegal kspace_modify command");
iarg += 2;
- } else error->all(FLERR,"Illegal kspace_modify command");
+ } else {
+ int n = modify_param(narg-iarg,&arg[iarg]);
+ if (n == 0) error->all(FLERR,"Illegal kspace_modify command");
+ iarg += n;
+ }
}
}
diff --git a/src/kspace.h b/src/kspace.h
index 28c7bcef2a..c25dc93f45 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -126,6 +126,8 @@ class KSpace : protected Pointers {
virtual int timing(int, double &, double &) {return 0;}
virtual int timing_1d(int, double &) {return 0;}
virtual int timing_3d(int, double &) {return 0;}
+
+ virtual int modify_param(int, char **) {return 0;}
virtual double memory_usage() {return 0.0;}
/* ----------------------------------------------------------------------
--
GitLab
From a62b65096bbdd10925feb9b08eea10d626b231fe Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 18 Jul 2018 15:48:17 -0600
Subject: [PATCH 039/332] more error checks for Scafacos usage
---
lib/scafacos/README | 7 +++++++
src/USER-SCAFACOS/scafacos.cpp | 5 +++++
2 files changed, 12 insertions(+)
create mode 100644 lib/scafacos/README
diff --git a/lib/scafacos/README b/lib/scafacos/README
new file mode 100644
index 0000000000..bdf167aef1
--- /dev/null
+++ b/lib/scafacos/README
@@ -0,0 +1,7 @@
+RENE - there needs to be a README like the one
+for lib/voronoi/README, explaining how
+to grab the correct version of Scafacos.
+
+And how to build, either via traditional make
+and the Install.py script, or via CMake
+
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 10721b33c8..fef4b4948f 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -77,6 +77,8 @@ void Scafacos::init()
{
// error checks
+ if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
+
if (domain->dimension == 2)
error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
@@ -86,6 +88,9 @@ void Scafacos::init()
if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8)
error->all(FLERR,"Scafacos atom count exceeds 2B");
+ if (atom->molecular > 0)
+ error->all(FLERR,"Cannot use Scafacos with molecular charged systems yet");
+
// one-time initialization of ScaFaCoS
scale = 1.0;
--
GitLab
From fba165d6b28451d9eca389d77fa3aa0a4ef30dff Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Thu, 19 Jul 2018 11:46:56 -0600
Subject: [PATCH 040/332] changed the files according to remarks by Steve
(compare to previous commit)
---
src/USER-SCAFACOS/scafacos.cpp | 74 ++++++++++++++++------------------
src/USER-SCAFACOS/scafacos.h | 2 +-
2 files changed, 35 insertions(+), 41 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index fef4b4948f..8779796a54 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -38,16 +38,24 @@ using namespace LAMMPS_NS;
Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
- if (narg != 2) error->all(FLERR,"Illegal scafacos command");
+ if (narg > 2) error->all(FLERR,"Illegal scafacos command");
int n = strlen(arg[0]) + 1;
method = new char[n];
strcpy(method,arg[0]);
- tolerance = force->numeric(FLERR,arg[1]);
+ // to allow 'kspace scafacos <method>' with default values
+ if (narg == 2)
+ tolerance = force->numeric(FLERR,arg[1]);
+ else
+ tolerance = 0.001;
// optional ScaFaCoS library setting defaults
-
- tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ // choose the correct default tolerance type for chosen method
+ // TODO: needs to be expanded for all solvers, currently mainly used ones
+ if (strcmp(method,"fmm") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0)
+ tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
// initializations
@@ -68,7 +76,8 @@ Scafacos::~Scafacos()
memory->destroy(epot);
memory->destroy(efield);
- // RENE: any clean-up/shut-down call to ScaFaCoS needed?
+ // clean up of the ScaFaCoS handle and internal arrays
+ fcs_destroy(fcs);
}
/* ---------------------------------------------------------------------- */
@@ -93,7 +102,6 @@ void Scafacos::init()
// one-time initialization of ScaFaCoS
- scale = 1.0;
qqrd2e = force->qqrd2e;
if (!initialized) {
@@ -129,9 +137,7 @@ void Scafacos::compute(int eflag, int vflag)
double *q = atom->q;
int nlocal = atom->nlocal;
- // RENE: why is scale needed?
-
- const double qscale = qqrd2e * scale;
+ const double qscale = qqrd2e;
if (eflag || vflag) ev_setup(eflag,vflag);
else eflag_atom = 0;
@@ -155,16 +161,6 @@ void Scafacos::compute(int eflag, int vflag)
}
- // initialize epot & efield
- // RENE: is this necessary? or does Scafacos just set them
-
- for (int i = 0; i < nlocal; i++) {
- epot[i] = 0.0;
- efield[i][0] = efield[i][1] = efield[i][2] = 0.0;
- }
-
- // ScaFaCoS calculation of full Coulombics
-
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
check_result(result);
@@ -196,7 +192,7 @@ void Scafacos::compute(int eflag, int vflag)
int Scafacos::modify_param(int narg, char **arg)
{
- // RENE: add any Scafacos options here you want to expose to LAMMPS
+ // add any Scafacos options here you want to expose to LAMMPS
// syntax: kspace_modify scafacos keyword value1 value2 ...
// keyword = tolerance
// value1 = energy, energy_rel, etc
@@ -245,17 +241,17 @@ void Scafacos::setup_handle()
{
// store simulation box params
+ // setup periodicity
old_periodicity[0] = domain->xperiodic;
old_periodicity[1] = domain->yperiodic;
old_periodicity[2] = domain->zperiodic;
- // RENE: what does SCFCS mean by offset?
- // it's an integer flag in LAMMPS, but being stored in a float?
-
- old_offset[0] = domain->boundary[0][0];
- old_offset[1] = domain->boundary[1][0];
- old_offset[2] = domain->boundary[2][0];
+ // setup box origin (lower left front corner of the system)
+ old_origin[0] = domain->boundary[0][0];
+ old_origin[1] = domain->boundary[1][0];
+ old_origin[2] = domain->boundary[2][0];
+ // setup box vectors (base vectors of the system box)
old_box_x[0] = domain->prd[0];
old_box_x[1] = old_box_x[2] = 0.0;
old_box_y[1] = domain->prd[1];
@@ -263,10 +259,10 @@ void Scafacos::setup_handle()
old_box_z[2] = domain->prd[2];
old_box_z[1] = old_box_z[0] = 0.0;
+ // setup number of atoms in the system
old_natoms = atom->natoms;
- // set all required ScaFaCoS params
-
+ // store parameters to ScaFaCoS handle
result = fcs_set_box_a(fcs,old_box_x);
check_result(result);
@@ -276,7 +272,7 @@ void Scafacos::setup_handle()
result = fcs_set_box_c(fcs,old_box_z);
check_result(result);
- result = fcs_set_box_origin(fcs,old_offset);
+ result = fcs_set_box_origin(fcs,old_origin);
check_result(result);
result = fcs_set_periodicity(fcs,old_periodicity);
@@ -285,11 +281,12 @@ void Scafacos::setup_handle()
result = fcs_set_total_particles(fcs,old_natoms);
check_result(result);
- // RENE: disable short-range calculations within LAMMPS
- // not sure what this is doing
- // is this the correct thing to do for now?
-
- int near_field_flag = 0;
+ // allow ScaFaCoS to calculate the near field computations for now
+ // TODO: allow the delegation of the near field computations
+ // within LAMMPS
+ // (near_field_flag = 1 -> enables the internal near field calcs
+ // 0 -> disables the internal near field calcs
+ int near_field_flag = 1;
result = fcs_set_near_field_flag(fcs,near_field_flag);
check_result(result);
}
@@ -307,9 +304,9 @@ bool Scafacos::box_has_changed()
(periodicity[0] != old_periodicity[0]) ||
(periodicity[1] != old_periodicity[1]) ||
(periodicity[2] != old_periodicity[2]) ||
- (domain->boundary[0][0] != old_offset[0]) ||
- (domain->boundary[1][0] != old_offset[1]) ||
- (domain->boundary[2][0] != old_offset[2]) ||
+ (domain->boundary[0][0] != old_origin[0]) ||
+ (domain->boundary[1][0] != old_origin[1]) ||
+ (domain->boundary[2][0] != old_origin[2]) ||
(prd[0] != old_box_x[0]) ||
(prd[1] != old_box_y[1]) ||
(prd[2] != old_box_z[2]) ||
@@ -333,9 +330,6 @@ void Scafacos::check_result(FCSResult result)
std::string err_msg = ss.str();
const char *str = err_msg.c_str();
- // RENE: will all procs have same error?
- // if so, then should call error->all(FLERR,str)
-
error->one(FLERR,str);
}
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index f3708129f1..3e549cf64e 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -51,7 +51,7 @@ class Scafacos : public KSpace {
// so ScaFaCoS can detect if changes, e.g. for NPT
fcs_float old_box_x[3],old_box_y[3],old_box_z[3];
- fcs_float old_offset[3];
+ fcs_float old_origin[3];
fcs_int old_periodicity[3];
fcs_int old_natoms;
--
GitLab
From 407708dcd294e86cfa676489253691f496a650de Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 20 Jul 2018 10:38:18 -0600
Subject: [PATCH 041/332] reverted change to kspace call and using
domain->boxlo for origin for now
---
src/USER-SCAFACOS/scafacos.cpp | 14 +++++---------
1 file changed, 5 insertions(+), 9 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 8779796a54..b9390aea47 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -38,16 +38,12 @@ using namespace LAMMPS_NS;
Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
- if (narg > 2) error->all(FLERR,"Illegal scafacos command");
+ if (narg != 2) error->all(FLERR,"Illegal scafacos command");
int n = strlen(arg[0]) + 1;
method = new char[n];
strcpy(method,arg[0]);
- // to allow 'kspace scafacos <method>' with default values
- if (narg == 2)
- tolerance = force->numeric(FLERR,arg[1]);
- else
- tolerance = 0.001;
+ tolerance = force->numeric(FLERR,arg[1]);
// optional ScaFaCoS library setting defaults
// choose the correct default tolerance type for chosen method
@@ -247,9 +243,9 @@ void Scafacos::setup_handle()
old_periodicity[2] = domain->zperiodic;
// setup box origin (lower left front corner of the system)
- old_origin[0] = domain->boundary[0][0];
- old_origin[1] = domain->boundary[1][0];
- old_origin[2] = domain->boundary[2][0];
+ old_origin[0] = domain->boxlo[0];
+ old_origin[1] = domain->boxlo[1];
+ old_origin[2] = domain->boxlo[2];
// setup box vectors (base vectors of the system box)
old_box_x[0] = domain->prd[0];
--
GitLab
From 5c934cdb6f111b6dc6b4a115776482e90cb341d1 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 20 Jul 2018 10:40:29 -0600
Subject: [PATCH 042/332] fixed examples to work with charged molecular
restriction and new kspace call format
---
examples/USER/scafacos/data.NaCl | 16 ++++++++--------
examples/USER/scafacos/in.scafacos | 3 ++-
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl
index 1a599b957d..2d804dec95 100644
--- a/examples/USER/scafacos/data.NaCl
+++ b/examples/USER/scafacos/data.NaCl
@@ -15,11 +15,11 @@
Atoms
- 1 1 1 1.0 0.0 0.0 0.0
- 2 1 2 -1.0 1.0 0.0 0.0
- 3 1 2 -1.0 0.0 1.0 0.0
- 4 1 1 1.0 1.0 1.0 0.0
- 5 1 2 -1.0 0.0 0.0 1.0
- 6 1 1 1.0 1.0 0.0 1.0
- 7 1 1 1.0 0.0 1.0 1.0
- 8 1 2 -1.0 1.0 1.0 1.0
+ 1 1 1.0 0.0 0.0 0.0
+ 2 2 -1.0 1.0 0.0 0.0
+ 3 2 -1.0 0.0 1.0 0.0
+ 4 1 1.0 1.0 1.0 0.0
+ 5 2 -1.0 0.0 0.0 1.0
+ 6 1 1.0 1.0 0.0 1.0
+ 7 1 1.0 0.0 1.0 1.0
+ 8 2 -1.0 1.0 1.0 1.0
diff --git a/examples/USER/scafacos/in.scafacos b/examples/USER/scafacos/in.scafacos
index f9b6733eef..9a1f0f321e 100644
--- a/examples/USER/scafacos/in.scafacos
+++ b/examples/USER/scafacos/in.scafacos
@@ -28,7 +28,8 @@ pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
-kspace_style scafacos p3m tolerance field 0.001
+kspace_style scafacos p3m 0.001
+kspace_style scafacos tolerance field
timestep 0.005
thermo 10
--
GitLab
From 0e0afdeb51b7eefaff3da277d7c4db437dc3e870 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 20 Jul 2018 10:41:19 -0600
Subject: [PATCH 043/332] fixed typo and removed comment
---
doc/src/Section_packages.txt | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index ea03bdb74e..18ae1a75e6 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -2731,8 +2731,6 @@ examples/reax :ul
:line
-RENE: check this section
-
USER-SCAFACOS package :link(USER-SCAFACOS),h4
[Contents:]
@@ -2764,7 +2762,7 @@ args:
make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
-make lib-voronoi args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
+make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
You can then install/un-install the package and build LAMMPS in the
usual manner:
--
GitLab
From 2f5598122429ae113b84623c338b5098293aeb07 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 23 Jul 2018 15:58:33 -0600
Subject: [PATCH 044/332] new MESSAGE package for client/server/coupling
---
doc/src/Section_commands.txt | 9 +-
doc/src/Section_howto.txt | 132 ++-
doc/src/Section_packages.txt | 47 ++
doc/src/Section_start.txt | 19 +
doc/src/fix_client_md.txt | 105 +++
doc/src/lammps.book | 12 +-
doc/src/message.txt | 159 ++++
doc/src/server.txt | 71 ++
doc/src/server_mc.txt | 112 +++
doc/src/server_md.txt | 122 +++
examples/COUPLE/README | 3 +
examples/COUPLE/lammps_mc/Makefile | 34 +
examples/COUPLE/lammps_mc/README | 106 +++
examples/COUPLE/lammps_mc/in.mc | 7 +
examples/COUPLE/lammps_mc/in.mc.server | 36 +
.../COUPLE/lammps_mc/log.23Jul18.file.g++.1 | 254 ++++++
.../COUPLE/lammps_mc/log.23Jul18.file.g++.4 | 254 ++++++
.../COUPLE/lammps_mc/log.23Jul18.zmq.g++.1 | 254 ++++++
.../COUPLE/lammps_mc/log.23Jul18.zmq.g++.4 | 254 ++++++
examples/COUPLE/lammps_mc/mc.cpp | 261 ++++++
examples/COUPLE/lammps_mc/mc.h | 40 +
examples/COUPLE/lammps_mc/random_park.cpp | 72 ++
examples/COUPLE/lammps_mc/random_park.h | 28 +
examples/COUPLE/lammps_vasp/INCAR | 53 ++
examples/COUPLE/lammps_vasp/KPOINTS | 6 +
examples/COUPLE/lammps_vasp/POSCAR_W | 11 +
examples/COUPLE/lammps_vasp/README | 90 ++
examples/COUPLE/lammps_vasp/data.W | 15 +
examples/COUPLE/lammps_vasp/in.client.W | 34 +
examples/COUPLE/lammps_vasp/log.client.output | 63 ++
examples/COUPLE/lammps_vasp/vasp_wrap.py | 234 ++++++
examples/README | 1 +
examples/message/README | 102 +++
examples/message/in.message | 27 +
examples/message/in.message.client | 38 +
examples/message/in.message.server | 29 +
.../log.23Jul18.message.client.file.g++.1 | 76 ++
.../log.23Jul18.message.client.file.g++.2 | 76 ++
.../log.23Jul18.message.client.mpione.g++.1 | 76 ++
.../log.23Jul18.message.client.mpione.g++.2 | 76 ++
.../log.23Jul18.message.client.mpitwo.g++.1 | 76 ++
.../log.23Jul18.message.client.mpitwo.g++.2 | 76 ++
.../log.23Jul18.message.client.zmq.g++.1 | 76 ++
.../log.23Jul18.message.client.zmq.g++.2 | 76 ++
examples/message/log.23Jul18.message.g++.1 | 83 ++
examples/message/log.23Jul18.message.g++.4 | 83 ++
.../log.23Jul18.message.server.file.g++.1 | 44 +
.../log.23Jul18.message.server.file.g++.4 | 44 +
.../log.23Jul18.message.server.mpione.g++.1 | 44 +
.../log.23Jul18.message.server.mpione.g++.4 | 44 +
.../log.23Jul18.message.server.mpitwo.g++.1 | 44 +
.../log.23Jul18.message.server.mpitwo.g++.4 | 44 +
.../log.23Jul18.message.server.zmq.g++.1 | 44 +
.../log.23Jul18.message.server.zmq.g++.4 | 44 +
lib/README | 2 +
lib/message/Install.py | 118 +++
lib/message/Makefile.lammps.nozmq | 5 +
lib/message/Makefile.lammps.zmq | 5 +
lib/message/README | 51 ++
lib/message/cslib/LICENSE | 501 ++++++++++++
lib/message/cslib/README | 21 +
lib/message/cslib/src/Makefile | 107 +++
lib/message/cslib/src/STUBS_MPI/mpi.h | 95 +++
lib/message/cslib/src/STUBS_ZMQ/zmq.h | 35 +
lib/message/cslib/src/cslib.cpp | 768 ++++++++++++++++++
lib/message/cslib/src/cslib.h | 87 ++
lib/message/cslib/src/cslib.py | 362 +++++++++
lib/message/cslib/src/cslib_wrap.cpp | 239 ++++++
lib/message/cslib/src/cslib_wrap.f90 | 147 ++++
lib/message/cslib/src/cslib_wrap.h | 54 ++
lib/message/cslib/src/msg.cpp | 110 +++
lib/message/cslib/src/msg.h | 52 ++
lib/message/cslib/src/msg_file.cpp | 143 ++++
lib/message/cslib/src/msg_file.h | 40 +
lib/message/cslib/src/msg_mpi_one.cpp | 82 ++
lib/message/cslib/src/msg_mpi_one.h | 38 +
lib/message/cslib/src/msg_mpi_two.cpp | 81 ++
lib/message/cslib/src/msg_mpi_two.h | 35 +
lib/message/cslib/src/msg_zmq.cpp | 140 ++++
lib/message/cslib/src/msg_zmq.h | 38 +
src/MESSAGE/Install.sh | 67 ++
src/MESSAGE/fix_client_md.cpp | 270 ++++++
src/MESSAGE/fix_client_md.h | 62 ++
src/MESSAGE/message.cpp | 90 ++
src/MESSAGE/message.h | 40 +
src/MESSAGE/server.cpp | 50 ++
src/MESSAGE/server.h | 40 +
src/MESSAGE/server_mc.cpp | 148 ++++
src/MESSAGE/server_mc.h | 29 +
src/MESSAGE/server_md.cpp | 333 ++++++++
src/MESSAGE/server_md.h | 33 +
src/Makefile | 6 +-
src/atom.cpp | 3 +-
src/domain.cpp | 6 +-
src/domain.h | 3 +-
src/lammps.cpp | 223 +++--
src/lammps.h | 4 +
97 files changed, 8882 insertions(+), 101 deletions(-)
create mode 100644 doc/src/fix_client_md.txt
create mode 100644 doc/src/message.txt
create mode 100644 doc/src/server.txt
create mode 100644 doc/src/server_mc.txt
create mode 100644 doc/src/server_md.txt
create mode 100644 examples/COUPLE/lammps_mc/Makefile
create mode 100644 examples/COUPLE/lammps_mc/README
create mode 100644 examples/COUPLE/lammps_mc/in.mc
create mode 100644 examples/COUPLE/lammps_mc/in.mc.server
create mode 100644 examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1
create mode 100644 examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4
create mode 100644 examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1
create mode 100644 examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4
create mode 100644 examples/COUPLE/lammps_mc/mc.cpp
create mode 100644 examples/COUPLE/lammps_mc/mc.h
create mode 100644 examples/COUPLE/lammps_mc/random_park.cpp
create mode 100644 examples/COUPLE/lammps_mc/random_park.h
create mode 100644 examples/COUPLE/lammps_vasp/INCAR
create mode 100644 examples/COUPLE/lammps_vasp/KPOINTS
create mode 100644 examples/COUPLE/lammps_vasp/POSCAR_W
create mode 100644 examples/COUPLE/lammps_vasp/README
create mode 100644 examples/COUPLE/lammps_vasp/data.W
create mode 100644 examples/COUPLE/lammps_vasp/in.client.W
create mode 100644 examples/COUPLE/lammps_vasp/log.client.output
create mode 100644 examples/COUPLE/lammps_vasp/vasp_wrap.py
create mode 100644 examples/message/README
create mode 100644 examples/message/in.message
create mode 100644 examples/message/in.message.client
create mode 100644 examples/message/in.message.server
create mode 100644 examples/message/log.23Jul18.message.client.file.g++.1
create mode 100644 examples/message/log.23Jul18.message.client.file.g++.2
create mode 100644 examples/message/log.23Jul18.message.client.mpione.g++.1
create mode 100644 examples/message/log.23Jul18.message.client.mpione.g++.2
create mode 100644 examples/message/log.23Jul18.message.client.mpitwo.g++.1
create mode 100644 examples/message/log.23Jul18.message.client.mpitwo.g++.2
create mode 100644 examples/message/log.23Jul18.message.client.zmq.g++.1
create mode 100644 examples/message/log.23Jul18.message.client.zmq.g++.2
create mode 100644 examples/message/log.23Jul18.message.g++.1
create mode 100644 examples/message/log.23Jul18.message.g++.4
create mode 100644 examples/message/log.23Jul18.message.server.file.g++.1
create mode 100644 examples/message/log.23Jul18.message.server.file.g++.4
create mode 100644 examples/message/log.23Jul18.message.server.mpione.g++.1
create mode 100644 examples/message/log.23Jul18.message.server.mpione.g++.4
create mode 100644 examples/message/log.23Jul18.message.server.mpitwo.g++.1
create mode 100644 examples/message/log.23Jul18.message.server.mpitwo.g++.4
create mode 100644 examples/message/log.23Jul18.message.server.zmq.g++.1
create mode 100644 examples/message/log.23Jul18.message.server.zmq.g++.4
create mode 100644 lib/message/Install.py
create mode 100644 lib/message/Makefile.lammps.nozmq
create mode 100644 lib/message/Makefile.lammps.zmq
create mode 100644 lib/message/README
create mode 100644 lib/message/cslib/LICENSE
create mode 100644 lib/message/cslib/README
create mode 100644 lib/message/cslib/src/Makefile
create mode 100644 lib/message/cslib/src/STUBS_MPI/mpi.h
create mode 100644 lib/message/cslib/src/STUBS_ZMQ/zmq.h
create mode 100644 lib/message/cslib/src/cslib.cpp
create mode 100644 lib/message/cslib/src/cslib.h
create mode 100644 lib/message/cslib/src/cslib.py
create mode 100644 lib/message/cslib/src/cslib_wrap.cpp
create mode 100644 lib/message/cslib/src/cslib_wrap.f90
create mode 100644 lib/message/cslib/src/cslib_wrap.h
create mode 100644 lib/message/cslib/src/msg.cpp
create mode 100644 lib/message/cslib/src/msg.h
create mode 100644 lib/message/cslib/src/msg_file.cpp
create mode 100644 lib/message/cslib/src/msg_file.h
create mode 100644 lib/message/cslib/src/msg_mpi_one.cpp
create mode 100644 lib/message/cslib/src/msg_mpi_one.h
create mode 100644 lib/message/cslib/src/msg_mpi_two.cpp
create mode 100644 lib/message/cslib/src/msg_mpi_two.h
create mode 100644 lib/message/cslib/src/msg_zmq.cpp
create mode 100644 lib/message/cslib/src/msg_zmq.h
create mode 100644 src/MESSAGE/Install.sh
create mode 100644 src/MESSAGE/fix_client_md.cpp
create mode 100644 src/MESSAGE/fix_client_md.h
create mode 100644 src/MESSAGE/message.cpp
create mode 100644 src/MESSAGE/message.h
create mode 100644 src/MESSAGE/server.cpp
create mode 100644 src/MESSAGE/server.h
create mode 100644 src/MESSAGE/server_mc.cpp
create mode 100644 src/MESSAGE/server_mc.h
create mode 100644 src/MESSAGE/server_md.cpp
create mode 100644 src/MESSAGE/server_md.h
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 32308b36cb..ec0c0dc454 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -482,6 +482,7 @@ in the command's documentation.
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
+"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
@@ -513,6 +514,7 @@ in the command's documentation.
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
+"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
@@ -574,6 +576,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
+"client/md"_fix_client_md.html,
"cmap"_fix_cmap.html,
"controller"_fix_controller.html,
"deform (k)"_fix_deform.html,
@@ -678,8 +681,6 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
@@ -932,9 +933,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded/polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
+"body"_pair_body.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 2784858f02..3a38ccedcb 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -37,7 +37,8 @@ This section describes how to perform common tasks using LAMMPS.
6.25 "Polarizable models"_#howto_25
6.26 "Adiabatic core/shell model"_#howto_26
6.27 "Drude induced dipoles"_#howto_27
-6.28 "Magnetic spins"_#howto_28 :all(b)
+6.28 "Magnetic spins"_#howto_28
+6.29 "Using LAMMPS in client/server mode"_#howto_29 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section 7"_Section_example.html also show how to
@@ -663,7 +664,7 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
-LAMMPS can be coupled to other codes in at least 3 ways. Each has
+LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
@@ -752,7 +753,8 @@ LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
-:line
+(4) Couple LAMMPS with another code in a client/server mode. This is
+described in a separate "howto section"_#howto_29.
6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
@@ -2955,6 +2957,130 @@ property/atom"_compute_property_atom.html. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
+:line
+
+6.29 Using LAMMPS in client/server mode :link(howto_29),h4
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages to a "server" code. The server responds to
+each request with a reply message. This enables the two codes to work
+in tandem to perform a simulation. LAMMPS can act as either a client
+or server code.
+
+Some advantages of client/server coupling are that the two codes run
+as stand-alone executables; they are not linked together. Thus
+neither code needs to have a library interface. This often makes it
+easier to run the two codes on different numbers of processors. If a
+message protocol (format and content) is defined for a particular kind
+of simulation, then in principle any code that implements the
+client-side protocol can be used in tandem with any code that
+implements the server-side protocol, without the two codes needing to
+know anything more specific about each other.
+
+A simple example of client/server coupling is where LAMMPS is the
+client code performing MD timestepping. Each timestep it sends a
+message to a server quantum code containing current coords of all the
+atoms. The quantum code computes energy and forces based on the
+coords. It returns them as a message to LAMMPS, which completes the
+timestep.
+
+Alternate methods for code coupling with LAMMPS are described in "this
+section"_#howto10.
+
+LAMMPS support for client/server coupling is in its "MESSAGE
+package"_Section_package.html#MESSAGE which implements several
+commands that enable LAMMPS to act as a client or server, as discussed
+below. The MESSAGE package also wraps a client/server library called
+CSlib which enables two codes to exchange messages in different ways,
+either via files, a socket, or MPI. The CSlib is provided with LAMMPS
+in the lib/message dir. It has its own
+"website"_http://cslib.sandia.gov (as of Aug 2018) with documentation
+and test programs.
+
+NOTE: For client/server coupling to work between LAMMPS and another
+code, the other code also has to use the CSlib. This can sometimes be
+done without any modifications to the other code by simply wrapping it
+with a Python script that exchanges CSlib messages with LAMMPS and
+prepares input for or processes output from the other code. The other
+code also has to implement a matching protocol for the format and
+content of messages that LAMMPS exchanges with it.
+
+These are the commands currently in the MESSAGE package for two
+protocols, MD and MC (Monte Carlo). New protocols can easily be
+defined and added to this directory, where LAMMPS acts as either the
+client or server.
+
+"message"_message.html
+"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
+"server md"_server_md.html = LAMMPS is a server for computing MD forces
+"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
+
+The server doc files give details of the message protocols
+for data that is exchanged bewteen the client and server.
+
+These example directories illustrate how to use LAMMPS as either a
+client or server code:
+
+examples/message
+examples/COUPLE/README
+examples/COUPLE/lammps_mc
+examples/COUPLE/lammps_vasp :ul
+
+The examples/message dir couples a client instance of LAMMPS to a
+server instance of LAMMPS.
+
+The lammps_mc dir shows how to couple LAMMPS as a server to a simple
+Monte Carlo client code as the driver.
+
+The lammps_vasp dir shows how to couple LAMMPS as a client code
+running MD timestepping to VASP acting as a server providing quantum
+DFT forces, thru a Python wrapper script on VASP.
+
+Here is how to launch a client and server code together for any of the
+4 modes of message exchange that the "message"_message.html command
+and the CSlib support. Here LAMMPS is used as both the client and
+server code. Another code could be subsitituted for either.
+
+The examples below show launching both codes from the same window (or
+batch script), using the "&" character to launch the first code in the
+background. For all modes except {mpi/one}, you could also launch the
+codes in separate windows on your desktop machine. It does not
+matter whether you launch the client or server first.
+
+In these examples either code can be run on one or more processors.
+If running in a non-MPI mode (file or zmq) you can launch a code on a
+single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch both codes via
+mpirun, even if one or both of them runs on a single processor. This
+is so that MPI can figure out how to connect both MPI processes
+together to exchange MPI messages between them.
+
+For message exchange in {file}, {zmq}, or {mpi/two} modes:
+
+% mpirun -np 1 lmp_mpi -log log.client < in.client &
+% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 4 lmp_mpi -log log.client < in.client &
+% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 2 lmp_mpi -log log.client < in.client &
+% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
+
+For message exchange in {mpi/one} mode:
+
+Launch both codes in a single mpirun command:
+
+mpirun -np 2 lmp_mpi -mpi 2 -in in.message.client -log log.client : -np 4 lmp_mpi -mpi 2 -in in.message.server -log log.server
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpi P
+command-line option as their first option, where P is the number of
+processors the first code in the mpirun command (client or server) is
+running on.
+
:line
:line
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 218866e271..a572574fa2 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -100,6 +100,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MESSAGE"_#MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_#MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
@@ -879,6 +880,52 @@ examples/meam :ul
:line
+MESSAGE package :link(MESSAGE),h4
+
+[Contents:]
+
+Commands to use LAMMPS as either a client or server
+and couple it to another application.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first build the
+CSlib library in lib/message. You can do this manually if you prefer;
+follow the instructions in lib/message/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/message/Install.py script with the specified
+args:
+
+make lib-message # print help message
+make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
+make lib-message args="-s" # build as serial lib with no ZMQ support
+
+The build should produce two files: lib/message/cslib/src/libmessage.a
+and lib/message/Makefile.lammps. The latter is copied from an
+existing Makefile.lammps.* and has settings to link with the
+open-source ZMQ library if requested in the build.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-message
+make machine :pre
+
+make no-message
+make machine :pre
+
+[Supporting info:]
+
+src/MESSAGE: filenames -> commands
+lib/message/README
+"message"_message.html
+"fix client/md"_fix_client_md.html
+"server md"_server_md.html
+"server mc"_server_mc.html
+examples/message :ul
+
+:line
+
MISC package :link(MISC),h4
[Contents:]
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 7d456171dc..f38339661b 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1204,6 +1204,7 @@ letter abbreviation can be used:
-i or -in
-k or -kokkos
-l or -log
+-m or -mpi
-nc or -nocite
-pk or -package
-p or -partition
@@ -1351,6 +1352,24 @@ specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
+-mpi P :pre
+
+If used, this must be the first command-line argument after the LAMMPS
+executable name. It is only used when running LAMMPS in client/server
+mode with the "mpi/one" mode of messaging provided by the
+"message"_message.html command and the CSlib library LAMMPS links with
+from the lib/message directory. See the "message"_message.html
+command for more details
+
+In the mpi/one mode of messaging, both executables (the client and the
+server) are launched by one mpirun command. P should be specified as
+the number of processors (MPI tasks) the first executable is running
+on (could be the client or the server code).
+
+This information is required so that both codes can shrink the
+MPI_COMM_WORLD communicator they are part of to the subset of
+processors they are actually running on.
+
-nocite :pre
Disable writing the log.cite file which is normally written to list
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
new file mode 100644
index 0000000000..53cd7c36c2
--- /dev/null
+++ b/doc/src/fix_client_md.txt
@@ -0,0 +1,105 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix client/md command :h3
+
+[Syntax:]
+
+fix ID group-ID client/md :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+client/md = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all client/md :pre
+
+[Description:]
+
+This fix style enables LAMMPS to run as a "client" code and
+communicate each timestep with a separate "server" code to perform an
+MD simulation together.
+
+"This section"_Section_howto.html#howto_29 gives an overview of
+client/server coupling of LAMMPS with another code where one code is
+the "client" and sends request messages to a "server" code. The
+server responds to each request with a reply message. This enables
+the two codes to work in tandem to perform a simulation.
+
+When using this fix, LAMMPS (as the client code) passes the current
+coordinates of all particles to the server code each timestep, which
+computes their interaction, and returns the energy, forces, and virial
+for the interacting particles to LAMMPS, so it can complete the
+timestep.
+
+The server code could be a quantum code, or another classical MD code
+which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
+does not have. In the quantum case, this fix is a mechanism for
+running {ab initio} MD with quantum forces.
+
+The group associated with this fix is ignored.
+
+The protocol for message format and content that LAMMPS exchanges with
+the server code is defined on the "server md"_server_md.html doc page.
+
+Note that when using LAMMPS in this mode, your LAMMPS input script
+should not normally contain force field commands, like a
+"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
+"kspace_style"_kspace_style.html commmand. However it is possible for
+a server code to only compute a portion of the full force-field, while
+LAMMPS computes the remaining part. Your LAMMPS script can also
+specify boundary conditions or force constraints in the usual way,
+which will be added to the per-atom forces returned by the server
+code.
+
+See the examples/message dir for example scripts where LAMMPS is both
+the "client" and/or "server" code for this kind of client/server MD
+simulation. The examples/message/README file explains how to launch
+LAMMPS and another code in tandem to perform a coupled simulation.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential energy computed by the server application to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the server application's contribution to the system's
+virial as part of "thermodynamic output"_thermo_style.html. The
+default is {virial yes}
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15. The scalar is the
+potential energy discussed above. The scalar value calculated by this
+fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the MESSAGE package. It is only enabled if LAMMPS
+was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other server code.
+
+[Related commands:]
+
+"message"_message.html, "server"_server.html
+
+[Default:] none
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 06f4bf3718..a75f2469ca 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -67,6 +67,7 @@ label.html
lattice.html
log.html
mass.html
+message.html
min_modify.html
min_style.html
minimize.html
@@ -94,6 +95,9 @@ reset_timestep.html
restart.html
run.html
run_style.html
+server.html
+server_mc.html
+server_md.html
set.html
shell.html
special_bonds.html
@@ -140,7 +144,8 @@ fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
-fix_box_relax.html
+fix_box_relax.htmlf
+fix_client_md.html
fix_cmap.html
fix_colvars.html
fix_controller.html
@@ -283,8 +288,6 @@ fix_vector.html
fix_viscosity.html
fix_viscous.html
fix_wall.html
-fix_wall_body_polygon.html
-fix_wall_body_polyhedron.html
fix_wall_ees.html
fix_wall_gran.html
fix_wall_gran_region.html
@@ -426,9 +429,8 @@ pair_agni.html
pair_airebo.html
pair_awpmd.html
pair_beck.html
-pair_body_nparticle.html
+pair_body.html
pair_body_rounded_polygon.html
-pair_body_rounded_polyhedron.html
pair_bop.html
pair_born.html
pair_brownian.html
diff --git a/doc/src/message.txt b/doc/src/message.txt
new file mode 100644
index 0000000000..bbea48f0f1
--- /dev/null
+++ b/doc/src/message.txt
@@ -0,0 +1,159 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+message command :h3
+
+[Syntax:]
+
+message which protocol mode arg :pre
+
+which = {client} or {server} :ulb,l
+protocol = {md} or {mc} :l
+mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
+ {file} arg = filename
+ filename = file used for message exchanges
+ {zmq} arg = socket-ID
+ socket-ID for client = localhost:5555, see description below
+ socket-ID for server = *:5555, see description below
+ {mpi/one} arg = none
+ {mpi/two} arg = filename
+ filename = file used to establish communication bewteen 2 MPI jobs :pre
+:ule
+
+[Examples:]
+
+message client md file tmp.couple
+message server md file tmp.couple :pre
+
+message client md zmq localhost:5555
+message server md zmq *:5555 :pre
+
+message client md mpi/one
+message server md mpi/one :pre
+
+message client md mpi/two tmp.couple
+message server md mpi/two tmp.couple :pre
+
+[Description:]
+
+Establish a messaging protocol between LAMMPS and another code for the
+purpose of client/server coupling.
+
+"This section"_Section_howto.html#howto_29 gives an overview of
+client/server coupling of LAMMPS with another code where one code is
+the "client" and sends request messages to a "server" code. The
+server responds to each request with a reply message. This enables
+the two codes to work in tandem to perform a simulation.
+
+:line
+
+The {which} argument defines LAMMPS to be the client or the server.
+
+:line
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+md = run dynamics with another code
+mc = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client or server. See the
+"server md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+The {mode} argument specifies how messages are exchanged between the
+client and server codes. Both codes must use the same mode and use
+consistent parameters.
+
+For mode {file}, the 2 codes communicate via binary files. They must
+use the same filename, which is actually a file prefix. Several files
+with that prefix will be created and deleted as a simulation runs.
+The filename can include a path. Both codes must be able to access
+the path/file in a common filesystem.
+
+For mode {zmq}, the 2 codes communicate via a socket on the server
+code's machine. The client specifies an IP address (IPv4 format) or
+the DNS name of the machine the server code is running on, followed by
+a 4-digit port ID for the socket, separated by a colon. E.g.
+
+localhost:5555 # client and server running on same machine
+192.168.1.1:5555 # server is 192.168.1.1
+deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre
+
+The server specifes "*:5555" where "*" represents all available
+interfaces on the server's machine, and the port ID must match
+what the client specifies.
+
+NOTE: What are allowed port IDs?
+
+NOTE: Additional explanation is needed here about how to use the {zmq}
+mode on a parallel machine, e.g. a cluster with many nodes.
+
+For mode {mpi/one}, the 2 codes communicate via MPI and are launched
+by the same mpirun command, e.g. with this syntax for OpenMPI:
+
+mpirun -np 2 lmp_mpi -mpi 2 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
+mpirun -np 2 othercode args : -np 4 lmp_mpi -mpi 2 -in in.server # LAMMPS is server :pre
+
+Note the use of the "-mpi P" command-line argument with LAMMPS. See
+the "command-line args"_Section_start.html#start_6 doc page for
+further explanation.
+
+For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
+be 2 separate mpirun commands. The specified {filename} argument is a
+file the 2 MPI processes will use to exchange info so that an MPI
+inter-communicator can be established to enable the 2 codes to send
+MPI messages to each other. Both codes must be able to access the
+path/file in a common filesystem.
+
+:line
+
+Normally, the message command should be used at the top of a LAMMPS
+input script. It performs an initial handshake with the other code to
+setup messaging and to verify that both codes are using the same
+message protocol and mode. Assuming both codes are launched at
+(nearly) the same time, the other code should perform the same kind of
+initialization.
+
+If LAMMPS is the client code, it will begin sending messages when a
+LAMMPS client command begins its operation. E.g. for the "fix
+client/md"_fix_client_md.html command, it is when a "run"_run.html
+command is executed.
+
+If LAMMPS is the server code, it will begin receiving messages when
+the "server"_server.html command is invoked.
+
+A fix client command will terminate its messaging with the server when
+LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
+server command will terminate its messaging with the client when the
+client signals it. Then the remainder of the LAMMPS input script will
+be processed.
+
+If both codes do something similar, this means a new round of
+client/server messaging can be initiated after termination by re-using
+a 2nd message command in your LAMMPS input script, followed by a new
+fix client or server command.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"server"_server.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/server.txt b/doc/src/server.txt
new file mode 100644
index 0000000000..ba6daa7fcf
--- /dev/null
+++ b/doc/src/server.txt
@@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+server command :h3
+
+[Syntax:]
+
+server protocol :pre
+
+protocol = {md} or {mc} :ul
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it receives
+messages from a separate "client" code and responds by sending a reply
+message back to the client. The specified {protocol} determines the
+format and content of messages LAMMPS expects to receive and how it
+responds.
+
+"This section"_Section_howto.html#howto_29 gives an overview of
+client/server coupling of LAMMPS with another code where one code is
+the "client" and sends request messages to a "server" code. The
+server responds to each request with a reply message. This enables
+the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+"md"_server_md.html = run dynamics with another code
+"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client (via the "fix
+client/md"_fix_client_md.html command) or server. See the "server
+md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
new file mode 100644
index 0000000000..44335efc95
--- /dev/null
+++ b/doc/src/server_mc.txt
@@ -0,0 +1,112 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+server mc command :h3
+
+[Syntax:]
+
+server mc :pre
+
+mc = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server mc :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {mc}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+"This section"_Section_howto.html#howto_29 gives an overview of
+client/server coupling of LAMMPS with another code where one code is
+the "client" and sends request messages to a "server" code. The
+server responds to each request with a reply message. This enables
+the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+See an example of how this command is used in
+examples/COUPLE/lammps_mc/in.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives
+instructions from a Monte Carlo (MC) driver to displace random atoms,
+compute the energy before and after displacement, and run dynamics to
+equilibrate the system.
+
+The MC driver performs the random displacements on random atoms,
+accepts or rejects the move in an MC sense, and orchestrates the MD
+runs.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax (as of Aug 2018).
+The "cs" object in this pseudo code is an instance of the CSlib that
+both the client and server codes store.
+
+See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
+these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
+example of how an MC driver code can use these messages.
+
+Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
+
+[Client sends one of these kinds of message]:
+
+cs.send(NATOMS,0) # msgID = 1 with no fields :pre
+
+cs.send(EINIT,0) # msgID = 2 with no fields :pre
+
+cs.send(DISPLACE,2) # msgID = 3 with 2 fields
+cs.pack(1,1,ID) # 1st field = ID of atom to displace
+cs.pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
+
+cs.send(ACCEPT,1) # msgID = 4 with 1 field
+cs.pack(1,1,flag) # 1st field = accept/reject flag :pre
+
+cs.send(RUN,1) # msgID = 5 with 1 field
+cs.pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
+
+[Server replies]:
+
+cs.send(NATOMS,1) # msgID = 1 with 1 field
+cs.pack(1,1,Natoms) # 1st field = number of atoms :pre
+
+cs.send(EINIT,2) # msgID = 2 with 2 fields
+cs.pack(1,1,poteng) # 1st field = potential energy of system
+cs.pack(2,3*Natoms,x) # 2nd field = 3N coords of Natoms :pre
+
+cs.send(DISPLACE,1) # msgID = 3 with 1 field
+cs.pack(1,1,poteng) # 1st field = new potential energy of system :pre
+
+cs.send(ACCEPT,0) # msgID = 4 with no fields
+
+cs.send(RUN,0) # msgID = 5 with no fields
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"message"_message.html
+
+[Default:] none
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
new file mode 100644
index 0000000000..422b207bed
--- /dev/null
+++ b/doc/src/server_md.txt
@@ -0,0 +1,122 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+server md command :h3
+
+[Syntax:]
+
+server md :pre
+
+md = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {md}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+"This section"_Section_howto.html#howto_29 gives an overview of
+client/server coupling of LAMMPS with another code where one code is
+the "client" and sends request messages to a "server" code. The
+server responds to each request with a reply message. This enables
+the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+See an example of how this command is used in
+examples/message/in.message.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives the
+current coordinates of all particles from the client code each
+timestep, computes their interaction, and returns the energy, forces,
+and virial for the interacting particles to the client code, so it can
+complete the timestep. This command could also be used with a client
+code that performs energy minimization, using the server to compute
+forces and energy each iteration of its minimizer.
+
+When using the "fix client/md" command, LAMMPS (as the client code)
+does the timestepping and receives needed energy, forces, and virial
+values from the server code.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax (as of Aug 2018).
+The "cs" object in this pseudo code is an instance of the CSlib that
+both the client and server codes store.
+
+See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
+files for details on how LAMMPS uses these messages. See the
+examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
+a quantum code (VASP) can use use these messages.
+
+The following code uses these values, defined as enums in LAMMPS:
+
+enum{SETUP=1,STEP};
+enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
+enum{FORCES=1,ENERGY,VIRIAL}; :pre
+
+[Client sends 2 kinds of messages]:
+
+# required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
+# optional fields: others in 2nd enum above :pre
+
+cs.send(SETUP,nfields) # msgID with nfields :pre
+
+cs.pack_string(UNITS,units) # units = "lj", "real", "metal", etc
+cs.pack_int(NATOMS,natoms) # total numer of atoms
+cs.pack_int(NTYPES,ntypes) # number of atom types
+cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
+cs.pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
+cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
+cs.pack(TYPES,natoms,type) # vector of per-atom types
+cs.pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs.pack(CHARGE,natoms,q) # vector of per-atom charge :pre
+
+# required fields: COORDS
+# optional fields: BOXLO, BOXHI, BOXTILT :pre
+
+cs.send(STEP,nfields) # msgID with nfields :pre
+
+cs.pack_int(NATOMS,natoms) # total numer of atoms
+cs.pack_int(NTYPES,ntypes) # number of atom types
+cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
+cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :pre
+
+[Server replies to either kind of message]:
+
+cs.send(msgID,3) # msgID = 1 with 3 fields
+cs.pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
+cs.pack(ENERGY,1,poteng) # total potential energy of system
+cs.pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index 83e7463531..2d09ed7d4b 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
+6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
In all of the examples included here, LAMMPS must first be built as a
library. Basically, in the src dir you type one of
@@ -33,9 +34,11 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
+lammps_mc client/server coupling Monte Carlo with LAMMPS MD
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
+lammps_vasp client/server coupling LAMMPS MD with VASP quantum DFT
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile
new file mode 100644
index 0000000000..821eb58134
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/Makefile
@@ -0,0 +1,34 @@
+# Makefile for MC
+
+SHELL = /bin/sh
+
+SRC = mc.cpp random_park.cpp
+OBJ = $(SRC:.cpp=.o)
+
+# change this line for your machine to path for CSlib src dir
+
+CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
+
+# compiler/linker settings
+
+CC = g++
+CCFLAGS = -g -O3 -I$(CSLIB)
+LINK = g++
+LINKFLAGS = -g -O -L$(CSLIB)
+
+# targets
+
+mc: $(OBJ)
+# this line if built the CSlib within lib/message with ZMQ support
+# note this is using the serial (no-mpi) version of the CSlib
+ $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
+# this line if built the CSlib without ZMQ support
+# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
+
+clean:
+ @rm -f *.o mc
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) -c $<
diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README
new file mode 100644
index 0000000000..512f7304de
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/README
@@ -0,0 +1,106 @@
+Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE)
+and Section_howto.html#howto10 for more details on how
+client/server coupling works in LAMMPS.
+
+In this dir, the mc.cpp/h files are a standalone "client" MC code. It
+should be run on a single processor, though it could become a parallel
+program at some point. LAMMPS is also run as a standalone executable
+as a "server" on as many processors as desired using its "server mc"
+command; see it's doc page for details.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the MC
+program became parallel, data could also be exchanged via MPI.
+
+The MC code makes simple MC moves, by displacing a single random atom
+by a small random amount. It uses LAMMPS to calculate the energy
+change, and to run dynamics between MC moves.
+
+----------------
+
+Build LAMMPS and the MC client code
+
+First, build LAMMPS with its MESSAGE package installed:
+
+cd lammps/lib/message
+python Install.py -m -z # build CSlib with MPI and ZMQ support
+cd lammps/src
+make yes-message
+make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+Next build the MC client code:
+
+First edit the Makefile in this dir. The CSLIB variable should be the
+path to where the LAMMPS lib/message dir is on your system. If you
+built the CSlib without ZMQ support you will also need to
+comment/uncomment two lines. Then you can just type "make" and you
+should get an "mc" executable.
+
+----------------
+
+To run in client/server mode:
+
+Both the client (MC) and server (LAMMPS) must use the same messaging
+mode, namely file or zmq. This is an argument to the MC code; it can
+be selected by setting the "mode" variable when you run LAMMPS. The
+default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The MC code is always run in serial.
+
+When you run, the server should print out thermodynamic info
+for every MD run it performs (between MC moves). The client
+will print nothing until the simulation ends, then it will
+print stats about the accepted MC moves.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
+
+--------------
+
+The input script for the MC program is in.mc. You can edit it to run
+longer simulations.
+
+500 nsteps = total # of steps of MD
+100 ndynamics = # of MD steps between MC moves
+0.1 delta = displacement size of MC move
+1.0 temperature = used in MC Boltzman factor
+12345 seed = random number seed
+
+--------------
+
+The problem size that LAMMPS is computing the MC energy for and
+running dynamics on is set by the x,y,z variables in the LAMMPS
+in.mc.server script. The default size is 500 particles. You can
+adjust the size as follows:
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
diff --git a/examples/COUPLE/lammps_mc/in.mc b/examples/COUPLE/lammps_mc/in.mc
new file mode 100644
index 0000000000..85052d09f1
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc
@@ -0,0 +1,7 @@
+# MC params
+
+500 nsteps
+100 ndynamics
+0.1 delta
+1.0 temperature
+12345 seed
diff --git a/examples/COUPLE/lammps_mc/in.mc.server b/examples/COUPLE/lammps_mc/in.mc.server
new file mode 100644
index 0000000000..8b10bb0f7b
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc.server
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server mc file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server mc zmq *:5555" &
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1 b/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1
new file mode 100644
index 0000000000..34e016e0c1
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000633001 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+46.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+314.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+314.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4 b/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4
new file mode 100644
index 0000000000..3b73e52595
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000604868 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 3.09944e-06 on 4 procs for 0 steps with 500 atoms
+
+72.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.099e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.33786e-06 on 4 procs for 0 steps with 500 atoms
+
+119.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.338e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.51667e-06 on 4 procs for 0 steps with 500 atoms
+
+113.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.517e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.92063e-06 on 4 procs for 0 steps with 500 atoms
+
+119.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.921e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 3.39746e-06 on 4 procs for 0 steps with 500 atoms
+
+117.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.397e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 3.39746e-06 on 4 procs for 0 steps with 500 atoms
+
+117.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.397e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1
new file mode 100644
index 0000000000..18af66d587
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000612974 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+46.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 0 on 1 procs for 0 steps with 500 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0 | | | 0.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 0 on 1 procs for 0 steps with 500 atoms
+
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0 | | | 0.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4
new file mode 100644
index 0000000000..480566635f
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000566006 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 4.29153e-06 on 4 procs for 0 steps with 500 atoms
+
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 4.292e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
+
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.576e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.09944e-06 on 4 procs for 0 steps with 500 atoms
+
+121.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.099e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 1.90735e-06 on 4 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
+
+151.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp
new file mode 100644
index 0000000000..24bb96641d
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.cpp
@@ -0,0 +1,261 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+// MC code used with LAMMPS in client/server mode
+// MC is the client, LAMMPS is the server
+
+// Syntax: mc infile mode modearg
+// mode = file, zmq
+// modearg = filename for file, localhost:5555 for zmq
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cslib.h"
+using namespace CSLIB_NS;
+
+#include "mc.h"
+#include "random_park.h"
+
+void error(const char *);
+CSlib *cs_create(char *, char *);
+
+#define MAXLINE 256
+
+/* ---------------------------------------------------------------------- */
+
+// main program
+
+int main(int narg, char **arg)
+{
+ if (narg != 4) {
+ error("Syntax: mc infile mode modearg");
+ exit(1);
+ }
+
+ // initialize CSlib
+
+ CSlib *cs = cs_create(arg[2],arg[3]);
+
+ // create MC class and perform run
+
+ MC *mc = new MC(arg[1],cs);
+ mc->run();
+
+ // final MC stats
+
+ int naccept = mc->naccept;
+ int nattempt = mc->nattempt;
+
+ printf("------ MC stats ------\n");
+ printf("MC attempts = %d\n",nattempt);
+ printf("MC accepts = %d\n",naccept);
+ printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
+
+ // clean up
+
+ delete cs;
+ delete mc;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void error(const char *str)
+{
+ printf("ERROR: %s\n",str);
+ exit(1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib *cs_create(char *mode, char *arg)
+{
+ CSlib *cs = new CSlib(0,mode,arg,NULL);
+
+ // initial handshake to agree on protocol
+
+ cs->send(0,1);
+ cs->pack_string(1,(char *) "mc");
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ return cs;
+}
+
+// ----------------------------------------------------------------------
+// MC class
+// ----------------------------------------------------------------------
+
+MC::MC(char *mcfile, CSlib *cs_caller)
+{
+ cs = cs_caller;
+
+ // setup MC params
+
+ options(mcfile);
+
+ // random # generator
+
+ random = new RanPark(seed);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MC::~MC()
+{
+ free(x);
+ delete random;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::run()
+{
+ int iatom,accept,msgID,nfield;
+ double pe_initial,pe_final,edelta;
+ double dx,dy,dz;
+ double xold[3],xnew[3];
+ int *fieldID,*fieldtype,*fieldlen;
+
+ enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+ // one-time request for atom count from MD
+ // allocate 1d coord buffer
+
+ cs->send(NATOMS,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ natoms = cs->unpack_int(1);
+
+ x = (double *) malloc(3*natoms*sizeof(double));
+
+ // loop over MC moves
+
+ naccept = nattempt = 0;
+
+ for (int iloop = 0; iloop < nloop; iloop++) {
+
+ // request current energy from MD
+ // recv energy, coords from MD
+
+ cs->send(EINIT,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_initial = cs->unpack_double(1);
+ double *x = (double *) cs->unpack(2);
+
+ // perform simple MC event
+ // displace a single atom by random amount
+
+ iatom = (int) natoms*random->uniform();
+ xold[0] = x[3*iatom+0];
+ xold[1] = x[3*iatom+1];
+ xold[2] = x[3*iatom+2];
+
+ dx = 2.0*delta*random->uniform() - delta;
+ dy = 2.0*delta*random->uniform() - delta;
+ dz = 2.0*delta*random->uniform() - delta;
+
+ xnew[0] = xold[0] + dx;
+ xnew[1] = xold[1] + dx;
+ xnew[2] = xold[2] + dx;
+
+ // send atom ID and its new coords to MD
+ // recv new energy
+
+ cs->send(DISPLACE,2);
+ cs->pack_int(1,iatom+1);
+ cs->pack(2,4,3,xnew);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_final = cs->unpack_double(1);
+
+ // decide whether to accept/reject MC event
+
+ if (pe_final <= pe_initial) accept = 1;
+ else if (temperature == 0.0) accept = 0;
+ else if (random->uniform() >
+ exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
+ else accept = 1;
+
+ nattempt++;
+ if (accept) naccept++;
+
+ // send accept (1) or reject (0) flag to MD
+
+ cs->send(ACCEPT,1);
+ cs->pack_int(1,accept);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // send dynamics timesteps
+
+ cs->send(RUN,1);
+ cs->pack_int(1,ndynamics);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ }
+
+ // send exit message to MD
+
+ cs->send(-1,0);
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::options(char *filename)
+{
+ // default params
+
+ nsteps = 0;
+ ndynamics = 100;
+ delta = 0.1;
+ temperature = 1.0;
+ seed = 12345;
+
+ // read and parse file
+
+ FILE *fp = fopen(filename,"r");
+ if (fp == NULL) error("Could not open MC file");
+
+ char line[MAXLINE];
+ char *keyword,*value;
+ char *eof = fgets(line,MAXLINE,fp);
+
+ while (eof) {
+ if (line[0] == '#') { // comment line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ value = strtok(line," \t\n\r\f");
+ if (value == NULL) { // blank line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ keyword = strtok(NULL," \t\n\r\f");
+ if (keyword == NULL) error("Missing keyword in MC file");
+
+ if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
+ else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
+ else if (strcmp(keyword,"delta") == 0) delta = atof(value);
+ else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
+ else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
+ else error("Unknown param in MC file");
+
+ eof = fgets(line,MAXLINE,fp);
+ }
+
+ // derived params
+
+ nloop = nsteps/ndynamics;
+}
diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h
new file mode 100644
index 0000000000..afeb3d06ab
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+#ifndef MC_H
+#define MC_H
+
+/* ---------------------------------------------------------------------- */
+
+class MC {
+ public:
+ int naccept; // # of accepted MC events
+ int nattempt; // # of attempted MC events
+
+ MC(char *, class CSlib *);
+ ~MC();
+ void run();
+
+ private:
+ int nsteps; // total # of MD steps
+ int ndynamics; // steps in one short dynamics run
+ int nloop; // nsteps/ndynamics
+ int natoms; // # of MD atoms
+
+ double delta; // MC displacement distance
+ double temperature; // MC temperature for Boltzmann criterion
+ double *x; // atom coords as 3N 1d vector
+ double energy; // global potential energy
+
+ int seed; // RNG seed
+ class RanPark *random;
+
+ class CSlib *cs; // messaging library
+
+ void options(char *);
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp
new file mode 100644
index 0000000000..61ac18c6c0
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.cpp
@@ -0,0 +1,72 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+// Park/Miller RNG
+
+#include <math.h>
+#include "random_park.h"
+//#include "error.h"
+
+#define IA 16807
+#define IM 2147483647
+#define AM (1.0/IM)
+#define IQ 127773
+#define IR 2836
+
+/* ---------------------------------------------------------------------- */
+
+RanPark::RanPark(int seed_init)
+{
+ //if (seed_init <= 0)
+ // error->one(FLERR,"Invalid seed for Park random # generator");
+ seed = seed_init;
+ save = 0;
+}
+
+/* ----------------------------------------------------------------------
+ uniform RN
+------------------------------------------------------------------------- */
+
+double RanPark::uniform()
+{
+ int k = seed/IQ;
+ seed = IA*(seed-k*IQ) - IR*k;
+ if (seed < 0) seed += IM;
+ double ans = AM*seed;
+ return ans;
+}
+
+/* ----------------------------------------------------------------------
+ gaussian RN
+------------------------------------------------------------------------- */
+
+double RanPark::gaussian()
+{
+ double first,v1,v2,rsq,fac;
+
+ if (!save) {
+ do {
+ v1 = 2.0*uniform()-1.0;
+ v2 = 2.0*uniform()-1.0;
+ rsq = v1*v1 + v2*v2;
+ } while ((rsq >= 1.0) || (rsq == 0.0));
+ fac = sqrt(-2.0*log(rsq)/rsq);
+ second = v1*fac;
+ first = v2*fac;
+ save = 1;
+ } else {
+ first = second;
+ save = 0;
+ }
+ return first;
+}
diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h
new file mode 100644
index 0000000000..0dc2081768
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.h
@@ -0,0 +1,28 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef RANPARK_H
+#define RANPARK_H
+
+class RanPark {
+ public:
+ RanPark(int);
+ double uniform();
+ double gaussian();
+
+ private:
+ int seed,save;
+ double second;
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_vasp/INCAR b/examples/COUPLE/lammps_vasp/INCAR
new file mode 100644
index 0000000000..ac2358e5fb
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/INCAR
@@ -0,0 +1,53 @@
+# Startparameter for this run:
+ NWRITE = 2 write-flag & timer
+ PREC = normal normal or accurate (medium, high low for compatibility)
+ ISTART = 0 job : 0-new 1-cont 2-samecut
+ ICHARG = 2 charge: 1-file 2-atom 10-const
+ ISPIN = 1 spin polarized calculation?
+ LSORBIT = F spin-orbit coupling
+ INIWAV = 1 electr: 0-lowe 1-rand 2-diag
+
+# Electronic Relaxation 1
+ ENCUT = 600.0 eV #Plane wave energy cutoff
+ ENINI = 600.0 initial cutoff
+ NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
+ EDIFF = 0.1E-05 stopping-criterion for ELM
+# Ionic relaxation
+ EDIFFG = 0.1E-02 stopping-criterion for IOM
+ NSW = 0 number of steps for IOM
+ NBLOCK = 1; KBLOCK = 1 inner block; outer block
+ IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
+ NFREE = 0 steps in history (QN), initial steepest desc. (CG)
+ ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
+ IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
+
+ POTIM = 0.5000 time-step for ionic-motion
+ TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
+ SMASS = -3.00 Nose mass-parameter (am)
+ estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
+ PSTRESS= 0.0 pullay stress
+
+# DOS related values:
+ EMIN = 10.00; EMAX =-10.00 energy-range for DOS
+ EFERMI = 0.00
+ ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
+
+# Electronic relaxation 2 (details)
+ IALGO = 48 algorithm
+
+# Write flags
+ LWAVE = T write WAVECAR
+ LCHARG = T write CHGCAR
+ LVTOT = F write LOCPOT, total local potential
+ LVHAR = F write LOCPOT, Hartree potential only
+ LELF = F write electronic localiz. function (ELF)
+
+# Dipole corrections
+ LMONO = F monopole corrections only (constant potential shift)
+ LDIPOL = F correct potential (dipole corrections)
+ IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
+ EPSILON= 1.0000000 bulk dielectric constant
+
+# Exchange correlation treatment:
+ GGA = -- GGA type
+
diff --git a/examples/COUPLE/lammps_vasp/KPOINTS b/examples/COUPLE/lammps_vasp/KPOINTS
new file mode 100644
index 0000000000..322509da30
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/KPOINTS
@@ -0,0 +1,6 @@
+K-Points
+ 0
+Monkhorst Pack
+ 15 15 15
+ 0 0 0
+
diff --git a/examples/COUPLE/lammps_vasp/POSCAR_W b/examples/COUPLE/lammps_vasp/POSCAR_W
new file mode 100644
index 0000000000..aba5df54a0
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/POSCAR_W
@@ -0,0 +1,11 @@
+W unit cell
+1.0
+3.16 0.00000000 0.00000000
+0.00000000 3.16 0.00000000
+0.00000000 0.00000000 3.16
+W
+2
+Direct
+ 0.00000000 0.00000000 0.00000000
+ 0.50000000 0.50000000 0.50000000
+
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
new file mode 100644
index 0000000000..3d83ff7dc1
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/README
@@ -0,0 +1,90 @@
+Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
+coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
+Section_howto.html#howto10 for more details on how client/server
+coupling works in LAMMPS.
+
+In this dir, the vasp_warp.py is a wrapper on the VASP quantum DFT
+code so it can work as a "server" code which LAMMPS drives as a
+"client" code to perform ab initio MD. LAMMPS performs the MD
+timestepping, sends VASP a current set of coordinates each timestep,
+VASP computes forces and energy and virial and returns that info to
+LAMMPS.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the
+vasp_wrap.py program became parallel, or the CSlib library calls were
+integrated into VASP directly, then data could also be exchanged via
+MPI.
+
+----------------
+
+Build LAMMPS with its MESSAGE package installed:
+
+cd lammps/lib/message
+python Install.py -m -z # build CSlib with MPI and ZMQ support
+cd lammps/src
+make yes-message
+make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+----------------
+
+To run in client/server mode:
+
+Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
+messaging mode, namely file or zmq. This is an argument to the
+vasp_wrap.py code; it can be selected by setting the "mode" variable
+when you run LAMMPS. The default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The vasp_wrap.py code is always run in serial, but it
+launches VASP from Python via an mpirun command which can run VASP
+itself in parallel.
+
+When you run, the server should print out thermodynamic info every
+timestep which corresponds to the forces and virial computed by VASP.
+VASP will also generate output files each timestep. The vasp_wrapper.py
+script could be generalized to archive these.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
+
+--------------
+
+The provided data.W file (for LAMMPS) and POSCAR_W file (for VASP) are
+for a simple 2-atom unit cell of bcc tungsten (W). You could
+replicate this with LAMMPS to create a larger system. The
+vasp_wrap.py script needs to be generalized to create an appropriate
+POSCAR_W file for a larger box.
+
+VASP input file include the sample INCAR and KPOINTS files provided.
+A POTCAR file is also needed, which should come from your VASP package
+installation.
diff --git a/examples/COUPLE/lammps_vasp/data.W b/examples/COUPLE/lammps_vasp/data.W
new file mode 100644
index 0000000000..8accd9ca79
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/data.W
@@ -0,0 +1,15 @@
+LAMMPS W data file
+
+2 atoms
+
+1 atom types
+
+0.0 3.16 xlo xhi
+0.0 3.16 ylo yhi
+0.0 3.16 zlo zhi
+
+Atoms
+
+1 1 0.000 0.000 0.000
+2 1 1.58 1.58 1.58
+
diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W
new file mode 100644
index 0000000000..3eaf99dcbb
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/in.client.W
@@ -0,0 +1,34 @@
+# small W unit cell for use with VASP
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+mass 1 183.85
+
+replicate $x $y $z
+
+velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 1
+run 3
+
diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output
new file mode 100644
index 0000000000..de37c7cbaf
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/log.client.output
@@ -0,0 +1,63 @@
+LAMMPS (20 Apr 2018)
+# small W unit cell for use with VASP
+
+#message client aimd file tmp.couple
+message client aimd zmq localhost:5555
+#message client aimd mpi/two tmp.couple
+#message client aimd mpi/one tmp.couple
+
+units real
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 2 atoms
+mass 1 1.0
+
+#velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all message/aimd
+fix_modify 2 energy yes
+
+thermo 1
+run 2
+Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 0 0 -48.069571 -172694.2
+ 1 0.063865861 0 0 -48.069381 -172693.93
+ 2 0.25546344 0 0 -48.06881 -172693.1
+Loop time of 0.281842 on 1 procs for 2 steps with 2 atoms
+
+Performance: 0.613 ns/day, 39.145 hours/ns, 7.096 timesteps/s
+0.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 3.0994e-06 | 3.0994e-06 | 3.0994e-06 | 0.0 | 0.00
+Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.03
+Modify | 0.28174 | 0.28174 | 0.28174 | 0.0 | 99.97
+Other | | 5.96e-06 | | | 0.00
+
+Nlocal: 2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7 ave 7 max 7 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds not checked
+
+Total wall time: 0:00:06
diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py
new file mode 100644
index 0000000000..35955b6adb
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py
@@ -0,0 +1,234 @@
+#!/usr/bin/env python
+
+# ----------------------------------------------------------------------
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+# ----------------------------------------------------------------------
+
+# Syntax: vasp_wrap.py file/zmq POSCARfile
+
+# wrapper on VASP to act as server program using CSlib
+# receives message with list of coords from client
+# creates VASP inputs
+# invokes VASP to calculate self-consistent energy of that config
+# reads VASP outputs
+# sends message with energy, forces, virial to client
+
+# NOTES:
+# check to insure basic VASP input files are in place?
+# worry about archiving VASP input/output in special filenames or dirs?
+# how to get ordering (by type) of VASP atoms vs LAMMPS atoms
+# create one initial permutation vector?
+# could make syntax for launching VASP more flexible
+# e.g. command-line arg for # of procs
+
+import sys
+import commands
+import xml.etree.ElementTree as ET
+from cslib import CSlib
+
+vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
+ "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
+
+# enums matching FixClientMD class in LAMMPS
+
+SETUP,STEP = range(1,2+1)
+UNITS,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE = range(1,10+1)
+FORCES,ENERGY,VIRIAL = range(1,3+1)
+
+# -------------------------------------
+# functions
+
+# error message and exit
+
+def error(txt):
+ print "ERROR:",txt
+ sys.exit(1)
+
+# -------------------------------------
+# read initial VASP POSCAR file to setup problem
+# return natoms,ntypes,box
+
+def vasp_setup(poscar):
+
+ ps = open(poscar,'r').readlines()
+
+ # box size
+
+ words = ps[2].split()
+ xbox = float(words[0])
+ words = ps[3].split()
+ ybox = float(words[1])
+ words = ps[4].split()
+ zbox = float(words[2])
+ box = [xbox,ybox,zbox]
+
+ ntypes = 0
+ natoms = 0
+ words = ps[6].split()
+ for word in words:
+ if word == '#': break
+ ntypes += 1
+ natoms += int(word)
+
+ return natoms,ntypes,box
+
+# -------------------------------------
+# write a new POSCAR file for VASP
+
+def poscar_write(poscar,natoms,ntypes,types,coords,box):
+
+ psold = open(poscar,'r').readlines()
+ psnew = open("POSCAR",'w')
+
+ # header, including box size
+
+ print >>psnew,psold[0],
+ print >>psnew,psold[1],
+ print >>psnew,"%g 0.0 0.0" % box[0]
+ print >>psnew,"0.0 %g 0.0" % box[1]
+ print >>psnew,"0.0 0.0 %g" % box[2]
+ print >>psnew,psold[5],
+ print >>psnew,psold[6],
+
+ # per-atom coords
+ # grouped by types
+
+ print >>psnew,"Cartesian"
+
+ for itype in range(1,ntypes+1):
+ for i in range(natoms):
+ if types[i] != itype: continue
+ x = coords[3*i+0]
+ y = coords[3*i+1]
+ z = coords[3*i+2]
+ aline = " %g %g %g" % (x,y,z)
+ print >>psnew,aline
+
+ psnew.close()
+
+# -------------------------------------
+# read a VASP output vasprun.xml file
+# uses ElementTree module
+# see https://docs.python.org/2/library/xml.etree.elementtree.html
+
+def vasprun_read():
+ tree = ET.parse('vasprun.xml')
+ root = tree.getroot()
+
+ #fp = open("vasprun.xml","r")
+ #root = ET.parse(fp)
+
+ scsteps = root.findall('calculation/scstep')
+ energy = scsteps[-1].find('energy')
+ for child in energy:
+ if child.attrib["name"] == "e_0_energy":
+ eout = float(child.text)
+
+ fout = []
+ sout = []
+
+ varrays = root.findall('calculation/varray')
+ for varray in varrays:
+ if varray.attrib["name"] == "forces":
+ forces = varray.findall("v")
+ for line in forces:
+ fxyz = line.text.split()
+ fxyz = [float(value) for value in fxyz]
+ fout += fxyz
+ if varray.attrib["name"] == "stress":
+ tensor = varray.findall("v")
+ stensor = []
+ for line in tensor:
+ sxyz = line.text.split()
+ sxyz = [float(value) for value in sxyz]
+ stensor.append(sxyz)
+ sxx = stensor[0][0]
+ syy = stensor[1][1]
+ szz = stensor[2][2]
+ sxy = 0.5 * (stensor[0][1] + stensor[1][0])
+ sxz = 0.5 * (stensor[0][2] + stensor[2][0])
+ syz = 0.5 * (stensor[1][2] + stensor[2][1])
+ sout = [sxx,syy,szz,sxy,sxz,syz]
+
+ #fp.close()
+
+ return eout,fout,sout
+
+# -------------------------------------
+# main program
+
+# command-line args
+
+if len(sys.argv) != 3:
+ print "Syntax: python vasp_wrap.py file/zmq POSCARfile"
+ sys.exit(1)
+
+mode = sys.argv[1]
+poscar_template = sys.argv[2]
+
+if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
+elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
+else:
+ print "Syntax: python vasp_wrap.py file/zmq POSCARfile"
+ sys.exit(1)
+
+natoms,ntypes,box = vasp_setup(poscar_template)
+
+# initial message for MD protocol
+
+msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+if msgID != 0: error("Bad initial client/server handshake")
+protocol = cs.unpack_string(1)
+if protocol != "md": error("Mismatch in client/server protocol")
+cs.send(0,0)
+
+# endless server loop
+
+while 1:
+
+ # recv message from client
+ # msgID = 0 = all-done message
+
+ msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+ if msgID < 0: break
+
+ # could generalize this to be more like ServerMD class
+ # allow for box size, atom types, natoms, etc
+
+ # unpack coords from client
+ # create VASP input
+ # NOTE: generalize this for general list of atom types
+
+ coords = cs.unpack(COORDS,1)
+ #types = cs.unpack(2);
+ types = 2*[1]
+
+ poscar_write(poscar_template,natoms,ntypes,types,coords,box)
+
+ # invoke VASP
+
+ print "Launching VASP ..."
+ print vaspcmd
+ out = commands.getoutput(vaspcmd)
+ print out
+
+ # process VASP output
+
+ energy,forces,virial = vasprun_read()
+
+ # return forces, energy, virial to client
+
+ cs.send(msgID,3);
+ cs.pack(FORCES,4,3*natoms,forces)
+ cs.pack_double(ENERGY,energy)
+ cs.pack(VIRIAL,4,6,virial)
+
+# final reply to client
+
+cs.send(0,0)
+
+# clean-up
+
+del cs
diff --git a/examples/README b/examples/README
index a8dfe63d92..599392e6b2 100644
--- a/examples/README
+++ b/examples/README
@@ -82,6 +82,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
+message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
diff --git a/examples/message/README b/examples/message/README
new file mode 100644
index 0000000000..213dbbde51
--- /dev/null
+++ b/examples/message/README
@@ -0,0 +1,102 @@
+This dir contains scripts that demonstrate how to use LAMMPS as both a
+client and server code to run a simple MD simulation. LAMMPS as a
+client performs the MD timestepping. LAMMPS as a server provides the
+energy and forces between interacting particles. Every timestep the
+LAMMPS client sends a message to the LAMMPS server and receives a
+response message in return.
+
+Another code could replace LAMMPS as the client, e.g. another MD code
+which wants to use a LAMMPS potential. Another code could replace
+LAMMPS as the server, e.g. a quantum code computing quantum forces, so
+that ab initio MD could be performed. See an example of the latter in
+examples/COUPLE/lammps_vasp.
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE)
+and Section_howto.html#howto10 for more details on how
+client/server coupling works in LAMMPS.
+
+--------------
+
+Note that you can adjust the problem size run by these scripts by
+setting "x,y,z" variables when you run LAMMPS. The default problem size
+is x = y = z = 5, which is 500 particles.
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
+
+This applies to either in.message or in.message.client
+
+The client and server script define a "mode" variable
+which can be set to file, zmq, mpi/one, or mpi/two,
+as illustrated below.
+
+--------------
+
+To run this problem in the traditional way (no client/server coupling)
+do one of these:
+
+% lmp_serial < in.message
+% mpirun -np 4 lmp_mpi < in.message
+
+--------------
+
+To run in client/server mode:
+
+Both the client and server script must use the same messaging mode.
+This can be selected by setting the "mode" variable when you run
+LAMMPS. The default mode = file. The other options for the mode
+variable are zmq, mpione, mpitwo.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means any of
+the 4 messaging modes can be used.
+
+The next sections illustrate how to launch LAMMPS twice, once as a
+client, once as a server, for each of the messaging modes.
+
+In all cases, the client should print out thermodynamic info for 50
+steps. The server should print out setup info, print nothing until
+the client exits, at which point the server should also exit.
+
+The examples below show launching LAMMPS twice from the same window
+(or batch script), using the "&" character to launch the first time in
+the background. For all modes except {mpi/one}, you could also launch
+twice in separate windows on your desktop machine. It does not matter
+whether you launch the client or server first.
+
+In these examples either the client or server can be run on one or
+more processors. If running in a non-MPI mode (file or zmq) you can
+launch LAMMPS on a single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both
+times via mpirun, even if one or both of them runs on a single
+processor. This is so that MPI can figure out how to connect both MPI
+processes together to exchange MPI messages between them.
+
+--------------
+
+File or ZMQ or mpi/two modes of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
+% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
+
+% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client &
+% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server
+
+% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
+% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
+
+--------------
+
+Mpi/one mode of messaging:
+
+Launch LAMMPS twice in a single mpirun command:
+
+mpirun -np 2 lmp_mpi -mpi 2 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 2 -in in.message.server -v mode mpione -log log.server
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpi P
+command-line option as their first option, where P is the number of
+processors the first code in the mpirun command (client or server) is
+running on.
diff --git a/examples/message/in.message b/examples/message/in.message
new file mode 100644
index 0000000000..951ff95e3b
--- /dev/null
+++ b/examples/message/in.message
@@ -0,0 +1,27 @@
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.client b/examples/message/in.message.client
new file mode 100644
index 0000000000..0c548ef2e5
--- /dev/null
+++ b/examples/message/in.message.client
@@ -0,0 +1,38 @@
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.server b/examples/message/in.message.server
new file mode 100644
index 0000000000..2fedd2ae00
--- /dev/null
+++ b/examples/message/in.message.server
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 1 0 1 0 1
+create_box 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/log.23Jul18.message.client.file.g++.1 b/examples/message/log.23Jul18.message.client.file.g++.1
new file mode 100644
index 0000000000..0e05f6dfd5
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.file.g++.1
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.00067687 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.12413 on 1 procs for 50 steps with 500 atoms
+
+Performance: 4215.352 tau/day, 9.758 timesteps/s
+0.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
+Comm | 0.0001719 | 0.0001719 | 0.0001719 | 0.0 | 0.00
+Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00
+Modify | 5.1232 | 5.1232 | 5.1232 | 0.0 | 99.98
+Other | | 0.0004876 | | | 0.01
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:19
diff --git a/examples/message/log.23Jul18.message.client.file.g++.2 b/examples/message/log.23Jul18.message.client.file.g++.2
new file mode 100644
index 0000000000..959c85439e
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.file.g++.2
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000554085 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.07392 on 2 procs for 50 steps with 500 atoms
+
+Performance: 4257.065 tau/day, 9.854 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.00
+Comm | 0.00022864 | 0.00023806 | 0.00024748 | 0.0 | 0.00
+Output | 0.00020814 | 0.00051165 | 0.00081515 | 0.0 | 0.01
+Modify | 5.0659 | 5.0695 | 5.073 | 0.2 | 99.91
+Other | | 0.003713 | | | 0.07
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:07
diff --git a/examples/message/log.23Jul18.message.client.mpione.g++.1 b/examples/message/log.23Jul18.message.client.mpione.g++.1
new file mode 100644
index 0000000000..95a3f99ef5
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.mpione.g++.1
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000674009 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0424271 on 1 procs for 50 steps with 500 atoms
+
+Performance: 509109.009 tau/day, 1178.493 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.02
+Comm | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.19
+Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.26
+Modify | 0.042014 | 0.042014 | 0.042014 | 0.0 | 99.03
+Other | | 0.0002129 | | | 0.50
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.client.mpione.g++.2 b/examples/message/log.23Jul18.message.client.mpione.g++.2
new file mode 100644
index 0000000000..6ba653a2be
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.mpione.g++.2
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000527859 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.027467 on 2 procs for 50 steps with 500 atoms
+
+Performance: 786397.868 tau/day, 1820.365 timesteps/s
+99.9% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 4.0531e-06 | 4.1723e-06 | 4.2915e-06 | 0.0 | 0.02
+Comm | 0.00017691 | 0.00018024 | 0.00018358 | 0.0 | 0.66
+Output | 9.3222e-05 | 0.00012612 | 0.00015903 | 0.0 | 0.46
+Modify | 0.026678 | 0.02676 | 0.026841 | 0.0 | 97.42
+Other | | 0.0003968 | | | 1.44
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.client.mpitwo.g++.1 b/examples/message/log.23Jul18.message.client.mpitwo.g++.1
new file mode 100644
index 0000000000..3822a0eb35
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.mpitwo.g++.1
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000490904 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0624809 on 1 procs for 50 steps with 500 atoms
+
+Performance: 345705.501 tau/day, 800.244 timesteps/s
+40.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 7.391e-06 | 7.391e-06 | 7.391e-06 | 0.0 | 0.01
+Comm | 8.5831e-05 | 8.5831e-05 | 8.5831e-05 | 0.0 | 0.14
+Output | 0.00011873 | 0.00011873 | 0.00011873 | 0.0 | 0.19
+Modify | 0.062024 | 0.062024 | 0.062024 | 0.0 | 99.27
+Other | | 0.0002449 | | | 0.39
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:07
diff --git a/examples/message/log.23Jul18.message.client.mpitwo.g++.2 b/examples/message/log.23Jul18.message.client.mpitwo.g++.2
new file mode 100644
index 0000000000..058fc9dbf7
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.mpitwo.g++.2
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000692129 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0186305 on 2 procs for 50 steps with 500 atoms
+
+Performance: 1159388.887 tau/day, 2683.771 timesteps/s
+50.7% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 2.861e-06 | 3.8147e-06 | 4.7684e-06 | 0.0 | 0.02
+Comm | 0.00017023 | 0.00017631 | 0.00018239 | 0.0 | 0.95
+Output | 0.00010896 | 0.00013852 | 0.00016809 | 0.0 | 0.74
+Modify | 0.017709 | 0.017821 | 0.017933 | 0.1 | 95.66
+Other | | 0.0004908 | | | 2.63
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/message/log.23Jul18.message.client.zmq.g++.1 b/examples/message/log.23Jul18.message.client.zmq.g++.1
new file mode 100644
index 0000000000..d895ee7556
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.zmq.g++.1
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000747919 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0769799 on 1 procs for 50 steps with 500 atoms
+
+Performance: 280592.815 tau/day, 649.520 timesteps/s
+12.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.01
+Comm | 9.5129e-05 | 9.5129e-05 | 9.5129e-05 | 0.0 | 0.12
+Output | 0.00011516 | 0.00011516 | 0.00011516 | 0.0 | 0.15
+Modify | 0.076471 | 0.076471 | 0.076471 | 0.0 | 99.34
+Other | | 0.0002928 | | | 0.38
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/message/log.23Jul18.message.client.zmq.g++.2 b/examples/message/log.23Jul18.message.client.zmq.g++.2
new file mode 100644
index 0000000000..4bdb8abecc
--- /dev/null
+++ b/examples/message/log.23Jul18.message.client.zmq.g++.2
@@ -0,0 +1,76 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000608921 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0453095 on 2 procs for 50 steps with 500 atoms
+
+Performance: 476720.759 tau/day, 1103.520 timesteps/s
+55.6% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.01
+Comm | 0.0001595 | 0.00015998 | 0.00016046 | 0.0 | 0.35
+Output | 8.893e-05 | 0.00011587 | 0.00014281 | 0.0 | 0.26
+Modify | 0.044439 | 0.044582 | 0.044724 | 0.1 | 98.39
+Other | | 0.0004481 | | | 0.99
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/message/log.23Jul18.message.g++.1 b/examples/message/log.23Jul18.message.g++.1
new file mode 100644
index 0000000000..53457c0129
--- /dev/null
+++ b/examples/message/log.23Jul18.message.g++.1
@@ -0,0 +1,83 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000540972 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.037292 on 1 procs for 50 steps with 500 atoms
+
+Performance: 579212.643 tau/day, 1340.770 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.028156 | 0.028156 | 0.028156 | 0.0 | 75.50
+Neigh | 0.0069656 | 0.0069656 | 0.0069656 | 0.0 | 18.68
+Comm | 0.0011504 | 0.0011504 | 0.0011504 | 0.0 | 3.08
+Output | 0.00013399 | 0.00013399 | 0.00013399 | 0.0 | 0.36
+Modify | 0.00049257 | 0.00049257 | 0.00049257 | 0.0 | 1.32
+Other | | 0.0003934 | | | 1.05
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18820 ave 18820 max 18820 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.g++.4 b/examples/message/log.23Jul18.message.g++.4
new file mode 100644
index 0000000000..09bd755380
--- /dev/null
+++ b/examples/message/log.23Jul18.message.g++.4
@@ -0,0 +1,83 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000635862 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.0152688 on 4 procs for 50 steps with 500 atoms
+
+Performance: 1414649.236 tau/day, 3274.651 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.006639 | 0.007916 | 0.0083909 | 0.8 | 51.84
+Neigh | 0.0015991 | 0.0018443 | 0.0019469 | 0.3 | 12.08
+Comm | 0.0041771 | 0.0047471 | 0.0063298 | 1.3 | 31.09
+Output | 9.6798e-05 | 0.00012475 | 0.00019407 | 0.0 | 0.82
+Modify | 0.00015974 | 0.0001967 | 0.00023103 | 0.0 | 1.29
+Other | | 0.0004399 | | | 2.88
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 1091 ave 1094 max 1089 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs: 4705 ave 4849 max 4648 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.file.g++.1 b/examples/message/log.23Jul18.message.server.file.g++.1
new file mode 100644
index 0000000000..159332c2b4
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.file.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.23Jul18.message.server.file.g++.4 b/examples/message/log.23Jul18.message.server.file.g++.4
new file mode 100644
index 0000000000..f5ea67196f
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.file.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.23Jul18.message.server.mpione.g++.1 b/examples/message/log.23Jul18.message.server.mpione.g++.1
new file mode 100644
index 0000000000..245461d4b2
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.mpione.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.mpione.g++.4 b/examples/message/log.23Jul18.message.server.mpione.g++.4
new file mode 100644
index 0000000000..d4d9a98189
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.mpione.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.mpitwo.g++.1 b/examples/message/log.23Jul18.message.server.mpitwo.g++.1
new file mode 100644
index 0000000000..440a03bad7
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.mpitwo.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.mpitwo.g++.4 b/examples/message/log.23Jul18.message.server.mpitwo.g++.4
new file mode 100644
index 0000000000..0265bda54c
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.mpitwo.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.zmq.g++.1 b/examples/message/log.23Jul18.message.server.zmq.g++.1
new file mode 100644
index 0000000000..4fa9244bfe
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.zmq.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.server.zmq.g++.4 b/examples/message/log.23Jul18.message.server.zmq.g++.4
new file mode 100644
index 0000000000..f094153e83
--- /dev/null
+++ b/examples/message/log.23Jul18.message.server.zmq.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (16 Jul 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/lib/README b/lib/README
index 3c8f46dd0a..12c27b2a39 100644
--- a/lib/README
+++ b/lib/README
@@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
meam modified embedded atom method (MEAM) potential, MEAM package
from Greg Wagner (Sandia)
+message client/server communication library via MPI, sockets, files
+ from Steve Plimpton (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
diff --git a/lib/message/Install.py b/lib/message/Install.py
new file mode 100644
index 0000000000..d3f31c986f
--- /dev/null
+++ b/lib/message/Install.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+# Install.py tool to build the CSlib library
+# used to automate the steps described in the README file in this dir
+
+from __future__ import print_function
+import sys,os,re,subprocess
+
+# help message
+
+help = """
+Syntax from src dir: make lib-message args="-m"
+ or: make lib-message args="-s -z"
+Syntax from lib dir: python Install.py -m
+ or: python Install.py -s -z
+
+specify zero or more options, order does not matter
+
+ -m = parallel build of CSlib library
+ -s = serial build of CSlib library
+ -z = build CSlib library with ZMQ socket support, default = no ZMQ support
+
+Example:
+
+make lib-message args="-m -z" # build parallel CSlib with ZMQ support
+make lib-message args="-s" # build serial CSlib with no ZMQ support
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print(help)
+ else: print("ERROR",str)
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+mpiflag = False
+serialflag = False
+zmqflag = False
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ mpiflag = True
+ iarg += 1
+ elif args[iarg] == "-s":
+ serialflag = True
+ iarg += 1
+ elif args[iarg] == "-z":
+ zmqflag = True
+ iarg += 1
+ else: error()
+
+if (not mpiflag and not serialflag):
+ error("Must use either -m or -s flag")
+
+if (mpiflag and serialflag):
+ error("Cannot use -m and -s flag at the same time")
+
+# build CSlib
+# copy resulting lib to cslib/src/libmessage.a
+# copy appropriate Makefile.lammps.* to Makefile.lammps
+
+print("Building CSlib ...")
+srcdir = fullpath("./cslib/src")
+
+if mpiflag and zmqflag:
+ cmd = "cd %s; make lib_parallel" % srcdir
+elif mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_parallel zmq=no" % srcdir
+elif not mpiflag and zmqflag:
+ cmd = "cd %s; make lib_serial" % srcdir
+elif not mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_serial zmq=no" % srcdir
+
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir
+else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps"
+else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps"
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
diff --git a/lib/message/Makefile.lammps.nozmq b/lib/message/Makefile.lammps.nozmq
new file mode 100644
index 0000000000..1bb10cc988
--- /dev/null
+++ b/lib/message/Makefile.lammps.nozmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB =
+message_SYSPATH =
diff --git a/lib/message/Makefile.lammps.zmq b/lib/message/Makefile.lammps.zmq
new file mode 100644
index 0000000000..759f2ce04b
--- /dev/null
+++ b/lib/message/Makefile.lammps.zmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB = -lzmq
+message_SYSPATH =
diff --git a/lib/message/README b/lib/message/README
new file mode 100644
index 0000000000..71e46a8286
--- /dev/null
+++ b/lib/message/README
@@ -0,0 +1,51 @@
+This directory contains the CSlib library which is required
+to use the MESSAGE package and its client/server commands
+in a LAMMPS input script.
+
+The CSlib libary is included in the LAMMPS distribution. A fuller
+version including documentation and test programs is available at
+http:cslib.sandia.gov (by Aug 2018) and was developed by Steve
+Plimpton at Sandia National Laboratories.
+
+You can type "make lib-message" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
+The CSlib can be optionally built with support for sockets using
+the open-source ZeroMQ (ZMQ) library. If it is not installed
+on your system, it is easy to download and install.
+
+Go to this website: http://zeromq.org
+
+-----------------
+
+Instructions:
+
+1. Compile CSlib from within cslib/src with one of the following:
+ % make lib_parallel # build parallel library with ZMQ socket support
+ % make lib_serial # build serial library with ZMQ support
+ % make lib_parallel zmq=no # build parallel lib with no ZMQ support
+ % make lib_serial zmq=no # build serial lib with no ZMQ support
+
+2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to
+ cslib/src/libmessage.a
+
+3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq
+ to lib/message/Makefile.lammps, depending on whether you
+ build the library with ZMQ support or not.
+ If your ZMQ library is not in a place your shell path finds,
+ you can set the INCLUDE and PATH variables in Makefile.lammps
+ to point to the dirs where the ZMQ include and library files are.
+
+-----------------
+
+When these steps are complete you can build LAMMPS
+with the MESSAGAE package installed:
+
+% cd lammps/src
+% make yes-message
+% make mpi (or whatever target you wish)
+
+Note that if you download and unpack a new LAMMPS tarball, you will
+need to re-build the CSlib in this dir.
diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE
new file mode 100644
index 0000000000..41ba9bbcd0
--- /dev/null
+++ b/lib/message/cslib/LICENSE
@@ -0,0 +1,501 @@
+GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 2.1, February 1999
+
+Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom
+to share and change it. By contrast, the GNU General Public Licenses
+are intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.
+
+This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations
+below.
+
+When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
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+it if you want it; that you can change the software and use pieces of
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+
+To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
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+We protect your rights with a two-step method: (1) we copyright the
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+
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+That's all there is to it!
diff --git a/lib/message/cslib/README b/lib/message/cslib/README
new file mode 100644
index 0000000000..1cc75861c6
--- /dev/null
+++ b/lib/message/cslib/README
@@ -0,0 +1,21 @@
+This is the July 2018 version of the Client/Server messaging library
+(CSlib). Only the source directory and license file are included here
+as part of the LAMMPS distribution. The full CSlib distribution,
+including documentation and test codes, can be found at the website:
+http://cslib.sandia.gov (as of Aug 2018).
+
+The contact author is
+
+Steve Plimpton
+Sandia National Laboratories
+sjplimp@sandia.gov
+http://www.sandia.gov/~sjplimp
+
+The CSlib is distributed as open-source code under the GNU LGPL
+license. See the accompanying LICENSE file.
+
+This directory contains the following:
+
+README this file
+LICENSE GNU LGPL license
+src source files for library
diff --git a/lib/message/cslib/src/Makefile b/lib/message/cslib/src/Makefile
new file mode 100644
index 0000000000..83cf902220
--- /dev/null
+++ b/lib/message/cslib/src/Makefile
@@ -0,0 +1,107 @@
+# Makefile for CSlib = client/server messaging library
+# type "make help" for options
+
+SHELL = /bin/sh
+
+# ----------------------------------------
+# should only need to change this section
+# compiler/linker settings
+# ----------------------------------------
+
+CC = g++
+CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI)
+SHFLAGS = -fPIC
+ARCHIVE = ar
+ARCHFLAGS = -rc
+SHLIBFLAGS = -shared
+
+# files
+
+LIB = libcsmpi.a
+SHLIB = libcsmpi.so
+SRC = $(wildcard *.cpp)
+INC = $(wildcard *.h)
+OBJ = $(SRC:.cpp=.o)
+
+# build with ZMQ support or not
+
+zmq = yes
+ZMQ = $(shell echo $(zmq) | tr a-z A-Z)
+
+ifeq ($(ZMQ),YES)
+ ZMQLIB = -lzmq
+else
+ CCFLAGS += -I./STUBS_ZMQ
+endif
+
+# build with MPI support or not
+
+mpi = yes
+MPI = $(shell echo $(mpi) | tr a-z A-Z)
+
+ifeq ($(MPI),YES)
+ CC = mpicxx
+else
+ CCFLAGS += -I./STUBS_MPI
+ LIB = libcsnompi.a
+ SHLIB = libcsnompi.so
+endif
+
+# targets
+
+shlib: shlib_parallel shlib_serial
+
+lib: lib_parallel lib_serial
+
+all: shlib lib
+
+help:
+ @echo 'make default = shlib'
+ @echo 'make shlib build 2 shared CSlibs: parallel & serial'
+ @echo 'make lib build 2 static CSlibs: parallel & serial'
+ @echo 'make all build 4 CSlibs: shlib and lib'
+ @echo 'make shlib_parallel build shared parallel CSlib'
+ @echo 'make shlib_serial build shared serial CSlib'
+ @echo 'make lib_parallel build static parallel CSlib'
+ @echo 'make lib_serial build static serial CSlib'
+ @echo 'make ... zmq=no build w/out ZMQ support'
+ @echo 'make clean remove all *.o files'
+ @echo 'make clean-all remove *.o and lib files'
+ @echo 'make tar create a tarball, 2 levels up'
+
+shlib_parallel:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=yes
+
+shlib_serial:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=no
+
+lib_parallel:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=yes
+
+lib_serial:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=no
+
+static: $(OBJ)
+ $(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ)
+
+shared: $(OBJ)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB)
+
+clean:
+ @rm -f *.o *.pyc
+
+clean-all:
+ @rm -f *.o *.pyc lib*.a lib*.so
+
+tar:
+ cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \
+ cslib/doc cslib/src cslib/test
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) $(SHFLAGS) -c $<
diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h
new file mode 100644
index 0000000000..fd2dbf8113
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_MPI/mpi.h
@@ -0,0 +1,95 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+// MPI constants and dummy functions
+
+#ifndef MPI_DUMMY_H
+#define MPI_DUMMY_H
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+
+namespace CSLIB_NS {
+
+typedef int MPI_Comm;
+typedef int MPI_Fint;
+typedef int MPI_Datatype;
+typedef int MPI_Status;
+typedef int MPI_Op;
+typedef int MPI_Info;
+
+#define MPI_COMM_WORLD 0
+#define MPI_MAX_PORT_NAME 0
+#define MPI_INFO_NULL 0
+#define MPI_INT 1
+#define MPI_LONG_LONG 2
+#define MPI_FLOAT 3
+#define MPI_DOUBLE 4
+#define MPI_CHAR 5
+#define MPI_SUM 0
+
+static void MPI_Init(int *, char ***) {}
+static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;}
+static void MPI_Comm_rank(MPI_Comm, int *) {}
+static void MPI_Comm_size(MPI_Comm, int *) {}
+
+static void MPI_Open_port(MPI_Info, char *) {}
+static void MPI_Close_port(const char *) {}
+static void MPI_Comm_accept(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+static void MPI_Comm_connect(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+
+static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {}
+static void MPI_Comm_free(MPI_Comm *) {}
+
+static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {}
+static void MPI_Recv(void *, int, MPI_Datatype, int, int,
+ MPI_Comm, MPI_Status *) {}
+
+static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type,
+ MPI_Op op, MPI_Comm)
+{
+ if (type == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype,
+ MPI_Op op,MPI_Comm)
+{
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+
+static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {}
+static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype,
+ void *out, int, MPI_Datatype, MPI_Comm)
+{
+ // assuming incount = 1
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype,
+ void *out, const int *, const int *,
+ MPI_Datatype, MPI_Comm)
+{
+ if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int));
+ else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t));
+ else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float));
+ else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double));
+ else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char));
+}
+
+static void MPI_Abort(MPI_Comm, int) {exit(1);}
+static void MPI_Finalize() {}
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
new file mode 100644
index 0000000000..af920974cd
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
@@ -0,0 +1,35 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+// ZMQ constants and dummy functions
+
+#ifndef ZMQ_DUMMY_H
+#define ZMQ_DUMMY_H
+
+namespace CSLIB_NS {
+
+#define ZMQ_REQ 0
+#define ZMQ_REP 0
+
+static void *zmq_ctx_new() {return NULL;}
+static void *zmq_connect(void *, char *) {return NULL;}
+static int zmq_bind(void *, char *) {return 0;}
+static void *zmq_socket(void *,int) {return NULL;}
+static void zmq_close(void *) {}
+static void zmq_ctx_destroy(void *) {}
+static void zmq_send(void *, void *, int, int) {}
+static void zmq_recv(void *, void *, int, int) {}
+
+};
+
+#endif
diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp
new file mode 100644
index 0000000000..8b4d27f134
--- /dev/null
+++ b/lib/message/cslib/src/cslib.cpp
@@ -0,0 +1,768 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include "cslib.h"
+#include "msg_file.h"
+#include "msg_zmq.h"
+#include "msg_mpi_one.h"
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+#define MAXTYPE 5 // # of defined field data types
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm)
+{
+ if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm);
+ else myworld = 0;
+
+#ifdef MPI_NO
+ if (pcomm)
+ error_all("constructor(): CSlib invoked with MPI_Comm "
+ "but built w/out MPI support");
+#endif
+#ifdef MPI_YES // NOTE: this could be OK to allow ??
+ // would allow a parallel app to invoke CSlib
+ // in parallel and/or in serial
+ if (!pcomm)
+ error_all("constructor(): CSlib invoked w/out MPI_Comm "
+ "but built with MPI support");
+#endif
+
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+ else error_all("constructor(): Invalid client/server arg");
+
+ if (pcomm == NULL) {
+ me = 0;
+ nprocs = 1;
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr);
+ else if (strcmp(mode,"mpi/one") == 0)
+ error_all("constructor(): No mpi/one mode for serial lib usage");
+ else if (strcmp(mode,"mpi/two") == 0)
+ error_all("constructor(): No mpi/two mode for serial lib usage");
+ else error_all("constructor(): Unknown mode");
+
+ } else if (pcomm) {
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world);
+ else error_all("constructor(): Unknown mode");
+ }
+
+ maxfield = 0;
+ fieldID = fieldtype = fieldlen = fieldoffset = NULL;
+ maxheader = 0;
+ header = NULL;
+ maxbuf = 0;
+ buf = NULL;
+
+ recvcounts = displs = NULL;
+ maxglobal = 0;
+ allids = NULL;
+ maxfieldbytes = 0;
+ fielddata = NULL;
+
+ pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::~CSlib()
+{
+ deallocate_fields();
+ sfree(header);
+ sfree(buf);
+
+ sfree(recvcounts);
+ sfree(displs);
+ sfree(allids);
+ sfree(fielddata);
+
+ delete msg;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send(int msgID_caller, int nfield_caller)
+{
+ if (nfield_caller < 0) error_all("send(): Invalid nfield");
+
+ msgID = msgID_caller;
+ nfield = nfield_caller;
+ allocate_fields();
+
+ fieldcount = 0;
+ nbuf = 0;
+
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int(int id, int value)
+{
+ pack(id,1,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int64(int id, int64_t value)
+{
+ pack(id,2,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_float(int id, float value)
+{
+ pack(id,3,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_double(int id, double value)
+{
+ pack(id,4,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_string(int id, char *value)
+{
+ pack(id,5,strlen(value)+1,value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack(int id, int ftype, int flen, void *data)
+{
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype");
+ if (flen < 0) error_all("pack(): Invalid flen");
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ memcpy(&buf[nbuf],data,nbytes);
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_parallel(int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack_parallel(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype");
+ if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ // NOTE: check for overflow of maxglobal and flen
+
+ int nglobal;
+ MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world);
+ int flen = nper*nglobal;
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ // nlocal datums, each of nper length, from all procs
+ // final data in buf = datums for all natoms, ordered by ids
+
+ if (recvcounts == NULL) {
+ recvcounts = (int *) smalloc(nprocs*sizeof(int));
+ displs = (int *) smalloc(nprocs*sizeof(int));
+ }
+
+ MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ if (ids && nglobal > maxglobal) {
+ sfree(allids);
+ maxglobal = nglobal;
+ // NOTE: maxglobal*sizeof(int) could overflow int
+ allids = (int *) smalloc(maxglobal*sizeof(int));
+ }
+
+ MPI_Allgatherv(ids,nlocal,MPI_INT,allids,
+ recvcounts,displs,MPI_INT,world);
+
+ int nlocalsize = nper*nlocal;
+ MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ if (ftype == 1) {
+ int *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int *) fielddata;
+ } else alldata = (int *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata,
+ recvcounts,displs,MPI_INT,world);
+ if (ids) {
+ int *bufptr = (int *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 2) {
+ int64_t *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int64_t *) fielddata;
+ } else alldata = (int64_t *) &buf[nbuf];
+ // NOTE: may be just MPI_LONG on some machines
+ MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata,
+ recvcounts,displs,MPI_LONG_LONG,world);
+ if (ids) {
+ int64_t *bufptr = (int64_t *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 3) {
+ float *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (float *) fielddata;
+ } else alldata = (float *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata,
+ recvcounts,displs,MPI_FLOAT,world);
+ if (ids) {
+ float *bufptr = (float *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 4) {
+ double *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (double *) fielddata;
+ } else alldata = (double *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata,
+ recvcounts,displs,MPI_DOUBLE,world);
+ if (ids) {
+ double *bufptr = (double *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (ftype == 5) {
+ char *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (char *) fielddata;
+ } else alldata = (char *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata,
+ recvcounts,displs,MPI_CHAR,world);
+ if (ids) {
+ char *bufptr = (char *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ memcpy(&bufptr[j],&alldata[m],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send_message()
+{
+ // setup header message
+
+ int m = 0;
+ header[m++] = msgID;
+ header[m++] = nfield;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ header[m++] = fieldID[ifield];
+ header[m++] = fieldtype[ifield];
+ header[m++] = fieldlen[ifield];
+ }
+
+ msg->send(nheader,header,nbuf,buf);
+ nsend++;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::recv(int &nfield_caller, int *&fieldID_caller,
+ int *&fieldtype_caller, int *&fieldlen_caller)
+{
+ msg->recv(maxheader,header,maxbuf,buf);
+ nrecv++;
+
+ // unpack header message
+
+ int m = 0;
+ msgID = header[m++];
+ nfield = header[m++];
+ allocate_fields();
+
+ int nbytes,nbytesround;
+
+ nbuf = 0;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ fieldID[ifield] = header[m++];
+ fieldtype[ifield] = header[m++];
+ fieldlen[ifield] = header[m++];
+ fieldoffset[ifield] = nbuf;
+ onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround);
+ nbuf += nbytesround;
+ }
+
+ // return message parameters
+
+ nfield_caller = nfield;
+ fieldID_caller = fieldID;
+ fieldtype_caller = fieldtype;
+ fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::unpack_int(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int(): Unknown field ID");
+ if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1");
+
+ int *ptr = (int *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int64_t CSlib::unpack_int64(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int64(): Unknown field ID");
+ if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1");
+
+ int64_t *ptr = (int64_t *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+float CSlib::unpack_float(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_float(): Unknown field ID");
+ if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1");
+
+ float *ptr = (float *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double CSlib::unpack_double(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_double(): Unknown field ID");
+ if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1");
+
+ double *ptr = (double *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+char *CSlib::unpack_string(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_string(): Unknown field ID");
+ if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype");
+
+ char *ptr = (char *) unpack(id);
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::unpack(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+ return &buf[fieldoffset[ifield]];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack(int id, void *data)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+
+ int ftype = fieldtype[ifield];
+ int nbytes = fieldlen[ifield];
+ if (ftype == 1) nbytes *= sizeof(int);
+ else if (ftype == 2) nbytes *= sizeof(int64_t);
+ else if (ftype == 3) nbytes *= sizeof(float);
+ else if (ftype == 4) nbytes *= sizeof(double);
+ memcpy(data,&buf[fieldoffset[ifield]],nbytes);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_parallel(): Unknown field ID");
+ if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ int upto;
+ if (!ids) {
+ MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world);
+ upto -= nlocal;
+ }
+
+ if (fieldtype[ifield] == 1) {
+ int *local = (int *) data;
+ int *global = (int *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 2) {
+ int64_t *local = (int64_t *) data;
+ int64_t *global = (int64_t *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 3) {
+ float *local = (float *) data;
+ float *global = (float *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 4) {
+ double *local = (double *) data;
+ double *global = (double *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (fieldtype[ifield] == 5) {
+ char *local = (char *) data;
+ char *global = (char *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ memcpy(&local[m],&global[j],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::extract(int flag)
+{
+ if (flag == 1) return nsend;
+ if (flag == 2) return nrecv;
+ error_all("extract(): Invalid flag");
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround)
+{
+ int64_t bigbytes,bigbytesround;
+ int64_t biglen = flen;
+
+ if (ftype == 1) bigbytes = biglen * sizeof(int);
+ else if (ftype == 2) bigbytes = biglen * sizeof(int64_t);
+ else if (ftype == 3) bigbytes = biglen * sizeof(float);
+ else if (ftype == 4) bigbytes = biglen * sizeof(double);
+ else if (ftype == 5) bigbytes = biglen * sizeof(char);
+ bigbytesround = roundup(bigbytes,8);
+
+ if (nbuf + bigbytesround > INT_MAX)
+ error_all("pack(): Message size exceeds 32-bit integer limit");
+
+ nbytes = (int) bigbytes;
+ nbytesround = (int) bigbytesround;
+ if (nbuf + nbytesround > maxbuf) {
+ maxbuf = nbuf + nbytesround;
+ buf = (char *) srealloc(buf,maxbuf);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::find_field(int id, int n)
+{
+ int ifield;
+ for (ifield = 0; ifield < n; ifield++)
+ if (id == fieldID[ifield]) return ifield;
+ return -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::allocate_fields()
+{
+ int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int);
+ if (bigbytes > INT_MAX)
+ error_all("send(): Message header size exceeds 32-bit integer limit");
+
+ nheader = 2;
+ nheader += 3 * nfield;
+
+ if (nfield > maxfield) {
+ deallocate_fields();
+ maxfield = nfield;
+ fieldID = new int[maxfield];
+ fieldtype = new int[maxfield];
+ fieldlen = new int[maxfield];
+ fieldoffset = new int[maxfield];
+ }
+
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::deallocate_fields()
+{
+ delete [] fieldID;
+ delete [] fieldtype;
+ delete [] fieldlen;
+ delete [] fieldoffset;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::srealloc(void *ptr, int nbytes)
+{
+ if (nbytes == 0) {
+ sfree(ptr);
+ return NULL;
+ }
+
+ ptr = realloc(ptr,nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ----------------------------------------------------------------------
+ round N up to multiple of nalign and return it
+ NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t
+------------------------------------------------------------------------- */
+
+int64_t CSlib::roundup(int64_t n, int nalign)
+{
+ if (n % nalign == 0) return n;
+ n = (n/nalign + 1) * nalign;
+ return n;
+}
diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h
new file mode 100644
index 0000000000..20d82a2469
--- /dev/null
+++ b/lib/message/cslib/src/cslib.h
@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef CSLIB_H
+#define CSLIB_H
+
+#include <stdint.h>
+
+namespace CSLIB_NS {
+
+class CSlib {
+ public:
+ int nsend,nrecv;
+
+ CSlib(int, const char *, const void *, const void *);
+ ~CSlib();
+
+ void send(int, int);
+
+ void pack_int(int, int);
+ void pack_int64(int, int64_t);
+ void pack_float(int, float);
+ void pack_double(int, double);
+ void pack_string(int, char *);
+ void pack(int, int, int, void *);
+ void pack_parallel(int, int, int, int *, int, void *);
+
+ int recv(int &, int *&, int *&, int *&);
+
+ int unpack_int(int);
+ int64_t unpack_int64(int);
+ float unpack_float(int);
+ double unpack_double(int);
+ char *unpack_string(int);
+ void *unpack(int);
+ void unpack(int, void *);
+ void unpack_parallel(int, int, int *, int, void *);
+
+ int extract(int);
+
+ private:
+ uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file
+ // so apps can include this file w/ no MPI on system
+ int me,nprocs;
+ int client,server;
+ int nfield,maxfield;
+ int msgID,fieldcount;
+ int nheader,maxheader;
+ int nbuf,maxbuf;
+ int maxglobal,maxfieldbytes;
+ int *fieldID,*fieldtype,*fieldlen,*fieldoffset;
+ int *header;
+ int *recvcounts,*displs; // nprocs size for Allgathers
+ int *allids; // nglobal size for pack_parallel()
+ char *buf; // maxbuf size for msg with all fields
+ char *fielddata; // maxfieldbytes size for one global field
+ const char *pad;
+
+ class Msg *msg;
+
+ void send_message();
+ void onefield(int, int, int &, int &);
+ int find_field(int, int);
+ void allocate_fields();
+ void deallocate_fields();
+ int64_t roundup(int64_t, int);
+ void *smalloc(int);
+ void *srealloc(void *, int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py
new file mode 100644
index 0000000000..e2ed78b61b
--- /dev/null
+++ b/lib/message/cslib/src/cslib.py
@@ -0,0 +1,362 @@
+# ------------------------------------------------------------------------
+# CSlib - Client/server library for code coupling
+# http://cslib.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright 2018 National Technology & Engineering Solutions of
+# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+# NTESS, the U.S. Government retains certain rights in this software.
+# This software is distributed under the GNU Lesser General Public
+# License (LGPL).
+#
+# See the README file in the top-level CSlib directory.
+# -------------------------------------------------------------------------
+
+# Python wrapper on CSlib library via ctypes
+
+# ctypes and Numpy data types:
+# 32-bit int = c_int = np.intc = np.int32
+# 64-bit int = c_longlong = np.int64
+# 32-bit floating point = c_float = np.float32
+# 64-bit floating point = c_double = np.float = np.float64
+
+import sys,traceback
+from ctypes import *
+
+# Numpy and mpi4py packages may not exist
+
+try:
+ import numpy as np
+ numpyflag = 1
+except:
+ numpyflag = 0
+
+try:
+ from mpi4py import MPI
+ mpi4pyflag = 1
+except:
+ mpi4pyflag = 0
+
+# wrapper class
+
+class CSlib:
+
+ # instantiate CSlib thru its C-interface
+
+ def __init__(self,csflag,mode,ptr,comm):
+
+ # load libcslib.so
+
+ try:
+ if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL)
+ else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL)
+ except:
+ etype,value,tb = sys.exc_info()
+ traceback.print_exception(etype,value,tb)
+ raise OSError,"Could not load CSlib dynamic library"
+
+ # define ctypes API for each library method
+
+ self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p,
+ POINTER(c_void_p)]
+ self.lib.cslib_open.restype = None
+
+ self.lib.cslib_close.argtypes = [c_void_p]
+ self.lib.cslib_close.restype = None
+
+ self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_send.restype = None
+
+ self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_pack_int.restype = None
+
+ self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong]
+ self.lib.cslib_pack_int64.restype = None
+
+ self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float]
+ self.lib.cslib_pack_float.restype = None
+
+ self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double]
+ self.lib.cslib_pack_double.restype = None
+
+ self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p]
+ self.lib.cslib_pack_string.restype = None
+
+ self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p]
+ self.lib.cslib_pack.restype = None
+
+ self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_pack_parallel.restype = None
+
+ self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int))]
+ self.lib.cslib_recv.restype = c_int
+
+ self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int.restype = c_int
+
+ self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int64.restype = c_longlong
+
+ self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_float.restype = c_float
+
+ self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_double.restype = c_double
+
+ self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_string.restype = c_char_p
+
+ # override return in unpack()
+ self.lib.cslib_unpack.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack.restype = c_void_p
+
+ self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p]
+ self.lib.cslib_unpack_data.restype = None
+
+ # override last arg in unpack_parallel()
+ self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_unpack_parallel.restype = None
+
+ self.lib.cslib_extract.argtypes = [c_void_p,c_int]
+ self.lib.cslib_extract.restype = c_int
+
+ # create an instance of CSlib with or w/out MPI communicator
+
+ self.cs = c_void_p()
+
+ if not comm:
+ self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs))
+ elif not mpi4pyflag:
+ print "Cannot pass MPI communicator to CSlib w/out mpi4py package"
+ sys.exit()
+ else:
+ address = MPI._addressof(comm)
+ comm_ptr = c_void_p(address)
+ if mode == "mpi/one":
+ address = MPI._addressof(ptr)
+ ptrcopy = c_void_p(address)
+ else: ptrcopy = ptr
+ self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs))
+
+ # destroy instance of CSlib
+
+ def __del__(self):
+ if self.cs: self.lib.cslib_close(self.cs)
+
+ def close(self):
+ self.lib.cslib_close(self.cs)
+ self.lib = None
+
+ # send a message
+
+ def send(self,msgID,nfield):
+ self.nfield = nfield
+ self.lib.cslib_send(self.cs,msgID,nfield)
+
+ # pack one field of message
+
+ def pack_int(self,id,value):
+ self.lib.cslib_pack_int(self.cs,id,value)
+
+ def pack_int64(self,id,value):
+ self.lib.cslib_pack_int64(self.cs,id,value)
+
+ def pack_float(self,id,value):
+ self.lib.cslib_pack_float(self.cs,id,value)
+
+ def pack_double(self,id,value):
+ self.lib.cslib_pack_double(self.cs,id,value)
+
+ def pack_string(self,id,value):
+ self.lib.cslib_pack_string(self.cs,id,value)
+
+ def pack(self,id,ftype,flen,data):
+ cdata = self.data_convert(ftype,flen,data)
+ self.lib.cslib_pack(self.cs,id,ftype,flen,cdata)
+
+ def pack_parallel(self,id,ftype,nlocal,ids,nper,data):
+ cids = self.data_convert(1,nlocal,ids)
+ cdata = self.data_convert(ftype,nper*nlocal,data)
+ self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata)
+
+ # convert input data to a ctypes vector to pass to CSlib
+
+ def data_convert(self,ftype,flen,data):
+
+ # tflag = type of data
+ # tflag = 1 if data is list or tuple
+ # tflag = 2 if data is Numpy array
+ # tflag = 3 if data is ctypes vector
+ # same usage of tflag as in unpack function
+
+ txttype = str(type(data))
+ if "numpy" in txttype: tflag = 2
+ elif "c_" in txttype: tflag = 3
+ else: tflag = 1
+
+ # create ctypes vector out of data to pass to lib
+ # cdata = ctypes vector to return
+ # NOTE: error check on ftype and tflag everywhere, also flen
+
+ if ftype == 1:
+ if tflag == 1: cdata = (flen * c_int)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int))
+ elif tflag == 3: cdata = data
+ elif ftype == 2:
+ if tflag == 1: cdata = (flen * c_longlong)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong))
+ elif tflag == 3: cdata = data
+ elif ftype == 3:
+ if tflag == 1: cdata = (flen * c_float)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float))
+ elif tflag == 3: cdata = data
+ elif ftype == 4:
+ if tflag == 1: cdata = (flen * c_double)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double))
+ elif tflag == 3: cdata = data
+
+ return cdata
+
+ # receive a message
+
+ def recv(self):
+ self.lib.cslib_recv.restype = c_int
+ nfield = c_int()
+ fieldID = POINTER(c_int)()
+ fieldtype = POINTER(c_int)()
+ fieldlen = POINTER(c_int)()
+ msgID = self.lib.cslib_recv(self.cs,byref(nfield),
+ byref(fieldID),byref(fieldtype),byref(fieldlen))
+
+ # copy returned C args to native Python int and lists
+ # store them in class so unpack() methods can access the info
+
+ self.nfield = nfield = nfield.value
+ self.fieldID = fieldID[:nfield]
+ self.fieldtype = fieldtype[:nfield]
+ self.fieldlen = fieldlen[:nfield]
+
+ return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen
+
+ # unpack one field of message
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+
+ def unpack_int(self,id):
+ return self.lib.cslib_unpack_int(self.cs,id)
+
+ def unpack_int64(self,id):
+ return self.lib.cslib_unpack_int64(self.cs,id)
+
+ def unpack_float(self,id):
+ return self.lib.cslib_unpack_float(self.cs,id)
+
+ def unpack_double(self,id):
+ return self.lib.cslib_unpack_double(self.cs,id)
+
+ def unpack_string(self,id):
+ return self.lib.cslib_unpack_string(self.cs,id)
+
+ def unpack(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # reset data type of return so can morph by tflag
+ # cannot do this for the generic c_void_p returned by CSlib
+
+ if self.fieldtype[index] == 1:
+ self.lib.cslib_unpack.restype = POINTER(c_int)
+ elif self.fieldtype[index] == 2:
+ self.lib.cslib_unpack.restype = POINTER(c_longlong)
+ elif self.fieldtype[index] == 3:
+ self.lib.cslib_unpack.restype = POINTER(c_float)
+ elif self.fieldtype[index] == 4:
+ self.lib.cslib_unpack.restype = POINTER(c_double)
+ #elif self.fieldtype[index] == 5:
+ # self.lib.cslib_unpack.restype = POINTER(c_char)
+
+ cdata = self.lib.cslib_unpack(self.cs,id)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+ # tflag = 2,3 should NOT perform a data copy
+
+ if tflag == 1:
+ data = cdata[:self.fieldlen[index]]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # handle data array like pack() or unpack_parallel() ??
+
+ def unpack_data(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # unpack one field of message in parallel
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+ # NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg?
+ # as opposed to creating this cdata
+ # does that make any performance difference ?
+ # e.g. should we allow CSlib to populate an existing Numpy array's memory
+
+ def unpack_parallel(self,id,nlocal,ids,nper,tflag=3):
+ cids = self.data_convert(1,nlocal,ids)
+
+ # allocate memory for the returned data
+ # pass cdata ptr to the memory to CSlib unpack_parallel()
+ # this resets data type of last unpack_parallel() arg
+
+ index = self.fieldID.index(id)
+ if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)()
+ elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)()
+ elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)()
+ elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)()
+ #elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)()
+
+ self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+
+ if tflag == 1:
+ data = cdata[:nper*nlocal]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ # NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int
+ # not sure why, reported as bug between ctypes and Numpy here:
+ # https://stackoverflow.com/questions/4964101/pep-3118-
+ # warning-when-using-ctypes-array-as-numpy-array
+ # but why not same warning when just using unpack() ??
+ # in Python these lines give same warning:
+ # >>> import ctypes,numpy
+ # >>> a = (10 * ctypes.c_longlong)()
+ # >>> b = numpy.ctypeslib.as_array(a)
+ data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # extract a library value
+
+ def extract(self,flag):
+ return self.lib.cslib_extract(self.cs,flag)
diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp
new file mode 100644
index 0000000000..453948f783
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.cpp
@@ -0,0 +1,239 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// C style library interface to CSlib class
+
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cslib_wrap.h"
+#include "cslib.h"
+
+using namespace CSLIB_NS;
+
+// ----------------------------------------------------------------------
+
+void cslib_open(int csflag, const char *mode, const void *ptr,
+ const void *pcomm, void **csptr)
+{
+ CSlib *cs = new CSlib(csflag,mode,ptr,pcomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran(int csflag, const char *mode, const char *str,
+ const void *pcomm, void **csptr)
+{
+ MPI_Comm ccomm;
+ void *pccomm = NULL;
+
+ if (pcomm) {
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+ }
+
+ CSlib *cs = new CSlib(csflag,mode,str,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran_mpi_one(int csflag, const char *mode,
+ const void *pboth, const void *pcomm,
+ void **csptr)
+{
+ MPI_Comm ccomm,cboth;
+ void *pccomm,*pcboth;
+
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+
+ MPI_Fint *fboth = (MPI_Fint *) pboth;
+ cboth = MPI_Comm_f2c(*fboth);
+ pcboth = &cboth;
+
+ CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_close(void *ptr)
+{
+ CSlib *cs = (CSlib *) ptr;
+ delete cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_send(void *ptr, int msgID, int nfield)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->send(msgID,nfield);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int(void *ptr, int id, int value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int64(void *ptr, int id, int64_t value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int64(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_float(void *ptr, int id, float value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_float(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_double(void *ptr, int id, double value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_double(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_string(void *ptr, int id, char *value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_string(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack(void *ptr, int id, int ftype, int flen, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack(id,ftype,flen,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_parallel(void *ptr, int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_parallel(id,ftype,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_recv(void *ptr, int *nfield_caller,
+ int **fieldID_caller, int **fieldtype_caller,
+ int **fieldlen_caller)
+{
+ CSlib *cs = (CSlib *) ptr;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ *nfield_caller = nfield;
+ *fieldID_caller = fieldID;
+ *fieldtype_caller = fieldtype;
+ *fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_unpack_int(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int(id);
+}
+// ----------------------------------------------------------------------
+
+int64_t cslib_unpack_int64(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int64(id);
+}
+
+// ----------------------------------------------------------------------
+
+float cslib_unpack_float(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_float(id);
+}
+
+// ----------------------------------------------------------------------
+
+double cslib_unpack_double(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_double(id);
+}
+
+// ----------------------------------------------------------------------
+
+char *cslib_unpack_string(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_string(id);
+}
+
+// ----------------------------------------------------------------------
+
+void *cslib_unpack(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack(id);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_data(void *ptr, int id, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack(id,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids,
+ int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack_parallel(id,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_extract(void *ptr, int flag)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->extract(flag);
+}
diff --git a/lib/message/cslib/src/cslib_wrap.f90 b/lib/message/cslib/src/cslib_wrap.f90
new file mode 100644
index 0000000000..cd2e058b78
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.f90
@@ -0,0 +1,147 @@
+! ISO_C_binding wrapper on CSlib C interface
+
+module cslib_wrap
+
+interface
+ subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*),str(*)
+ type(c_ptr), value :: pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran
+
+ subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*)
+ type(c_ptr), value :: pboth,pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran_mpi_one
+
+ subroutine cslib_close(ptr) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ end subroutine cslib_close
+
+ subroutine cslib_send(ptr,msgID,nfield) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: msgID,nfield
+ end subroutine cslib_send
+
+ subroutine cslib_pack_int(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int), value :: value
+ end subroutine cslib_pack_int
+
+ subroutine cslib_pack_int64(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int64_t), value :: value
+ end subroutine cslib_pack_int64
+
+ subroutine cslib_pack_float(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_float), value :: value
+ end subroutine cslib_pack_float
+
+ subroutine cslib_pack_double(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_double), value :: value
+ end subroutine cslib_pack_double
+
+ subroutine cslib_pack_string(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ character(c_char) :: value(*)
+ end subroutine cslib_pack_string
+
+ subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,flen
+ type(c_ptr), value :: data
+ end subroutine cslib_pack
+
+ subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_pack_parallel
+
+ function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_recv
+ type(c_ptr), value :: ptr
+ integer(c_int) :: nfield
+ type(c_ptr) :: fieldID,fieldtype,fieldlen
+ end function cslib_recv
+
+ function cslib_unpack_int(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_unpack_int
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int
+
+ function cslib_unpack_int64(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int64_t) :: cslib_unpack_int64
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int64
+
+ function cslib_unpack_float(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_float) :: cslib_unpack_float
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_float
+
+ function cslib_unpack_double(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_double) :: cslib_unpack_double
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_double
+
+ function cslib_unpack_string(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack_string
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_string
+
+ function cslib_unpack(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack
+
+ subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_unpack_parallel
+
+ function cslib_extract(ptr,flag) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_extract
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: flag
+ end function cslib_extract
+end interface
+
+end module cslib_wrap
diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h
new file mode 100644
index 0000000000..42d095f452
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.h
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+/* C style library interface to CSlib class
+ ifdefs allow this file to be included in a C program
+*/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void cslib_open(int, const char *, const void *, const void *, void **);
+void cslib_open_fortran(int, const char *, const char *, const void *, void **);
+void cslib_open_fortran_mpi_one(int, const char *, const void *,
+ const void *, void **);
+void cslib_close(void *);
+
+void cslib_send(void *, int, int);
+
+void cslib_pack_int(void *, int, int);
+void cslib_pack_int64(void *, int, int64_t);
+void cslib_pack_float(void *, int, float);
+void cslib_pack_double(void *, int, double);
+void cslib_pack_string(void *, int, char *);
+void cslib_pack(void *, int, int, int, void *);
+void cslib_pack_parallel(void *, int, int, int, int *, int, void *);
+
+int cslib_recv(void *, int *, int **, int **, int **);
+
+int cslib_unpack_int(void *, int);
+int64_t cslib_unpack_int64(void *, int);
+float cslib_unpack_float(void *, int);
+double cslib_unpack_double(void *, int);
+char *cslib_unpack_string(void *, int);
+void *cslib_unpack(void *, int);
+void cslib_unpack_data(void *, int, void *);
+void cslib_unpack_parallel(void *, int, int, int *, int, void *);
+
+int cslib_extract(void *, int);
+
+#ifdef __cplusplus
+}
+#endif
diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp
new file mode 100644
index 0000000000..1ba24d2b48
--- /dev/null
+++ b/lib/message/cslib/src/msg.cpp
@@ -0,0 +1,110 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "msg.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
+{
+ world = cworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr)
+{
+ world = 0;
+ me = 0;
+ nprocs = 1;
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::init(int csflag)
+{
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::allocate(int nheader, int &maxheader, int *&header,
+ int nbuf, int &maxbuf, char *&buf)
+{
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+
+ if (nbuf > maxbuf) {
+ sfree(buf);
+ maxbuf = nbuf;
+ buf = (char *) smalloc(maxbuf*sizeof(char));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *Msg::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = (void *) malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"Failed to allocate %d bytes",nbytes);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h
new file mode 100644
index 0000000000..48805a0f4f
--- /dev/null
+++ b/lib/message/cslib/src/msg.h
@@ -0,0 +1,52 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_H
+#define MSG_H
+
+#include <mpi.h>
+
+namespace CSLIB_NS {
+
+class Msg {
+ public:
+ int nsend,nrecv;
+ MPI_Comm world;
+
+ Msg(int, const void *, MPI_Comm);
+ Msg(int, const void *);
+ virtual ~Msg() {}
+ virtual void send(int, int *, int, char *) = 0;
+ virtual void recv(int &, int *&, int &, char *&) = 0;
+
+ protected:
+ int me,nprocs;
+ int client,server;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int lengths[2];
+
+ void init(int);
+ void allocate(int, int &, int *&, int, int &, char *&);
+ void *smalloc(int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp
new file mode 100644
index 0000000000..31126b8444
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <unistd.h>
+
+#include "msg_file.h"
+
+using namespace CSLIB_NS;
+
+#define MAXLINE 256
+#define SLEEP 0.1 // delay in CPU secs to check for message file
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::~MsgFile()
+{
+ delete [] fileroot;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::init(char *filename)
+{
+ int n = strlen(filename) + 1;
+ fileroot = new char[n];
+ strcpy(fileroot,filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::send(int nheader, int *header, int nbuf, char *buf)
+{
+ char filename[MAXLINE];
+
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server");
+
+ fp = fopen(filename,"wb");
+ if (!fp) error_one("send(): Could not open send message file");
+ fwrite(lengths,sizeof(int),2,fp);
+ fwrite(header,sizeof(int),nheader,fp);
+ fwrite(buf,1,nbuf,fp);
+ fclose(fp);
+ }
+
+ // create empty signal file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ fp = fopen(filename,"w");
+ fclose(fp);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ char filename[MAXLINE];
+
+ // wait until signal file exists to open message file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+
+ int delay = (int) (1000000 * SLEEP);
+ while (1) {
+ fp = fopen(filename,"r");
+ if (fp) break;
+ usleep(delay);
+ }
+ fclose(fp);
+
+ if (client) sprintf(filename,"%s.%s",fileroot,"server");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client");
+ fp = fopen(filename,"rb");
+ if (!fp) error_one("recv(): Could not open recv message file");
+ }
+
+ // read and broadcast data
+
+ if (me == 0) fread(lengths,sizeof(int),2,fp);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) fread(header,sizeof(int),nheader,fp);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) fread(buf,1,nbuf,fp);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+
+ // delete both message and signal file
+
+ if (me == 0) {
+ fclose(fp);
+ unlink(filename);
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ unlink(filename);
+ }
+}
diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h
new file mode 100644
index 0000000000..6d7c7017f6
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_FILE_H
+#define MSG_FILE_H
+
+#include <stdio.h>
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgFile : public Msg {
+ public:
+ MsgFile(int, const void *, MPI_Comm);
+ MsgFile(int, const void *);
+ ~MsgFile();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ char *fileroot;
+ FILE *fp;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp
new file mode 100644
index 0000000000..c028961abc
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.cpp
@@ -0,0 +1,82 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_one.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ // NOTE: ideally would skip this call if mpi/two
+ init(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::init(const void *ptr)
+{
+ MPI_Comm *pbothcomm = (MPI_Comm *) ptr;
+ bothcomm = *pbothcomm;
+
+ if (client) {
+ MPI_Comm_size(world,&nprocs);
+ otherroot = nprocs;
+ } else if (server) {
+ otherroot = 0;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ MPI_Status status;
+
+ if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h
new file mode 100644
index 0000000000..8f1b781bc6
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_ONE_H
+#define MSG_MPI_ONE_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgMPIOne : public Msg {
+ public:
+ MsgMPIOne(int, const void *, MPI_Comm);
+ virtual ~MsgMPIOne() {}
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ protected:
+ MPI_Comm bothcomm;
+ int otherroot;
+
+ void init(const void *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp
new file mode 100644
index 0000000000..4c8f593939
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.cpp
@@ -0,0 +1,81 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) :
+ MsgMPIOne(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::~MsgMPITwo()
+{
+ // free the inter comm that spans both client and server
+
+ MPI_Comm_free(&bothcomm);
+ MPI_Close_port(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPITwo::init(char *filename)
+{
+ if (client) {
+ if (me == 0) {
+ FILE *fp = NULL;
+ while (!fp) {
+ fp = fopen(filename,"r");
+ if (!fp) sleep(1);
+ }
+ fgets(port,MPI_MAX_PORT_NAME,fp);
+ //printf("Client port: %s\n",port);
+ fclose(fp);
+ }
+
+ MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world);
+ MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("CLIENT comm connect\n");
+ if (me == 0) unlink(filename);
+
+ } else if (server) {
+ MPI_Open_port(MPI_INFO_NULL,port);
+
+ if (me == 0) {
+ //printf("Server name: %s\n",port);
+ FILE *fp = fopen(filename,"w");
+ fprintf(fp,"%s",port);
+ fclose(fp);
+ }
+
+ MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("SERVER comm accept\n");
+ }
+
+ otherroot = 0;
+}
diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h
new file mode 100644
index 0000000000..40dd95e7ea
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.h
@@ -0,0 +1,35 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_TWO_H
+#define MSG_MPI_TWO_H
+
+#include "msg_mpi_one.h"
+
+namespace CSLIB_NS {
+
+class MsgMPITwo : public MsgMPIOne {
+ public:
+ MsgMPITwo(int, const void *, MPI_Comm);
+ ~MsgMPITwo();
+
+ private:
+ char port[MPI_MAX_PORT_NAME];
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp
new file mode 100644
index 0000000000..dcbeedaaa0
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.cpp
@@ -0,0 +1,140 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <zmq.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+
+#include "msg_zmq.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::~MsgZMQ()
+{
+ if (me == 0) {
+ zmq_close(socket);
+ zmq_ctx_destroy(context);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgZMQ::init(char *port)
+{
+#ifdef ZMQ_NO
+ error_all("constructor(): Library not built with ZMQ support");
+#endif
+
+ if (me == 0) {
+ int n = strlen(port) + 8;
+ char *socket_name = new char[n];
+ strcpy(socket_name,"tcp://");
+ strcat(socket_name,port);
+
+ if (client) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REQ);
+ zmq_connect(socket,socket_name);
+ } else if (server) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REP);
+ int rc = zmq_bind(socket,socket_name);
+ if (rc) error_one("constructor(): Server could not make socket connection");
+ }
+
+ delete [] socket_name;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ send below has a following ZMQ recv, except last one
+ if client calls send(), it will next call recv()
+ if server calls send(), it will next call recv() from its wait loop
+ in either case, recv() issues a ZMQ recv to match last ZMQ send here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ zmq_send(socket,lengths,2*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) {
+ zmq_send(socket,header,nheader*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) zmq_send(socket,buf,nbuf,0);
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ recv below has a following ZMQ send, except last one
+ if client calls recv(), it will next call send() to ping server again,
+ if server calls recv(), it will next call send() to respond to client
+ in either case, send() issues a ZMQ send to match last ZMQ recv here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ if (me == 0) {
+ zmq_recv(socket,lengths,2*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) {
+ zmq_recv(socket,header,nheader*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) zmq_recv(socket,buf,nbuf,0);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h
new file mode 100644
index 0000000000..5f6dd7f26b
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the GNU Lesser General Public
+ License (LGPL).
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_ZMQ_H
+#define MSG_ZMQ_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgZMQ : public Msg {
+ public:
+ MsgZMQ(int, const void *, MPI_Comm);
+ MsgZMQ(int, const void *);
+ ~MsgZMQ();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ void *context,*socket;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/src/MESSAGE/Install.sh b/src/MESSAGE/Install.sh
new file mode 100644
index 0000000000..853dbddcdd
--- /dev/null
+++ b/src/MESSAGE/Install.sh
@@ -0,0 +1,67 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# arg1 = file, arg2 = file it depends on
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+action () {
+ if (test $mode = 0) then
+ rm -f ../$1
+ elif (! cmp -s $1 ../$1) then
+ if (test -z "$2" || test -e ../$2) then
+ cp $1 ..
+ if (test $mode = 2) then
+ echo " updating src/$1"
+ fi
+ fi
+ elif (test -n "$2") then
+ if (test ! -e ../$2) then
+ rm -f ../$1
+ fi
+ fi
+}
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+ test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ # multiline form needed for BSD sed on Macs
+ sed -i -e '4 i \
+include ..\/..\/lib\/message\/Makefile.lammps
+' ../Makefile.package.settings
+ fi
+
+elif (test $1 = 0) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ fi
+
+fi
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
new file mode 100644
index 0000000000..20b56e031d
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -0,0 +1,270 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstdio>
+#include <cstring>
+#include "fix_client_md.h"
+#include "cslib.h"
+#include "atom.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+#include "comm.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+using namespace FixConst;
+
+enum{SETUP=1,STEP};
+enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
+enum{FORCES=1,ENERGY,VIRIAL};
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ if (lmp->clientserver != 1)
+ error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
+ if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");
+
+ if (sizeof(tagint) != 4)
+ error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
+
+ scalar_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ virial_flag = 1;
+ thermo_virial = 1;
+
+ maxatom = 0;
+ xpbc = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::~FixClientMD()
+{
+ memory->destroy(xpbc);
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // all-done message to server
+
+ cs->send(-1,0);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // clean-up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixClientMD::setmask()
+{
+ int mask = 0;
+ mask |= POST_FORCE;
+ mask |= MIN_POST_FORCE;
+ mask |= THERMO_ENERGY;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::init()
+{
+ if (3*atom->natoms > INT_MAX)
+ error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::setup(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
+ // optional fields: others in enum above
+
+ int nfields = 6;
+ if (domain->dimension == 2) nfields++;
+ if (domain->triclinic) nfields++;
+ if (atom->q_flag) nfields++;
+
+ cs->send(SETUP,nfields);
+
+ cs->pack_int(NATOMS,atom->natoms);
+ cs->pack_int(NTYPES,atom->ntypes);
+ cs->pack(BOXLO,4,3,domain->boxlo);
+ cs->pack(BOXHI,4,3,domain->boxhi);
+ cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (domain->dimension == 2) cs->pack_int(DIM,domain->dimension);
+ if (domain->triclinic) {
+ double boxtilt[3];
+ boxtilt[0] = domain->xy;
+ if (domain->dimension == 3) {
+ boxtilt[1] = domain->xz;
+ boxtilt[2] = domain->yz;
+ } else boxtilt[1] = boxtilt[2] = 0.0;
+ cs->pack(BOXTILT,4,3,boxtilt);
+ }
+ if (atom->q_flag)
+ cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
+
+ // receive initial forces, energy, virial
+
+ receive_fev(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_setup(int vflag)
+{
+ setup(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::post_force(int vflag)
+{
+ int i,j,m;
+
+ // energy and virial setup
+
+ if (vflag) v_setup(vflag);
+ else evflag = 0;
+
+ // required fields: COORDS
+ // optional fields: BOXLO, BOXHI, BOXTILT
+
+ // send coords
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfields = 1;
+ if (domain->box_change) nfields += 2;
+ if (domain->box_change && domain->triclinic) nfields++;;
+
+ cs->send(STEP,nfields);
+
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (domain->box_change) {
+ cs->pack(BOXLO,4,3,domain->boxlo);
+ cs->pack(BOXHI,4,3,domain->boxhi);
+ if (domain->triclinic) {
+ double boxtilt[3];
+ boxtilt[0] = domain->xy;
+ if (domain->dimension == 3) {
+ boxtilt[1] = domain->xz;
+ boxtilt[2] = domain->yz;
+ } else boxtilt[1] = boxtilt[2] = 0.0;
+ cs->pack(BOXTILT,4,3,boxtilt);
+ }
+ }
+
+ // recv forces, energy, virial
+
+ receive_fev(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_post_force(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ potential energy from QM code
+------------------------------------------------------------------------- */
+
+double FixClientMD::compute_scalar()
+{
+ return eng;
+}
+
+/* ----------------------------------------------------------------------
+ pack local coords into xpbc, enforcing PBC
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_coords()
+{
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+
+ if (nlocal > maxatom) {
+ memory->destroy(xpbc);
+ maxatom = atom->nmax;
+ memory->create(xpbc,3*maxatom,"message:xpbc");
+ }
+
+ memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
+
+ int j = 0;
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ receive message from server with forces, energy, virial
+------------------------------------------------------------------------- */
+
+void FixClientMD::receive_fev(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ double *forces = (double *) cs->unpack(FORCES);
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ bigint natoms = atom->natoms;
+ int m;
+
+ int j = 0;
+ for (tagint id = 1; id <= natoms; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ f[m][0] += forces[j++];
+ f[m][1] += forces[j++];
+ f[m][2] += forces[j++];
+ }
+ }
+
+ eng = cs->unpack_double(ENERGY);
+
+ if (vflag) {
+ double *v = (double *) cs->unpack(VIRIAL);
+ double invnprocs = 1.0 / comm->nprocs;
+ for (int i = 0; i < 6; i++)
+ virial[i] = invnprocs*v[i];
+ }
+}
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
new file mode 100644
index 0000000000..8e4ec0c6de
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.h
@@ -0,0 +1,62 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(client/md,FixClientMD)
+
+#else
+
+#ifndef LMP_FIX_CLIENT_MD_H
+#define LMP_FIX_CLIENT_MD_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixClientMD : public Fix {
+ public:
+ FixClientMD(class LAMMPS *, int, char **);
+ ~FixClientMD();
+ int setmask();
+ void init();
+ void setup(int);
+ void min_setup(int);
+ void post_force(int);
+ void min_post_force(int);
+ double compute_scalar();
+
+ private:
+ void *cslib;
+ int maxatom;
+ double eng;
+ double *xpbc;
+
+ void pack_coords();
+ void receive_fev(int );
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
new file mode 100644
index 0000000000..67e0a49046
--- /dev/null
+++ b/src/MESSAGE/message.cpp
@@ -0,0 +1,90 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "message.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+// customize by adding a new server protocol enum
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Message::command(int narg, char **arg)
+{
+ if (narg < 3) error->all(FLERR,"Illegal message command");
+
+ int clientserver;
+ if (strcmp(arg[0],"client") == 0) clientserver = 1;
+ else if (strcmp(arg[0],"server") == 0) clientserver = 2;
+ else error->all(FLERR,"Illegal message command");
+ lmp->clientserver = clientserver;
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[1],"md") == 0) protocol = MD;
+ else if (strcmp(arg[1],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ // instantiate CSlib with chosen communication mode
+
+ if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 ||
+ strcmp(arg[2],"mpi/two") == 0) {
+ if (narg != 4) error->all(FLERR,"Illegal message command");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world);
+
+ } else if (strcmp(arg[2],"mpi/one") == 0) {
+ if (narg != 3) error->all(FLERR,"Illegal message command");
+ if (!lmp->cscomm)
+ error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world);
+
+ } else error->all(FLERR,"Illegal message command");
+
+ // perform initial handshake between client and server
+ // other code being coupled to must perform similar operation
+ // client sends protocol with msgID = 0
+ // server matches it and replies
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ if (clientserver == 1) {
+ cs->send(0,1);
+ cs->pack_string(1,arg[1]);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+
+ } else {
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+ char *pstr = cs->unpack_string(1);
+ if (strcmp(pstr,arg[1]) != 0)
+ error->one(FLERR,"Mismatch in client/server protocol");
+
+ cs->send(0,0);
+ }
+}
diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h
new file mode 100644
index 0000000000..c384a5a7b7
--- /dev/null
+++ b/src/MESSAGE/message.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(message,Message)
+
+#else
+
+#ifndef LMP_MESSAGE_H
+#define LMP_MESSAGE_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Message : protected Pointers {
+ public:
+ Message(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
new file mode 100644
index 0000000000..cbf769be74
--- /dev/null
+++ b/src/MESSAGE/server.cpp
@@ -0,0 +1,50 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "server.h"
+#include "error.h"
+
+// customize by adding a new server protocol include and enum
+
+#include "server_md.h"
+#include "server_mc.h"
+
+using namespace LAMMPS_NS;
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Server::command(int narg, char **arg)
+{
+ if (narg != 1) error->all(FLERR,"Illegal server command");
+
+ if (lmp->clientserver != 2)
+ error->all(FLERR,"Message command not used to setup LAMMPS as a server");
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[0],"md") == 0) protocol = MD;
+ else if (strcmp(arg[0],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ if (protocol == MD) {
+ ServerMD *server = new ServerMD(lmp);
+ server->loop();
+ } else if (protocol == MC) {
+ ServerMC *server = new ServerMC(lmp);
+ server->loop();
+ }
+}
diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h
new file mode 100644
index 0000000000..579f6ab6f1
--- /dev/null
+++ b/src/MESSAGE/server.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(server,Server)
+
+#else
+
+#ifndef LMP_SERVER_H
+#define LMP_SERVER_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Server : protected Pointers {
+ public:
+ Server(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp
new file mode 100644
index 0000000000..8a7344e86b
--- /dev/null
+++ b/src/MESSAGE/server_mc.cpp
@@ -0,0 +1,148 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "server_mc.h"
+#include "atom.h"
+#include "update.h"
+#include "integrate.h"
+#include "input.h"
+#include "output.h"
+#include "thermo.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+/* ---------------------------------------------------------------------- */
+
+ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMC::loop()
+{
+ int i,j,m;
+ double xold[3],xnew[3];
+ tagint atomid;
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // require atom map
+
+ if (!atom->map_style) error->all(FLERR,"Server mode requires atom map");
+
+ // initialize LAMMPS for dynamics
+
+ input->one("run 0");
+
+ //update->whichflag = 1;
+ //lmp->init();
+
+ // loop on messages
+ // receive a message, process it, send return message if necessary
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ if (msgID == NATOMS) {
+
+ cs->send(msgID,1);
+ cs->pack_int(1,atom->natoms);
+
+ } else if (msgID == EINIT) {
+
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,2);
+ cs->pack_double(1,dval);
+ double *coords = NULL;
+ if (atom->nlocal) coords = &atom->x[0][0];
+ cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords);
+
+ } else if (msgID == DISPLACE) {
+
+ atomid = cs->unpack_int(1);
+ double *xnew = (double *) cs->unpack(2);
+ double **x = atom->x;
+
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ xold[0] = x[m][0];
+ xold[1] = x[m][1];
+ xold[2] = x[m][2];
+ x[m][0] = xnew[0];
+ x[m][1] = xnew[1];
+ x[m][2] = xnew[2];
+ }
+
+ input->one("run 0");
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,1);
+ cs->pack_double(1,dval);
+
+ } else if (msgID == ACCEPT) {
+
+ int accept = cs->unpack_int(1);
+ double **x = atom->x;
+
+ if (!accept) {
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ x[m][0] = xold[0];
+ x[m][1] = xold[1];
+ x[m][2] = xold[2];
+ }
+ }
+
+ cs->send(msgID,0);
+
+ } else if (msgID == RUN) {
+
+ int nsteps = cs->unpack_int(1);
+
+ //input->one("run 100");
+
+ update->nsteps = nsteps;
+ update->firststep = update->ntimestep;
+ update->laststep = update->ntimestep + nsteps;
+
+ update->integrate->setup(1);
+ update->integrate->run(nsteps);
+
+ cs->send(msgID,0);
+
+ } else error->all(FLERR,"Server received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h
new file mode 100644
index 0000000000..d0fb489429
--- /dev/null
+++ b/src/MESSAGE/server_mc.h
@@ -0,0 +1,29 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MC_H
+#define LMP_SERVER_MC_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMC : protected Pointers {
+ public:
+ ServerMC(class LAMMPS *);
+ void loop();
+};
+
+}
+
+#endif
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
new file mode 100644
index 0000000000..88fe1abe5f
--- /dev/null
+++ b/src/MESSAGE/server_md.cpp
@@ -0,0 +1,333 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "mpi.h"
+#include <cstring>
+#include "server_md.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "update.h"
+#include "integrate.h"
+#include "kspace.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{SETUP=1,STEP};
+enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
+enum{FORCES=1,ENERGY,VIRIAL};
+
+// NOTE: features that could be added to this interface
+// allow client to set periodicity vs shrink-wrap
+// currently just assume server is same as client
+// test that triclinic boxes actually work
+// send new box size/shape every step, for NPT client
+// unit check between client/server with unit conversion if needed
+// option for client to send other per-atom quantities, e.g. rmass
+// more precise request of energy/virial (global or peratom) by client
+// maybe Verlet should have a single(eflag,vflag) method to more easily comply
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
+{
+ if (domain->box_exist == 0)
+ error->all(FLERR,"Server command before simulation box is defined");
+
+ if (!atom->map_style) error->all(FLERR,"Server md mode requires atom map");
+ if (atom->tag_enable == 0) error->all(FLERR,"Server md mode requires atom IDs");
+ if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMD::loop()
+{
+ int i,j,m;
+
+ // cs = instance of CSlib
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // counters
+
+ int forcecalls = 0;
+ int neighcalls = 0;
+
+ // loop on messages
+ // receive a message, process it, send return message
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ // SETUP call at beginning of each run
+ // required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
+ // optional fields: others in enum above
+
+ if (msgID == SETUP) {
+
+ int natoms = -1;
+ int ntypes = -1;
+ double *boxlo = NULL;
+ double *boxhi = NULL;
+ double *boxtilt = NULL;
+ int *types = NULL;
+ double *coords = NULL;
+ double *charge = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == UNITS) {
+ char *units = cs->unpack_string(UNITS);
+ if (strcmp(units,update->unit_style) != 0)
+ error->all(FLERR,"Server md units mis-match with client");
+ } else if (fieldID[ifield] == DIM) {
+ int dim = cs->unpack_int(DIM);
+ if (dim != domain->dimension)
+ error->all(FLERR,"Server md dimension mis-match with client");
+ } else if (fieldID[ifield] == NATOMS) {
+ natoms = cs->unpack_int(NATOMS);
+ if (3*natoms > INT_MAX)
+ error->all(FLERR,"Server md max atoms is 1/3 of 2^31");
+ } else if (fieldID[ifield] == NTYPES) {
+ ntypes = cs->unpack_int(NTYPES);
+ if (ntypes != atom->ntypes)
+ error->all(FLERR,"Server md ntypes mis-match with client");
+ } else if (fieldID[ifield] == BOXLO) {
+ boxlo = (double *) cs->unpack(BOXLO);
+ } else if (fieldID[ifield] == BOXHI) {
+ boxhi = (double *) cs->unpack(BOXHI);
+ } else if (fieldID[ifield] == BOXTILT) {
+ boxtilt = (double *) cs->unpack(BOXTILT);
+ } else if (fieldID[ifield] == TYPES) {
+ types = (int *) cs->unpack(TYPES);
+ } else if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+ } else if (fieldID[ifield] == CHARGE) {
+ charge = (double *) cs->unpack(CHARGE);
+ } else error->all(FLERR,"Server md setup field unknown");
+ }
+
+ if (natoms < 0 || ntypes < 0 || !boxlo || !boxhi || !types || !coords)
+ error->all(FLERR,"Required server md setup field not received");
+
+ if (charge && atom->q_flag == 0)
+ error->all(FLERR,"Server md does not define atom attribute q");
+
+ // reset box, global and local
+ // reset proc decomposition
+
+ box_change(boxlo,boxhi,boxtilt);
+
+ domain->set_initial_box();
+ domain->set_global_box();
+ comm->set_proc_grid();
+ domain->set_local_box();
+
+ // clear all atoms
+
+ atom->nlocal = 0;
+ atom->nghost = 0;
+
+ // add atoms that are in my sub-box
+
+ int nlocal = 0;
+ for (int i = 0; i < natoms; i++) {
+ if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue;
+ atom->avec->create_atom(types[i],&coords[3*i]);
+ atom->tag[nlocal] = i+1;
+ if (charge) atom->q[nlocal] = charge[i];
+ nlocal++;
+ }
+
+ int ntotal;
+ MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
+ if (ntotal != natoms)
+ error->all(FLERR,"Server md atom cound does not match client");
+
+ atom->map_init();
+ atom->map_set();
+ atom->natoms = natoms;
+
+ // perform system setup() for dynamics
+ // also OK for minimization, since client runs minimizer
+ // return forces, energy, virial to client
+
+ update->whichflag = 1;
+ lmp->init();
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ forcecalls++;
+
+ send_fev(msgID);
+
+ // STEP call at each timestep of run or minimization
+ // required fields: COORDS
+ // optional fields: BOXLO, BOXHI, BOXTILT
+
+ } else if (msgID == STEP) {
+
+ double *boxlo = NULL;
+ double *boxhi = NULL;
+ double *boxtilt = NULL;
+ double *coords = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == BOXLO) {
+ boxlo = (double *) cs->unpack(BOXLO);
+ } else if (fieldID[ifield] == BOXHI) {
+ boxhi = (double *) cs->unpack(BOXHI);
+ } else if (fieldID[ifield] == BOXTILT) {
+ boxtilt = (double *) cs->unpack(BOXTILT);
+ } else if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+ } else error->all(FLERR,"Server md step field unknown");
+ }
+
+ if (!coords)
+ error->all(FLERR,"Required server md step field not received");
+
+ // change box size/shape, only if both box lo/hi received
+
+ if (boxlo && boxhi) box_change(boxlo,boxhi,boxtilt);
+
+ // assign received coords to owned atoms
+ // closest_image() insures xyz matches current server PBC
+
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+ int nall = atom->natoms;
+
+ j = 0;
+ for (tagint id = 1; id <= nall; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ domain->closest_image(x[m],&coords[j],x[m]);
+ j += 3;
+ }
+ }
+
+ // if no need to reneighbor, just ghost comm
+ // else setup_minimal(1) which includes reneigh
+ // setup_minimal computes forces for 0 or 1
+
+ int nflag = neighbor->decide();
+ if (nflag == 0) {
+ comm->forward_comm();
+ update->integrate->setup_minimal(0);
+ } else {
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ }
+
+ forcecalls++;
+
+ send_fev(msgID);
+
+ } else error->all(FLERR,"Server MD received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // stats
+
+ if (comm->me == 0) {
+ if (screen) {
+ fprintf(screen,"Server MD calls = %d\n",forcecalls);
+ fprintf(screen,"Server MD reneighborings = %d\n",neighcalls);
+ }
+ if (logfile) {
+ fprintf(logfile,"Server MD calls = %d\n",forcecalls);
+ fprintf(logfile,"Server MD reneighborings %d\n",neighcalls);
+ }
+ }
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ box change due to received message
+------------------------------------------------------------------------- */
+
+void ServerMD::box_change(double *boxlo, double *boxhi, double *boxtilt)
+{
+ domain->boxlo[0] = boxlo[0];
+ domain->boxhi[0] = boxhi[0];
+ domain->boxlo[1] = boxlo[1];
+ domain->boxhi[1] = boxhi[1];
+ if (domain->dimension == 3) {
+ domain->boxlo[2] = boxlo[2];
+ domain->boxhi[2] = boxhi[2];
+ }
+
+ if (boxtilt) {
+ if (!domain->triclinic)
+ error->all(FLERR,"Server md not setup for triclinic box");
+ domain->xy = boxtilt[0];
+ if (domain->dimension == 3) {
+ domain->xz = boxtilt[1];
+ domain->yz = boxtilt[2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ send return message with forces, energy, pressure tensor
+ pressure tensor should be just pair style virial
+------------------------------------------------------------------------- */
+
+void ServerMD::send_fev(int msgID)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ cs->send(msgID,3);
+
+ double *forces = NULL;
+ if (atom->nlocal) forces = &atom->f[0][0];
+ cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces);
+
+ double eng = force->pair->eng_vdwl + force->pair->eng_coul;
+ double engall;
+ MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
+ cs->pack_double(ENERGY,engall);
+
+ double v[6],vall[6];
+ for (int i = 0; i < 6; i++)
+ v[i] = force->pair->virial[i];
+ if (force->kspace)
+ for (int i = 0; i < 6; i++)
+ v[i] += force->kspace->virial[i];
+
+ MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
+ cs->pack(VIRIAL,4,6,vall);
+}
+
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
new file mode 100644
index 0000000000..70134cbff9
--- /dev/null
+++ b/src/MESSAGE/server_md.h
@@ -0,0 +1,33 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MD_H
+#define LMP_SERVER_MD_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMD : protected Pointers {
+ public:
+ ServerMD(class LAMMPS *);
+ void loop();
+
+ private:
+ void box_change(double *, double *, double *);
+ void send_fev(int);
+};
+
+}
+
+#endif
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe..b9cabfd67b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -53,7 +53,7 @@ endif
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
- granular kim kokkos kspace latte manybody mc meam misc \
+ granular kim kokkos kspace latte manybody mc meam message misc \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap spin srd voronoi
@@ -65,14 +65,14 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
-PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
+PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-qmmm user-quip user-smd user-vtk
PACKSYS = compress mpiio python user-lb
-PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
+PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
user-h5md user-molfile user-netcdf user-qmmm user-quip \
diff --git a/src/atom.cpp b/src/atom.cpp
index cf4d20a71e..798861364c 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1533,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int narg, char **arg)
}
/* ----------------------------------------------------------------------
- set all masses as read in from restart file
+ set all masses
+ called from reading of restart file, also from ServerMD
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)
diff --git a/src/domain.cpp b/src/domain.cpp
index 4c1d12018b..c00a716613 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1208,13 +1208,9 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
- not currently used (Jan 2017):
- used to be called by pair TIP4P styles but no longer,
- due to use of other closest_image() method
------------------------------------------------------------------------- */
-void Domain::closest_image(const double * const xi, const double * const xj,
- double * const xjimage)
+void Domain::closest_image(double *xi, double *xj, double *xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];
diff --git a/src/domain.h b/src/domain.h
index 5581f9a45f..ed24116cf4 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -116,8 +116,7 @@ class Domain : protected Pointers {
void minimum_image_once(double *);
int closest_image(int, int);
int closest_image(double *, int);
- void closest_image(const double * const, const double * const,
- double * const);
+ void closest_image(double *, double *, double *);
void remap(double *, imageint &);
void remap(double *);
void remap_near(double *, double *);
diff --git a/src/lammps.cpp b/src/lammps.cpp
index df6519f9f4..282250c642 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -47,8 +47,8 @@
#include "accelerator_omp.h"
#include "timer.h"
#include "python.h"
-#include "memory.h"
#include "version.h"
+#include "memory.h"
#include "error.h"
#include "lmpinstalledpkgs.h"
@@ -73,12 +73,50 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
output = NULL;
python = NULL;
+ clientserver = 0;
+ cslib = NULL;
+ cscomm = 0;
+
screen = NULL;
logfile = NULL;
infile = NULL;
initclock = MPI_Wtime();
+ // check if -mpi is first arg
+ // if so, then 2 apps were launched with one mpirun command
+ // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
+ // e.g. for client/server coupling with another code
+ // communicator needs to shrink to be just LAMMPS
+ // syntax: -mpi P1 means P1 procs for one app, P-P1 procs for second app
+ // LAMMPS could be either app, based on proc IDs
+ // do the following:
+ // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
+ // NOTE: assuming other app is doing the same thing, else will hang!
+ // re-create universe with subcomm
+ // store full two-app comm in cscomm
+ // cscomm is used by CSLIB package to exchange messages w/ other app
+ // eventually should extend to N > 2 apps launched with one mpirun command
+
+ int iarg = 1;
+ if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0)) {
+ int me,nprocs;
+ MPI_Comm_rank(communicator,&me);
+ MPI_Comm_size(communicator,&nprocs);
+ int p1 = atoi(arg[iarg+1]);
+ if (p1 <= 0 || p1 >= nprocs)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ int which = 0;
+ if (me >= p1) which = 1;
+ MPI_Comm subcomm;
+ MPI_Comm_split(communicator,which,me,&subcomm);
+ cscomm = communicator;
+ communicator = subcomm;
+ delete universe;
+ universe = new Universe(this,communicator);
+ }
+
// parse input switches
int inflag = 0;
@@ -107,59 +145,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int *pfirst = NULL;
int *plast = NULL;
- int iarg = 1;
+ iarg = 1;
while (iarg < narg) {
- if (strcmp(arg[iarg],"-partition") == 0 ||
- strcmp(arg[iarg],"-p") == 0) {
- universe->existflag = 1;
+
+ if (strcmp(arg[iarg],"-echo") == 0 ||
+ strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- iarg++;
- while (iarg < narg && arg[iarg][0] != '-') {
- universe->add_world(arg[iarg]);
- iarg++;
- }
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-help") == 0 ||
+ strcmp(arg[iarg],"-h") == 0) {
+ if (iarg+1 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ helpflag = 1;
+ citeflag = 0;
+ iarg += 1;
+
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-screen") == 0 ||
- strcmp(arg[iarg],"-sc") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- screenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-log") == 0 ||
- strcmp(arg[iarg],"-l") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- logflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-var") == 0 ||
- strcmp(arg[iarg],"-v") == 0) {
- if (iarg+3 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 3;
- while (iarg < narg && arg[iarg][0] != '-') iarg++;
- } else if (strcmp(arg[iarg],"-echo") == 0 ||
- strcmp(arg[iarg],"-e") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 2;
- } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
- strcmp(arg[iarg],"-ps") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partscreenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-plog") == 0 ||
- strcmp(arg[iarg],"-pl") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partlogflag = iarg + 1;
- iarg += 2;
+
} else if (strcmp(arg[iarg],"-kokkos") == 0 ||
strcmp(arg[iarg],"-k") == 0) {
if (iarg+2 > narg)
@@ -172,6 +181,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
kkfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
kklast = iarg;
+
+ } else if (strcmp(arg[iarg],"-log") == 0 ||
+ strcmp(arg[iarg],"-l") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ logflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-nocite") == 0 ||
+ strcmp(arg[iarg],"-nc") == 0) {
+ citeflag = 0;
+ iarg++;
+
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@@ -188,31 +217,32 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
else break;
}
plast[npack++] = iarg;
- } else if (strcmp(arg[iarg],"-suffix") == 0 ||
- strcmp(arg[iarg],"-sf") == 0) {
+
+ } else if (strcmp(arg[iarg],"-partition") == 0 ||
+ strcmp(arg[iarg],"-p") == 0) {
+ universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- delete [] suffix;
- delete [] suffix2;
- suffix2 = NULL;
- suffix_enable = 1;
- // hybrid option to set fall-back for suffix2
- if (strcmp(arg[iarg+1],"hybrid") == 0) {
- if (iarg+4 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- int n = strlen(arg[iarg+2]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+2]);
- n = strlen(arg[iarg+3]) + 1;
- suffix2 = new char[n];
- strcpy(suffix2,arg[iarg+3]);
- iarg += 4;
- } else {
- int n = strlen(arg[iarg+1]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+1]);
- iarg += 2;
+ iarg++;
+ while (iarg < narg && arg[iarg][0] != '-') {
+ universe->add_world(arg[iarg]);
+ iarg++;
}
+
+ } else if (strcmp(arg[iarg],"-plog") == 0 ||
+ strcmp(arg[iarg],"-pl") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partlogflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
+ strcmp(arg[iarg],"-ps") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partscreenflag = iarg + 1;
+ iarg += 2;
+
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
if (iarg+3 > narg)
@@ -221,6 +251,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
+
} else if (strcmp(arg[iarg],"-restart") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
@@ -241,17 +272,47 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
wdfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wdlast = iarg;
- } else if (strcmp(arg[iarg],"-nocite") == 0 ||
- strcmp(arg[iarg],"-nc") == 0) {
- citeflag = 0;
- iarg++;
- } else if (strcmp(arg[iarg],"-help") == 0 ||
- strcmp(arg[iarg],"-h") == 0) {
- if (iarg+1 > narg)
+
+ } else if (strcmp(arg[iarg],"-screen") == 0 ||
+ strcmp(arg[iarg],"-sc") == 0) {
+ if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- helpflag = 1;
- citeflag = 0;
- iarg += 1;
+ screenflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-suffix") == 0 ||
+ strcmp(arg[iarg],"-sf") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ delete [] suffix;
+ delete [] suffix2;
+ suffix2 = NULL;
+ suffix_enable = 1;
+ // hybrid option to set fall-back for suffix2
+ if (strcmp(arg[iarg+1],"hybrid") == 0) {
+ if (iarg+4 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ int n = strlen(arg[iarg+2]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+2]);
+ n = strlen(arg[iarg+3]) + 1;
+ suffix2 = new char[n];
+ strcpy(suffix2,arg[iarg+3]);
+ iarg += 4;
+ } else {
+ int n = strlen(arg[iarg+1]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+1]);
+ iarg += 2;
+ }
+
+ } else if (strcmp(arg[iarg],"-var") == 0 ||
+ strcmp(arg[iarg],"-v") == 0) {
+ if (iarg+3 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 3;
+ while (iarg < narg && arg[iarg][0] != '-') iarg++;
+
} else error->universe_all(FLERR,"Invalid command-line argument");
}
@@ -595,6 +656,14 @@ LAMMPS::~LAMMPS()
delete [] suffix;
delete [] suffix2;
+ // free the MPI comm created by -mpi command-line arg
+ // it was passed to universe as if origianl universe world
+ // may have been split later by partitions, universe will free the splits
+ // free a copy of uorig here, so check in universe destructor will still work
+
+ MPI_Comm copy = universe->uorig;
+ if (cscomm) MPI_Comm_free(©);
+
delete input;
delete universe;
delete error;
diff --git a/src/lammps.h b/src/lammps.h
index b2c8673471..5ccef3026e 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -51,6 +51,10 @@ class LAMMPS {
int num_package; // number of cmdline package commands
int cite_enable; // 1 if generating log.cite, 0 if disabled
+ int clientserver; // 0 = neither, 1 = client, 2 = server
+ void *cslib; // client/server messaging via CSlib
+ MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode
+
class KokkosLMP *kokkos; // KOKKOS accelerator class
class AtomKokkos *atomKK; // KOKKOS version of Atom class
class MemoryKokkos *memoryKK; // KOKKOS version of Memory class
--
GitLab
From ef3fd1374a1ddc557c78abd8631415234d874db4 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 23 Jul 2018 16:11:18 -0600
Subject: [PATCH 045/332] added kspace_style for internal fmm tuning (for
inhomogenous systems) and fixed the call to fcs_set_tolerance
---
src/USER-SCAFACOS/scafacos.cpp | 43 +++++++++++++++++++++++++++++-----
src/USER-SCAFACOS/scafacos.h | 2 ++
2 files changed, 39 insertions(+), 6 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index b9390aea47..352a298b86 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -49,7 +49,10 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
// choose the correct default tolerance type for chosen method
// TODO: needs to be expanded for all solvers, currently mainly used ones
if (strcmp(method,"fmm") == 0)
+ {
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
+ fmm_tuning_flag = 0;
+ }
else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
@@ -81,6 +84,8 @@ Scafacos::~Scafacos()
void Scafacos::init()
{
// error checks
+ if (screen && me == 0) fprintf(screen,"Setting up ScaFaCoS with solver %s ...\n",method);
+ if (logfile && me == 0) fprintf(logfile,"Setting up ScaFaCoS with solver %s ...\n",method);
if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
@@ -106,18 +111,31 @@ void Scafacos::init()
setup_handle();
- result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
- check_result(result);
-
+ // using other methods lead to termination of the program,
+ // since they have no tolerance tuning methods
+ if ( strcmp(method,"fmm") == 0 ||
+ strcmp(method,"p3m") == 0 ||
+ strcmp(method,"p2nfft") == 0 ||
+ strcmp(method,"ewald") == 0)
+ {
+ result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
+ check_result(result);
+ }
if (me == 0) fcs_print_parameters(fcs);
double **x = atom->x;
double *q = atom->q;
int nlocal = atom->nlocal;
+ if (strcmp(method,"fmm") == 0)
+ {
+ if (fmm_tuning_flag == 1)
+ fcs_fmm_set_internal_tuning(fcs,fmm_tuning_flag);
+ }
+
result = fcs_tune(fcs,nlocal,&x[0][0],q);
+ check_result(result);
}
-
initialized = 1;
}
@@ -197,7 +215,7 @@ int Scafacos::modify_param(int narg, char **arg)
if (strcmp(arg[0],"scafacos") != 0) return 0;
if (strcmp(arg[1],"tolerance") == 0) {
- if (narg < 2) error->all(FLERR,"Illegal kspace_modify command");
+ if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (tolerance)");
if (strcmp(arg[2],"energy") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
else if (strcmp(arg[2],"energy_rel") == 0)
@@ -210,7 +228,20 @@ int Scafacos::modify_param(int narg, char **arg)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
else if (strcmp(arg[2],"potential_rel") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
- else error->all(FLERR,"Illegal kspace_modify command");
+ else error->all(FLERR,"Illegal kspace_modify command (tolerance argument)");
+ return 3;
+ }
+
+ // keyword = fmm_inhomogen_tuning
+ // value1 = 0, 1
+ // 0 -> homogenous system (default)
+ // 1 -> inhomogenous system (more internal tuning is provided (sequential!))
+ if (strcmp(arg[1],"fmm_tuning") == 0)
+ {
+ if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg);
+ if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg);
+ if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)");
+ fmm_tuning_flag = atoi(arg[2]);
return 3;
}
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index 3e549cf64e..857036bb7a 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -44,6 +44,8 @@ class Scafacos : public KSpace {
int tolerance_type;
int initialized,maxatom;
+ int fmm_tuning_flag;
+
FCS fcs; // ScaFaCoS handle
FCSResult result; // result for each ScaFaCoS call
--
GitLab
From a90e019ec7d9315fc359cb5eff01ac941e007921 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 23 Jul 2018 16:13:15 -0600
Subject: [PATCH 046/332] updated ScaFaCoS examples, added open-boundary
Hammersley distributed sphere and charged cloud near a charged wall examples
---
examples/USER/scafacos/data.NaCl | 50 +-
examples/USER/scafacos/data.cloud_wall | 316 +++++
.../USER/scafacos/data.hammersley_shphere | 1016 +++++++++++++++++
examples/USER/scafacos/in.scafacos.cw.ewald | 31 +
examples/USER/scafacos/in.scafacos.cw.fmm | 37 +
examples/USER/scafacos/in.scafacos.cw.p2nfft | 31 +
examples/USER/scafacos/in.scafacos.ewald | 37 +
examples/USER/scafacos/in.scafacos.fmm | 37 +
.../USER/scafacos/in.scafacos.hsph.direct | 34 +
examples/USER/scafacos/in.scafacos.hsph.fmm | 37 +
.../USER/scafacos/in.scafacos.hsph.p2nfft | 36 +
examples/USER/scafacos/in.scafacos.p2nfft | 37 +
.../log.23Jul18.scafacos.cw.g++.ewald.16 | 92 ++
.../log.23Jul18.scafacos.cw.g++.ewald.8 | 92 ++
.../log.23Jul18.scafacos.cw.g++.fmm.1 | 99 ++
.../log.23Jul18.scafacos.cw.g++.fmm.16 | 99 ++
.../log.23Jul18.scafacos.cw.g++.fmm.2 | 99 ++
.../log.23Jul18.scafacos.cw.g++.fmm.4 | 99 ++
.../log.23Jul18.scafacos.cw.g++.fmm.8 | 99 ++
.../log.23Jul18.scafacos.cw.g++.p2nfft.1 | 92 ++
.../log.23Jul18.scafacos.cw.g++.p2nfft.16 | 92 ++
.../log.23Jul18.scafacos.cw.g++.p2nfft.2 | 92 ++
.../log.23Jul18.scafacos.cw.g++.p2nfft.4 | 92 ++
.../log.23Jul18.scafacos.cw.g++.p2nfft.8 | 92 ++
.../log.23Jul18.scafacos.g++.ewald.16 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.ewald.8 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.fmm.1 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.fmm.16 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.fmm.2 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.fmm.4 | 102 ++
.../scafacos/log.23Jul18.scafacos.g++.fmm.8 | 102 ++
.../log.23Jul18.scafacos.g++.p2nfft.1 | 102 ++
.../log.23Jul18.scafacos.g++.p2nfft.16 | 102 ++
.../log.23Jul18.scafacos.g++.p2nfft.2 | 102 ++
.../log.23Jul18.scafacos.g++.p2nfft.4 | 102 ++
.../log.23Jul18.scafacos.g++.p2nfft.8 | 102 ++
.../log.23Jul18.scafacos.hsph.g++.direct.1 | 105 ++
.../log.23Jul18.scafacos.hsph.g++.direct.2 | 105 ++
.../log.23Jul18.scafacos.hsph.g++.direct.4 | 105 ++
.../log.23Jul18.scafacos.hsph.g++.direct.8 | 105 ++
.../log.23Jul18.scafacos.hsph.g++.fmm.1 | 109 ++
.../log.23Jul18.scafacos.hsph.g++.fmm.2 | 109 ++
.../log.23Jul18.scafacos.hsph.g++.fmm.4 | 109 ++
.../log.23Jul18.scafacos.hsph.g++.fmm.8 | 109 ++
.../log.23Jul18.scafacos.hsph.g++.p2nfft.1 | 107 ++
.../log.23Jul18.scafacos.hsph.g++.p2nfft.2 | 107 ++
.../log.23Jul18.scafacos.hsph.g++.p2nfft.4 | 107 ++
.../log.23Jul18.scafacos.hsph.g++.p2nfft.8 | 107 ++
48 files changed, 5321 insertions(+), 25 deletions(-)
create mode 100644 examples/USER/scafacos/data.cloud_wall
create mode 100644 examples/USER/scafacos/data.hammersley_shphere
create mode 100644 examples/USER/scafacos/in.scafacos.cw.ewald
create mode 100644 examples/USER/scafacos/in.scafacos.cw.fmm
create mode 100644 examples/USER/scafacos/in.scafacos.cw.p2nfft
create mode 100644 examples/USER/scafacos/in.scafacos.ewald
create mode 100644 examples/USER/scafacos/in.scafacos.fmm
create mode 100644 examples/USER/scafacos/in.scafacos.hsph.direct
create mode 100644 examples/USER/scafacos/in.scafacos.hsph.fmm
create mode 100644 examples/USER/scafacos/in.scafacos.hsph.p2nfft
create mode 100644 examples/USER/scafacos/in.scafacos.p2nfft
create mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
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diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl
index 2d804dec95..23807e23d5 100644
--- a/examples/USER/scafacos/data.NaCl
+++ b/examples/USER/scafacos/data.NaCl
@@ -1,25 +1,25 @@
- LAMMPS Description
-
- 8 atoms
-
- 2 atom types
-
- 0.0000000000000000 2.000000000000000 xlo xhi
- 0.0000000000000000 2.000000000000000 ylo yhi
- 0.0000000000000000 2.000000000000000 zlo zhi
-
- Masses
-
- 1 22.98976928
- 2 35.45
-
- Atoms
-
- 1 1 1.0 0.0 0.0 0.0
- 2 2 -1.0 1.0 0.0 0.0
- 3 2 -1.0 0.0 1.0 0.0
- 4 1 1.0 1.0 1.0 0.0
- 5 2 -1.0 0.0 0.0 1.0
- 6 1 1.0 1.0 0.0 1.0
- 7 1 1.0 0.0 1.0 1.0
- 8 2 -1.0 1.0 1.0 1.0
+LAMMPS Description
+
+8 atoms
+
+2 atom types
+
+0 2 xlo xhi
+0 2 ylo yhi
+0 2 zlo zhi
+
+Masses
+
+1 22.98976928
+2 35.45
+
+Atoms
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+3 1 -1 0 1 0
+4 2 1 1 1 0
+5 1 -1 0 0 1
+6 2 1 1 0 1
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+8 1 -1 1 1 1
diff --git a/examples/USER/scafacos/data.cloud_wall b/examples/USER/scafacos/data.cloud_wall
new file mode 100644
index 0000000000..1592ec666a
--- /dev/null
+++ b/examples/USER/scafacos/data.cloud_wall
@@ -0,0 +1,316 @@
+LAMMPS Description
+
+300 atoms
+
+1 atom types
+
+0 10 xlo xhi
+0 10 ylo yhi
+0 10 zlo zhi
+
+Masses
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diff --git a/examples/USER/scafacos/data.hammersley_shphere b/examples/USER/scafacos/data.hammersley_shphere
new file mode 100644
index 0000000000..e0d067adfb
--- /dev/null
+++ b/examples/USER/scafacos/data.hammersley_shphere
@@ -0,0 +1,1016 @@
+LAMMPS Description
+
+1000 atoms
+
+1 atom types
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+-50.5 51.5 ylo yhi
+-50.5 51.5 zlo zhi
+
+Masses
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+955 1 -1 0.360273 0.656078 0.954
+956 1 -1 0.638272 0.345546 0.955
+957 1 1 0.51132 0.704782 0.956
+958 1 -1 0.488803 0.297452 0.957
+959 1 -1 0.299717 0.511072 0.958
+960 1 1 0.697988 0.489055 0.959
+961 1 1 0.69513 0.51801 0.96
+962 1 -1 0.307224 0.482207 0.961
+963 1 1 0.482427 0.690387 0.962
+964 1 -1 0.517349 0.312037 0.963
+965 1 1 0.619063 0.643276 0.964
+966 1 -1 0.382542 0.358654 0.965
+967 1 -1 0.360616 0.615828 0.966
+968 1 1 0.63739 0.385829 0.967
+969 1 1 0.655724 0.582012 0.968
+970 1 1 0.346649 0.419238 0.969
+971 1 -1 0.42051 0.650935 0.97
+972 1 1 0.578194 0.351525 0.971
+973 1 1 0.548857 0.657572 0.972
+974 1 1 0.451999 0.345188 0.973
+975 1 -1 0.348003 0.547128 0.974
+976 1 1 0.649121 0.453763 0.975
+977 1 -1 0.646729 0.543528 0.976
+978 1 -1 0.356287 0.457366 0.977
+979 1 -1 0.458282 0.640626 0.978
+980 1 1 0.54078 0.362537 0.979
+981 1 -1 0.566752 0.623062 0.98
+982 1 -1 0.434905 0.379993 0.981
+983 1 -1 0.383134 0.563391 0.982
+984 1 -1 0.613631 0.438364 0.983
+985 1 -1 0.59748 0.579004 0.984
+986 1 1 0.405567 0.423466 0.985
+987 1 -1 0.426024 0.591277 0.986
+988 1 -1 0.571322 0.411999 0.987
+989 1 1 0.511337 0.608293 0.988
+990 1 1 0.48914 0.396264 0.989
+991 1 -1 0.401042 0.51036 0.99
+992 1 1 0.593927 0.490167 0.991
+993 1 1 0.587477 0.516843 0.992
+994 1 1 0.418131 0.484237 0.993
+995 1 1 0.485399 0.575834 0.994
+996 1 -1 0.513336 0.430738 0.995
+997 1 -1 0.535388 0.552265 0.996
+998 1 -1 0.469337 0.454714 0.997
+999 1 1 0.463006 0.525048 0.998
+1000 1 -1 0.526172 0.482279 0.999
diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/USER/scafacos/in.scafacos.cw.ewald
new file mode 100644
index 0000000000..f8444dd01f
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.cw.ewald
@@ -0,0 +1,31 @@
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/USER/scafacos/in.scafacos.cw.fmm
new file mode 100644
index 0000000000..24a2739581
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.cw.fmm
@@ -0,0 +1,37 @@
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/USER/scafacos/in.scafacos.cw.p2nfft
new file mode 100644
index 0000000000..7a2391bc77
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.cw.p2nfft
@@ -0,0 +1,31 @@
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.ewald b/examples/USER/scafacos/in.scafacos.ewald
new file mode 100644
index 0000000000..6c26c71884
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.ewald
@@ -0,0 +1,37 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+
+replicate 8 8 8
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/USER/scafacos/in.scafacos.fmm
new file mode 100644
index 0000000000..18d7464fb8
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.fmm
@@ -0,0 +1,37 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+
+replicate 8 8 8
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/USER/scafacos/in.scafacos.hsph.direct
new file mode 100644
index 0000000000..60448880ec
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.hsph.direct
@@ -0,0 +1,34 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/USER/scafacos/in.scafacos.hsph.fmm
new file mode 100644
index 0000000000..515809dbde
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.hsph.fmm
@@ -0,0 +1,37 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+
+timestep 0.005
+thermo 1
+
+run 20
diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/USER/scafacos/in.scafacos.hsph.p2nfft
new file mode 100644
index 0000000000..d690a29e49
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.hsph.p2nfft
@@ -0,0 +1,36 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
diff --git a/examples/USER/scafacos/in.scafacos.p2nfft b/examples/USER/scafacos/in.scafacos.p2nfft
new file mode 100644
index 0000000000..7fa2ccdd9e
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.p2nfft
@@ -0,0 +1,37 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+
+replicate 8 8 8
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
new file mode 100644
index 0000000000..ffdc7e3a3c
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49647271 0 0.49647271 0
+ 10 300 0.061254978 0.014582562 0.44286522 0.02180093 0.46466616 0
+ 20 300 0.12240911 0.058693359 0.37869251 0.087746571 0.46643909 0
+ 30 300 0.18348265 0.13468789 0.26730177 0.2013584 0.46866017 0
+ 40 300 0.24441123 0.50949535 0.083356437 0.76169555 0.84505198 0
+ 50 300 0.30493236 1.1731116 -0.055261984 1.7538018 1.6985399 0
+ 60 300 0.36615515 1.3589639 -0.33351524 2.031651 1.6981358 0
+ 70 300 0.42717433 1.6482648 -0.76570045 2.4641559 1.6984554 0
+ 80 300 0.48137259 2.8640899 -2.4038488 4.2818144 1.8779656 0
+ 90 300 0.5323379 93.168442 -2.5911448 139.28682 136.69568 0
+ 100 300 0.5756321 94.146897 -1.3480439 140.74961 139.40157 0
+Loop time of 0.575655 on 16 procs for 100 steps with 300 atoms
+
+Performance: 75045.007 tau/day, 173.715 timesteps/s
+98.7% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2159e-05 | 1.739e-05 | 2.3127e-05 | 0.0 | 0.00
+Kspace | 0.57008 | 0.57086 | 0.57137 | 0.1 | 99.17
+Neigh | 0.00025606 | 0.00061357 | 0.001369 | 0.0 | 0.11
+Comm | 0.0023558 | 0.0027267 | 0.003104 | 0.4 | 0.47
+Output | 0.00029898 | 0.00032344 | 0.00037599 | 0.0 | 0.06
+Modify | 8.2493e-05 | 0.00014143 | 0.00021815 | 0.0 | 0.02
+Other | | 0.0009701 | | | 0.17
+
+Nlocal: 18.75 ave 39 max 6 min
+Histogram: 6 1 1 0 1 2 2 1 1 1
+Nghost: 122.812 ave 195 max 63 min
+Histogram: 8 0 0 0 0 0 0 1 3 4
+Neighs: 160.625 ave 598 max 13 min
+Histogram: 8 2 1 1 1 0 0 2 0 1
+
+Total # of neighbors = 2570
+Ave neighs/atom = 8.56667
+Neighbor list builds = 23
+Dangerous builds = 16
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
new file mode 100644
index 0000000000..52d887f475
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49647271 0 0.49647271 0
+ 10 300 0.067519665 0.014718629 0.45088339 0.02200435 0.47288774 0
+ 20 300 0.13502312 0.05922597 0.38470912 0.088542825 0.47325194 0
+ 30 300 0.20248008 0.13587829 0.27058048 0.20313804 0.47371852 0
+ 40 300 0.26985955 0.51353118 0.088432648 0.76772911 0.85616176 0
+ 50 300 0.33801103 1.1760001 -0.058088247 1.7581201 1.7000319 0
+ 60 300 0.40665984 1.3627885 -0.33736672 2.0373688 1.7000021 0
+ 70 300 0.47533679 1.6529365 -0.77082139 2.4711401 1.7003187 0
+ 80 300 0.54396391 2.9569837 -2.4624654 4.4206907 1.9582253 0
+ 90 300 0.61429667 81.642726 -2.5370215 122.05588 119.51885 0
+ 100 300 0.68513632 85.047974 -1.128107 127.14672 126.01861 0
+Loop time of 0.685155 on 8 procs for 100 steps with 300 atoms
+
+Performance: 63051.442 tau/day, 145.952 timesteps/s
+99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.0967e-05 | 1.4216e-05 | 1.8358e-05 | 0.0 | 0.00
+Kspace | 0.67942 | 0.67981 | 0.6803 | 0.0 | 99.22
+Neigh | 0.00073242 | 0.0010653 | 0.0015635 | 0.8 | 0.16
+Comm | 0.0029492 | 0.0031102 | 0.0033047 | 0.2 | 0.45
+Output | 0.00021768 | 0.00023454 | 0.00028443 | 0.0 | 0.03
+Modify | 0.00016046 | 0.00018132 | 0.00019431 | 0.0 | 0.03
+Other | | 0.0007433 | | | 0.11
+
+Nlocal: 37.5 ave 46 max 31 min
+Histogram: 2 0 0 2 1 0 2 0 0 1
+Nghost: 203.875 ave 212 max 192 min
+Histogram: 1 0 1 0 0 2 1 0 0 3
+Neighs: 321.625 ave 599 max 112 min
+Histogram: 1 2 0 1 1 0 1 1 0 1
+
+Total # of neighbors = 2573
+Ave neighs/atom = 8.57667
+Neighbor list builds = 23
+Dangerous builds = 16
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
new file mode 100644
index 0000000000..47e0be01ce
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
@@ -0,0 +1,99 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49646402 0 0.49646402 0
+ 10 300 0.036603451 0.015455559 0.47335833 0.02310606 0.49646439 0
+ 20 300 0.073534727 0.06229069 0.40334177 0.093124582 0.49646635 0
+ 30 300 0.10984373 0.14310163 0.28254277 0.21393694 0.49647971 0
+ 40 300 0.14610171 0.52929788 0.089669015 0.79130033 0.88096934 0
+ 50 300 0.18255496 1.1963022 -0.082792461 1.7884718 1.7056794 0
+ 60 300 0.2194376 1.3928167 -0.37659239 2.082261 1.7056686 0
+ 70 300 0.25588369 1.7069009 -0.84571914 2.5518169 1.7060978 0
+ 80 300 0.29101205 15.358343 -3.368063 22.960722 19.592659 0
+ 90 300 0.32697225 42.280432 -2.1623864 63.209247 61.04686 0
+ 100 300 0.36395645 41.48079 -0.89904529 62.013782 61.114736 0
+Loop time of 0.363968 on 1 procs for 100 steps with 300 atoms
+
+Performance: 118691.709 tau/day, 274.749 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00
+Kspace | 0.35715 | 0.35715 | 0.35715 | 0.0 | 98.13
+Neigh | 0.0039768 | 0.0039768 | 0.0039768 | 0.0 | 1.09
+Comm | 0.0012023 | 0.0012023 | 0.0012023 | 0.0 | 0.33
+Output | 0.0001502 | 0.0001502 | 0.0001502 | 0.0 | 0.04
+Modify | 0.0009768 | 0.0009768 | 0.0009768 | 0.0 | 0.27
+Other | | 0.0005031 | | | 0.14
+
+Nlocal: 300 ave 300 max 300 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 374 ave 374 max 374 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2459 ave 2459 max 2459 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
new file mode 100644
index 0000000000..f104355d87
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
@@ -0,0 +1,99 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49646402 0 0.49646402 0
+ 10 300 0.018873215 0.015455559 0.47335833 0.02310606 0.49646439 0
+ 20 300 0.035197735 0.06229069 0.40334177 0.093124582 0.49646635 0
+ 30 300 0.051513195 0.14310163 0.28254277 0.21393694 0.49647971 0
+ 40 300 0.067400217 0.52929788 0.089669015 0.79130033 0.88096934 0
+ 50 300 0.083569527 1.1963022 -0.082792461 1.7884718 1.7056794 0
+ 60 300 0.099931955 1.3928167 -0.37659239 2.082261 1.7056686 0
+ 70 300 0.11602688 1.7069009 -0.84571914 2.5518169 1.7060978 0
+ 80 300 0.13271379 15.358343 -3.368063 22.960722 19.592659 0
+ 90 300 0.15055513 42.280432 -2.1623864 63.209247 61.04686 0
+ 100 300 0.16817498 41.48079 -0.89904529 62.013782 61.114736 0
+Loop time of 0.168194 on 16 procs for 100 steps with 300 atoms
+
+Performance: 256846.586 tau/day, 594.552 timesteps/s
+97.7% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.4544e-05 | 2.0206e-05 | 2.6941e-05 | 0.0 | 0.01
+Kspace | 0.16313 | 0.16373 | 0.16423 | 0.1 | 97.34
+Neigh | 0.00016737 | 0.00039591 | 0.00084519 | 0.0 | 0.24
+Comm | 0.0021157 | 0.0026083 | 0.0032525 | 0.7 | 1.55
+Output | 0.00026298 | 0.00030228 | 0.00035977 | 0.0 | 0.18
+Modify | 0.00010705 | 0.00015062 | 0.00020647 | 0.0 | 0.09
+Other | | 0.0009913 | | | 0.59
+
+Nlocal: 18.75 ave 36 max 6 min
+Histogram: 4 3 1 0 0 1 2 1 2 2
+Nghost: 127 ave 196 max 71 min
+Histogram: 8 0 0 0 0 0 0 1 6 1
+Neighs: 153.688 ave 491 max 10 min
+Histogram: 8 1 1 1 1 1 0 0 0 3
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
new file mode 100644
index 0000000000..43ded2d4da
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
@@ -0,0 +1,99 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49646402 0 0.49646402 0
+ 10 300 0.021326542 0.015455559 0.47335833 0.02310606 0.49646439 0
+ 20 300 0.043129683 0.06229069 0.40334177 0.093124582 0.49646635 0
+ 30 300 0.064425707 0.14310163 0.28254277 0.21393694 0.49647971 0
+ 40 300 0.085822344 0.52929788 0.089669015 0.79130033 0.88096934 0
+ 50 300 0.10737753 1.1963022 -0.082792461 1.7884718 1.7056794 0
+ 60 300 0.12947297 1.3928167 -0.37659239 2.082261 1.7056686 0
+ 70 300 0.15108895 1.7069009 -0.84571914 2.5518169 1.7060978 0
+ 80 300 0.17378163 15.358343 -3.368063 22.960722 19.592659 0
+ 90 300 0.19809985 42.280432 -2.1623864 63.209247 61.04686 0
+ 100 300 0.22268319 41.48079 -0.89904529 62.013782 61.114736 0
+Loop time of 0.222696 on 2 procs for 100 steps with 300 atoms
+
+Performance: 193986.156 tau/day, 449.042 timesteps/s
+98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1683e-05 | 1.5378e-05 | 1.9073e-05 | 0.0 | 0.01
+Kspace | 0.21627 | 0.2168 | 0.21734 | 0.1 | 97.35
+Neigh | 0.0016344 | 0.0021609 | 0.0026875 | 1.1 | 0.97
+Comm | 0.0022857 | 0.0023286 | 0.0023715 | 0.1 | 1.05
+Output | 0.00015521 | 0.00019228 | 0.00022936 | 0.0 | 0.09
+Modify | 0.00052834 | 0.00054049 | 0.00055265 | 0.0 | 0.24
+Other | | 0.0006541 | | | 0.29
+
+Nlocal: 150 ave 159 max 141 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 392 ave 395 max 389 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 1229.5 ave 1773 max 686 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
new file mode 100644
index 0000000000..12c74993e9
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
@@ -0,0 +1,99 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49646402 0 0.49646402 0
+ 10 300 0.017563343 0.015455559 0.47335833 0.02310606 0.49646439 0
+ 20 300 0.034884214 0.06229069 0.40334177 0.093124582 0.49646635 0
+ 30 300 0.052014828 0.14310163 0.28254277 0.21393694 0.49647971 0
+ 40 300 0.069101095 0.52929788 0.089669015 0.79130033 0.88096934 0
+ 50 300 0.085633039 1.1963022 -0.082792461 1.7884718 1.7056794 0
+ 60 300 0.10165119 1.3928167 -0.37659239 2.082261 1.7056686 0
+ 70 300 0.11729789 1.7069009 -0.84571914 2.5518169 1.7060978 0
+ 80 300 0.1342802 15.358343 -3.368063 22.960722 19.592659 0
+ 90 300 0.15266848 42.280432 -2.1623864 63.209247 61.04686 0
+ 100 300 0.17004442 41.48079 -0.89904529 62.013782 61.114736 0
+Loop time of 0.170072 on 4 procs for 100 steps with 300 atoms
+
+Performance: 254010.216 tau/day, 587.987 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.5497e-05 | 1.6868e-05 | 1.9789e-05 | 0.0 | 0.01
+Kspace | 0.16417 | 0.16472 | 0.16507 | 0.1 | 96.86
+Neigh | 0.00082564 | 0.0012031 | 0.0015855 | 0.9 | 0.71
+Comm | 0.0026572 | 0.0029335 | 0.003197 | 0.4 | 1.72
+Output | 0.00019169 | 0.00021791 | 0.00026536 | 0.0 | 0.13
+Modify | 0.00031304 | 0.00032955 | 0.00035334 | 0.0 | 0.19
+Other | | 0.0006474 | | | 0.38
+
+Nlocal: 75 ave 81 max 70 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 282.5 ave 290 max 274 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs: 614.75 ave 981 max 285 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
new file mode 100644
index 0000000000..1fea13cd13
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
@@ -0,0 +1,99 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49646402 0 0.49646402 0
+ 10 300 0.016258478 0.015455559 0.47335833 0.02310606 0.49646439 0
+ 20 300 0.031442165 0.06229069 0.40334177 0.093124582 0.49646635 0
+ 30 300 0.046462774 0.14310163 0.28254277 0.21393694 0.49647971 0
+ 40 300 0.061176538 0.52929788 0.089669015 0.79130033 0.88096934 0
+ 50 300 0.076244354 1.1963022 -0.082792461 1.7884718 1.7056794 0
+ 60 300 0.091396809 1.3928167 -0.37659239 2.082261 1.7056686 0
+ 70 300 0.10625911 1.7069009 -0.84571914 2.5518169 1.7060978 0
+ 80 300 0.1204896 15.358343 -3.368063 22.960722 19.592659 0
+ 90 300 0.13657618 42.280432 -2.1623864 63.209247 61.04686 0
+ 100 300 0.15163732 41.48079 -0.89904529 62.013782 61.114736 0
+Loop time of 0.151654 on 8 procs for 100 steps with 300 atoms
+
+Performance: 284858.554 tau/day, 659.395 timesteps/s
+97.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.3828e-05 | 1.6987e-05 | 1.955e-05 | 0.0 | 0.01
+Kspace | 0.14633 | 0.14689 | 0.14725 | 0.1 | 96.86
+Neigh | 0.00047135 | 0.00067887 | 0.00094771 | 0.0 | 0.45
+Comm | 0.0027649 | 0.0029218 | 0.0032592 | 0.3 | 1.93
+Output | 0.00022578 | 0.00024724 | 0.00030136 | 0.0 | 0.16
+Modify | 0.00018954 | 0.00021681 | 0.0002358 | 0.0 | 0.14
+Other | | 0.0006794 | | | 0.45
+
+Nlocal: 37.5 ave 45 max 31 min
+Histogram: 1 1 1 1 1 0 1 0 1 1
+Nghost: 200 ave 209 max 189 min
+Histogram: 1 0 0 0 1 4 0 0 0 2
+Neighs: 307.375 ave 514 max 115 min
+Histogram: 2 1 0 1 1 0 0 0 1 2
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
new file mode 100644
index 0000000000..bd9325dc4b
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49683273 0 0.49683273 0
+ 10 300 0.082981586 0.015479312 0.47369009 0.023141571 0.49683166 0
+ 20 300 0.16677213 0.062386358 0.40356181 0.093267605 0.49682941 0
+ 30 300 0.2506392 0.14331637 0.2825636 0.21425798 0.49682157 0
+ 40 300 0.33466673 0.53041843 0.089505208 0.79297556 0.88248077 0
+ 50 300 0.41812825 1.1948397 -0.083317439 1.7862853 1.7029679 0
+ 60 300 0.50167894 1.3915614 -0.37745551 2.0803842 1.7029287 0
+ 70 300 0.58574796 1.7061978 -0.84746071 2.5507657 1.703305 0
+ 80 300 0.6700325 20.692093 -3.32971 30.93468 27.60497 0
+ 90 300 0.75608635 48.999403 -2.1632167 73.254107 71.090891 0
+ 100 300 0.84190726 51.199785 -0.81127924 76.543678 75.732399 0
+Loop time of 0.841921 on 1 procs for 100 steps with 300 atoms
+
+Performance: 51311.251 tau/day, 118.776 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1206e-05 | 1.1206e-05 | 1.1206e-05 | 0.0 | 0.00
+Kspace | 0.835 | 0.835 | 0.835 | 0.0 | 99.18
+Neigh | 0.0040102 | 0.0040102 | 0.0040102 | 0.0 | 0.48
+Comm | 0.0012431 | 0.0012431 | 0.0012431 | 0.0 | 0.15
+Output | 0.0001545 | 0.0001545 | 0.0001545 | 0.0 | 0.02
+Modify | 0.0010202 | 0.0010202 | 0.0010202 | 0.0 | 0.12
+Other | | 0.000484 | | | 0.06
+
+Nlocal: 300 ave 300 max 300 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 381 ave 381 max 381 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2461 ave 2461 max 2461 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
new file mode 100644
index 0000000000..1e385c5fda
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49683273 0 0.49683273 0
+ 10 300 0.029647827 0.015479312 0.47369009 0.023141571 0.49683166 0
+ 20 300 0.059298515 0.062386358 0.40356181 0.093267605 0.49682941 0
+ 30 300 0.088926077 0.14331637 0.2825636 0.21425798 0.49682157 0
+ 40 300 0.11850166 0.53041843 0.089505208 0.79297556 0.88248077 0
+ 50 300 0.14820433 1.1948397 -0.083317439 1.7862853 1.7029679 0
+ 60 300 0.17807317 1.3915614 -0.37745551 2.0803842 1.7029287 0
+ 70 300 0.20803642 1.7061978 -0.84746071 2.5507657 1.703305 0
+ 80 300 0.23797083 20.692093 -3.32971 30.93468 27.60497 0
+ 90 300 0.26835561 48.999403 -2.1632167 73.254107 71.090891 0
+ 100 300 0.29766583 51.199785 -0.81127924 76.543678 75.732399 0
+Loop time of 0.297693 on 16 procs for 100 steps with 300 atoms
+
+Performance: 145116.000 tau/day, 335.917 timesteps/s
+98.8% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1683e-05 | 1.6928e-05 | 2.4557e-05 | 0.0 | 0.01
+Kspace | 0.29245 | 0.29325 | 0.29366 | 0.1 | 98.51
+Neigh | 0.00017214 | 0.00042973 | 0.0010228 | 0.0 | 0.14
+Comm | 0.0021176 | 0.0024613 | 0.0028479 | 0.5 | 0.83
+Output | 0.00028467 | 0.00033538 | 0.00041103 | 0.0 | 0.11
+Modify | 8.893e-05 | 0.00015014 | 0.00027537 | 0.0 | 0.05
+Other | | 0.001048 | | | 0.35
+
+Nlocal: 18.75 ave 33 max 6 min
+Histogram: 2 6 0 0 0 0 2 1 2 3
+Nghost: 128.875 ave 198 max 71 min
+Histogram: 7 1 0 0 0 0 0 1 5 2
+Neighs: 153.812 ave 490 max 14 min
+Histogram: 8 0 3 0 1 1 0 0 1 2
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
new file mode 100644
index 0000000000..3f54069ffd
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49683273 0 0.49683273 0
+ 10 300 0.049199581 0.015479312 0.47369009 0.023141571 0.49683166 0
+ 20 300 0.09860301 0.062386358 0.40356181 0.093267605 0.49682941 0
+ 30 300 0.14826894 0.14331637 0.2825636 0.21425798 0.49682157 0
+ 40 300 0.19769144 0.53041843 0.089505208 0.79297556 0.88248077 0
+ 50 300 0.24735355 1.1948397 -0.083317439 1.7862853 1.7029679 0
+ 60 300 0.29692888 1.3915614 -0.37745551 2.0803842 1.7029287 0
+ 70 300 0.34639764 1.7061978 -0.84746071 2.5507657 1.703305 0
+ 80 300 0.39633083 20.692093 -3.32971 30.93468 27.60497 0
+ 90 300 0.44779778 48.999403 -2.1632167 73.254107 71.090891 0
+ 100 300 0.49988627 51.199785 -0.81127924 76.543678 75.732399 0
+Loop time of 0.499909 on 2 procs for 100 steps with 300 atoms
+
+Performance: 86415.782 tau/day, 200.037 timesteps/s
+99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.0599e-06 | 1.3709e-05 | 1.8358e-05 | 0.0 | 0.00
+Kspace | 0.49314 | 0.49365 | 0.49416 | 0.1 | 98.75
+Neigh | 0.0016146 | 0.0021083 | 0.0026021 | 1.1 | 0.42
+Comm | 0.002754 | 0.0028276 | 0.0029013 | 0.1 | 0.57
+Output | 0.00015783 | 0.00019348 | 0.00022912 | 0.0 | 0.04
+Modify | 0.00049257 | 0.00049472 | 0.00049686 | 0.0 | 0.10
+Other | | 0.0006217 | | | 0.12
+
+Nlocal: 150 ave 157 max 143 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 399 ave 402 max 396 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 1230.5 ave 1756 max 705 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
new file mode 100644
index 0000000000..8b94402658
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49683273 0 0.49683273 0
+ 10 300 0.031973124 0.015479312 0.47369009 0.023141571 0.49683166 0
+ 20 300 0.064628601 0.062386358 0.40356181 0.093267605 0.49682941 0
+ 30 300 0.096747875 0.14331637 0.2825636 0.21425798 0.49682157 0
+ 40 300 0.12864041 0.53041843 0.089505208 0.79297556 0.88248077 0
+ 50 300 0.161134 1.1948397 -0.083317439 1.7862853 1.7029679 0
+ 60 300 0.19359422 1.3915614 -0.37745551 2.0803842 1.7029287 0
+ 70 300 0.22573543 1.7061978 -0.84746071 2.5507657 1.703305 0
+ 80 300 0.25922132 20.692093 -3.32971 30.93468 27.60497 0
+ 90 300 0.29452014 48.999403 -2.1632167 73.254107 71.090891 0
+ 100 300 0.33031607 51.199785 -0.81127924 76.543678 75.732399 0
+Loop time of 0.330333 on 4 procs for 100 steps with 300 atoms
+
+Performance: 130777.056 tau/day, 302.725 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.0014e-05 | 1.3471e-05 | 1.5497e-05 | 0.0 | 0.00
+Kspace | 0.32504 | 0.3255 | 0.3258 | 0.1 | 98.54
+Neigh | 0.00083303 | 0.0011883 | 0.0015609 | 0.8 | 0.36
+Comm | 0.0024087 | 0.0025436 | 0.0026674 | 0.2 | 0.77
+Output | 0.00017405 | 0.00020278 | 0.00024986 | 0.0 | 0.06
+Modify | 0.00028658 | 0.00031012 | 0.00033331 | 0.0 | 0.09
+Other | | 0.0005748 | | | 0.17
+
+Nlocal: 75 ave 81 max 69 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost: 287 ave 296 max 278 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 615.25 ave 964 max 286 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
new file mode 100644
index 0000000000..3de3c25017
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
@@ -0,0 +1,92 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul
+ 0 300 0 0 0.49683273 0 0.49683273 0
+ 10 300 0.023941755 0.015479312 0.47369009 0.023141571 0.49683166 0
+ 20 300 0.047938108 0.062386358 0.40356181 0.093267605 0.49682941 0
+ 30 300 0.071953773 0.14331637 0.2825636 0.21425798 0.49682157 0
+ 40 300 0.095941782 0.53041843 0.089505208 0.79297556 0.88248077 0
+ 50 300 0.12011361 1.1948397 -0.083317439 1.7862853 1.7029679 0
+ 60 300 0.14433384 1.3915614 -0.37745551 2.0803842 1.7029287 0
+ 70 300 0.16875505 1.7061978 -0.84746071 2.5507657 1.703305 0
+ 80 300 0.193331 20.692093 -3.32971 30.93468 27.60497 0
+ 90 300 0.21844888 48.999403 -2.1632167 73.254107 71.090891 0
+ 100 300 0.24417853 51.199785 -0.81127924 76.543678 75.732399 0
+Loop time of 0.244198 on 8 procs for 100 steps with 300 atoms
+
+Performance: 176905.349 tau/day, 409.503 timesteps/s
+99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.7752e-06 | 1.4246e-05 | 1.955e-05 | 0.0 | 0.01
+Kspace | 0.23946 | 0.23972 | 0.24009 | 0.0 | 98.17
+Neigh | 0.00049043 | 0.00071204 | 0.00095773 | 0.0 | 0.29
+Comm | 0.0025063 | 0.0026675 | 0.0027597 | 0.2 | 1.09
+Output | 0.00019646 | 0.00021604 | 0.00026321 | 0.0 | 0.09
+Modify | 0.00017905 | 0.0001913 | 0.00020766 | 0.0 | 0.08
+Other | | 0.0006773 | | | 0.28
+
+Nlocal: 37.5 ave 42 max 33 min
+Histogram: 2 1 0 1 0 0 1 0 1 2
+Nghost: 202.25 ave 212 max 194 min
+Histogram: 1 0 2 1 0 2 0 1 0 1
+Neighs: 307.625 ave 505 max 129 min
+Histogram: 3 0 0 1 1 0 0 0 1 2
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
new file mode 100644
index 0000000000..f2223064e0
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000503302 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87413076 0 1.3753199 1.4996338
+ 10 1.5001167 -0.84976141 0 1.3998642 1.4997504
+ 20 1.5002402 -0.84977464 0 1.4000363 1.499874
+ 30 1.5003611 -0.84978325 0 1.4002089 1.4999948
+ 40 1.5004736 -0.84977869 0 1.4003823 1.5001073
+ 50 1.5005703 -0.8497468 0 1.4005591 1.5002039
+ 60 1.5006418 -0.84967646 0 1.4007366 1.5002754
+ 70 1.5006785 -0.84955497 0 1.4009132 1.5003121
+ 80 1.5006711 -0.849369 0 1.4010881 1.5003047
+ 90 1.500611 -0.84910811 0 1.4012589 1.5002446
+ 100 1.5004911 -0.84870167 0 1.4014854 1.5001247
+Loop time of 46.4857 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 929.317 tau/day, 2.151 timesteps/s
+99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00023437 | 0.00024788 | 0.00026894 | 0.0 | 0.00
+Kspace | 46.476 | 46.476 | 46.476 | 0.0 | 99.98
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0062859 | 0.0067717 | 0.0072649 | 0.3 | 0.01
+Output | 0.0004127 | 0.00044075 | 0.00050807 | 0.0 | 0.00
+Modify | 0.00099325 | 0.0010343 | 0.0010939 | 0.1 | 0.00
+Other | | 0.001459 | | | 0.00
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 1265 ave 1265 max 1265 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 4096 ave 4096 max 4096 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:47
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
new file mode 100644
index 0000000000..8d3702a8b3
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000281811 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87413076 0 1.3753199 1.4996338
+ 10 1.5001095 -0.85040058 0 1.3992143 1.4997433
+ 20 1.5002258 -0.85039456 0 1.3993947 1.4998595
+ 30 1.5003395 -0.85038368 0 1.3995761 1.4999732
+ 40 1.5004452 -0.85035944 0 1.3997589 1.5000789
+ 50 1.5005354 -0.85030783 0 1.3999457 1.500169
+ 60 1.5006008 -0.85021779 0 1.4001339 1.5002344
+ 70 1.500632 -0.8500769 0 1.4003215 1.5002656
+ 80 1.5006197 -0.84987187 0 1.4005081 1.5002533
+ 90 1.5005554 -0.84959251 0 1.400691 1.500189
+ 100 1.500432 -0.84916846 0 1.4009301 1.5000657
+Loop time of 86.1477 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 501.464 tau/day, 1.161 timesteps/s
+99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.000314 | 0.00033289 | 0.00035048 | 0.0 | 0.00
+Kspace | 86.136 | 86.136 | 86.136 | 0.0 | 99.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0069821 | 0.0073864 | 0.0077834 | 0.3 | 0.01
+Output | 0.00038719 | 0.00041264 | 0.00047517 | 0.0 | 0.00
+Modify | 0.0018711 | 0.0019454 | 0.0020905 | 0.1 | 0.00
+Other | | 0.001762 | | | 0.00
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 1685 ave 1685 max 1685 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 8192 ave 8192 max 8192 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:28
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
new file mode 100644
index 0000000000..0749de3832
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 1 by 1 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000584364 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87378819 0 1.3756625 1.4996338
+ 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
+ 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
+ 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
+ 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
+ 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
+ 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
+ 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
+ 80 1.4995842 -0.87316464 0 1.3756624 1.499218
+ 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
+ 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
+Loop time of 5.26537 on 1 procs for 100 steps with 4096 atoms
+
+Performance: 8204.550 tau/day, 18.992 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0011349 | 0.0011349 | 0.0011349 | 0.0 | 0.02
+Kspace | 5.2375 | 5.2375 | 5.2375 | 0.0 | 99.47
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0090225 | 0.0090225 | 0.0090225 | 0.0 | 0.17
+Output | 0.0004127 | 0.0004127 | 0.0004127 | 0.0 | 0.01
+Modify | 0.012851 | 0.012851 | 0.012851 | 0.0 | 0.24
+Other | | 0.004441 | | | 0.08
+
+Nlocal: 4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 5165 ave 5165 max 5165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 65536 ave 65536 max 65536 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
new file mode 100644
index 0000000000..6af26f7b81
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000507593 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87378819 0 1.3756625 1.4996338
+ 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
+ 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
+ 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
+ 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
+ 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
+ 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
+ 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
+ 80 1.4995842 -0.87316464 0 1.3756624 1.499218
+ 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
+ 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
+Loop time of 0.570389 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 75737.813 tau/day, 175.319 timesteps/s
+99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00024104 | 0.00025283 | 0.00029206 | 0.0 | 0.04
+Kspace | 0.56153 | 0.56176 | 0.56189 | 0.0 | 98.49
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0055203 | 0.0057825 | 0.0061858 | 0.2 | 1.01
+Output | 0.00038505 | 0.00040831 | 0.00048184 | 0.0 | 0.07
+Modify | 0.00096965 | 0.00099662 | 0.0010159 | 0.0 | 0.17
+Other | | 0.001192 | | | 0.21
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 1265 ave 1265 max 1265 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 4096 ave 4096 max 4096 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
new file mode 100644
index 0000000000..bcc61485ca
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 1 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000455141 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87378819 0 1.3756625 1.4996338
+ 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
+ 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
+ 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
+ 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
+ 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
+ 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
+ 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
+ 80 1.4995842 -0.87316464 0 1.3756624 1.499218
+ 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
+ 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
+Loop time of 2.73149 on 2 procs for 100 steps with 4096 atoms
+
+Performance: 15815.560 tau/day, 36.610 timesteps/s
+99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00070763 | 0.00071537 | 0.00072312 | 0.0 | 0.03
+Kspace | 2.7111 | 2.7112 | 2.7112 | 0.0 | 99.26
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0096555 | 0.0097489 | 0.0098424 | 0.1 | 0.36
+Output | 0.00036025 | 0.0003823 | 0.00040436 | 0.0 | 0.01
+Modify | 0.0063472 | 0.0064594 | 0.0065715 | 0.1 | 0.24
+Other | | 0.00299 | | | 0.11
+
+Nlocal: 2048 ave 2048 max 2048 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 3685 ave 3685 max 3685 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 32768 ave 32768 max 32768 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
new file mode 100644
index 0000000000..54e010c8fd
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000329494 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87378819 0 1.3756625 1.4996338
+ 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
+ 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
+ 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
+ 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
+ 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
+ 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
+ 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
+ 80 1.4995842 -0.87316464 0 1.3756624 1.499218
+ 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
+ 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
+Loop time of 1.53742 on 4 procs for 100 steps with 4096 atoms
+
+Performance: 28099.005 tau/day, 65.044 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00044894 | 0.00045562 | 0.0004611 | 0.0 | 0.03
+Kspace | 1.5223 | 1.5225 | 1.5225 | 0.0 | 99.03
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0085156 | 0.0086777 | 0.0088782 | 0.1 | 0.56
+Output | 0.00034738 | 0.0003686 | 0.0004015 | 0.0 | 0.02
+Modify | 0.0032606 | 0.0033693 | 0.0034289 | 0.1 | 0.22
+Other | | 0.002084 | | | 0.14
+
+Nlocal: 1024 ave 1024 max 1024 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 2525 ave 2525 max 2525 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 16384 ave 16384 max 16384 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
new file mode 100644
index 0000000000..d5d38d6804
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000284672 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87378819 0 1.3756625 1.4996338
+ 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
+ 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
+ 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
+ 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
+ 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
+ 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
+ 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
+ 80 1.4995842 -0.87316464 0 1.3756624 1.499218
+ 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
+ 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
+Loop time of 0.902102 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 47888.152 tau/day, 110.852 timesteps/s
+99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00030732 | 0.00031349 | 0.00032663 | 0.0 | 0.03
+Kspace | 0.89112 | 0.89138 | 0.8916 | 0.0 | 98.81
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0064399 | 0.0066807 | 0.0070164 | 0.2 | 0.74
+Output | 0.00034571 | 0.00036666 | 0.00041723 | 0.0 | 0.04
+Modify | 0.0018673 | 0.0019273 | 0.0020192 | 0.1 | 0.21
+Other | | 0.001431 | | | 0.16
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 1685 ave 1685 max 1685 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 8192 ave 8192 max 8192 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
new file mode 100644
index 0000000000..d8b782e41d
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 1 by 1 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000631332 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87394226 0 1.3755084 1.4996338
+ 10 1.5000144 -0.87365638 0 1.375816 1.4996482
+ 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
+ 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
+ 40 1.5000313 -0.8736496 0 1.375848 1.4996651
+ 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
+ 60 1.4999432 -0.87350118 0 1.3758644 1.499577
+ 70 1.499838 -0.87333517 0 1.3758726 1.4994719
+ 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
+ 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
+ 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
+Loop time of 9.59682 on 1 procs for 100 steps with 4096 atoms
+
+Performance: 4501.489 tau/day, 10.420 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0011375 | 0.0011375 | 0.0011375 | 0.0 | 0.01
+Kspace | 9.5688 | 9.5688 | 9.5688 | 0.0 | 99.71
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.009017 | 0.009017 | 0.009017 | 0.0 | 0.09
+Output | 0.0004344 | 0.0004344 | 0.0004344 | 0.0 | 0.00
+Modify | 0.012987 | 0.012987 | 0.012987 | 0.0 | 0.14
+Other | | 0.004481 | | | 0.05
+
+Nlocal: 4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 5165 ave 5165 max 5165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 65536 ave 65536 max 65536 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:10
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
new file mode 100644
index 0000000000..43bcfb6770
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000500917 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87394226 0 1.3755084 1.4996338
+ 10 1.5000144 -0.87365638 0 1.375816 1.4996482
+ 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
+ 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
+ 40 1.5000313 -0.8736496 0 1.375848 1.4996651
+ 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
+ 60 1.4999432 -0.87350118 0 1.3758644 1.499577
+ 70 1.499838 -0.87333517 0 1.3758726 1.4994719
+ 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
+ 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
+ 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
+Loop time of 1.20528 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 35842.175 tau/day, 82.968 timesteps/s
+99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00021839 | 0.00025332 | 0.00029278 | 0.0 | 0.02
+Kspace | 1.1945 | 1.1948 | 1.195 | 0.0 | 99.13
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0066545 | 0.0069329 | 0.0072389 | 0.2 | 0.58
+Output | 0.0003922 | 0.00042732 | 0.00054955 | 0.0 | 0.04
+Modify | 0.0010166 | 0.0011965 | 0.0014412 | 0.3 | 0.10
+Other | | 0.001724 | | | 0.14
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 1265 ave 1265 max 1265 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 4096 ave 4096 max 4096 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
new file mode 100644
index 0000000000..9f4f44153b
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 1 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.00044775 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87394226 0 1.3755084 1.4996338
+ 10 1.5000144 -0.87365638 0 1.375816 1.4996482
+ 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
+ 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
+ 40 1.5000313 -0.8736496 0 1.375848 1.4996651
+ 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
+ 60 1.4999432 -0.87350118 0 1.3758644 1.499577
+ 70 1.499838 -0.87333517 0 1.3758726 1.4994719
+ 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
+ 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
+ 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
+Loop time of 5.14681 on 2 procs for 100 steps with 4096 atoms
+
+Performance: 8393.542 tau/day, 19.429 timesteps/s
+99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00070882 | 0.00072873 | 0.00074863 | 0.0 | 0.01
+Kspace | 5.1257 | 5.1258 | 5.1258 | 0.0 | 99.59
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.010188 | 0.010291 | 0.010394 | 0.1 | 0.20
+Output | 0.00042391 | 0.00044322 | 0.00046253 | 0.0 | 0.01
+Modify | 0.0063772 | 0.006551 | 0.0067248 | 0.2 | 0.13
+Other | | 0.003026 | | | 0.06
+
+Nlocal: 2048 ave 2048 max 2048 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 3685 ave 3685 max 3685 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 32768 ave 32768 max 32768 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
new file mode 100644
index 0000000000..d6a78bb193
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 1 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000317335 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87394226 0 1.3755084 1.4996338
+ 10 1.5000144 -0.87365638 0 1.375816 1.4996482
+ 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
+ 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
+ 40 1.5000313 -0.8736496 0 1.375848 1.4996651
+ 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
+ 60 1.4999432 -0.87350118 0 1.3758644 1.499577
+ 70 1.499838 -0.87333517 0 1.3758726 1.4994719
+ 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
+ 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
+ 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
+Loop time of 2.94274 on 4 procs for 100 steps with 4096 atoms
+
+Performance: 14680.187 tau/day, 33.982 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00048852 | 0.00049287 | 0.00050163 | 0.0 | 0.02
+Kspace | 2.9277 | 2.9279 | 2.928 | 0.0 | 99.49
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0081494 | 0.0083126 | 0.0084655 | 0.1 | 0.28
+Output | 0.00034475 | 0.00040233 | 0.00043464 | 0.0 | 0.01
+Modify | 0.0034239 | 0.0035145 | 0.0036252 | 0.1 | 0.12
+Other | | 0.00216 | | | 0.07
+
+Nlocal: 1024 ave 1024 max 1024 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 2525 ave 2525 max 2525 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 16384 ave 16384 max 16384 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
new file mode 100644
index 0000000000..70716bbcbd
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
@@ -0,0 +1,102 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (2 2 2)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (16 16 16)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000422239 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 16 16 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.87394226 0 1.3755084 1.4996338
+ 10 1.5000144 -0.87365638 0 1.375816 1.4996482
+ 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
+ 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
+ 40 1.5000313 -0.8736496 0 1.375848 1.4996651
+ 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
+ 60 1.4999432 -0.87350118 0 1.3758644 1.499577
+ 70 1.499838 -0.87333517 0 1.3758726 1.4994719
+ 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
+ 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
+ 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
+Loop time of 1.75933 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 24554.819 tau/day, 56.840 timesteps/s
+99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00030684 | 0.00031838 | 0.00032926 | 0.0 | 0.02
+Kspace | 1.7474 | 1.7477 | 1.748 | 0.0 | 99.34
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0068667 | 0.0072413 | 0.0075011 | 0.2 | 0.41
+Output | 0.00036955 | 0.00038695 | 0.00044942 | 0.0 | 0.02
+Modify | 0.0018206 | 0.0019438 | 0.0020213 | 0.1 | 0.11
+Other | | 0.001739 | | | 0.10
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 1685 ave 1685 max 1685 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 8192 ave 8192 max 8192 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 65536
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
new file mode 100644
index 0000000000..37d12bb37d
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
@@ -0,0 +1,105 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777512 0 272.51604 0.17489112
+ 5 286.36222 -4.382053 0 424.73173 0.26957567
+ 6 481.42206 -4.3095567 0 717.1014 0.4532011
+ 7 488.59167 -3.8685194 0 728.2861 0.45995044
+ 8 497.85287 -3.0417966 0 742.99073 0.46866874
+ 9 499.61615 -3.419003 0 745.2558 0.47032866
+ 10 502.63684 -2.8360961 0 750.36521 0.47317227
+ 11 504.4846 -2.7628105 0 753.20736 0.47491172
+ 12 506.54485 -2.8460356 0 756.21142 0.47685119
+ 13 508.27211 -2.730935 0 758.91482 0.4784772
+ 14 510.57045 -2.6094877 0 762.48033 0.48064081
+ 15 513.14798 -2.7150827 0 766.23717 0.48306726
+ 16 515.78124 -2.3961811 0 770.50201 0.48554615
+ 17 515.70265 -2.2982683 0 770.48215 0.48547216
+ 18 515.7081 -2.1515983 0 770.63699 0.4854773
+ 19 515.74906 -2.0581436 0 770.79182 0.48551586
+ 20 515.70883 -1.8922577 0 770.89742 0.48547798
+Loop time of 0.52055 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 16597.836 tau/day, 38.421 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
+Kspace | 0.35879 | 0.35879 | 0.35879 | 0.0 | 68.93
+Neigh | 0.15946 | 0.15946 | 0.15946 | 0.0 | 30.63
+Comm | 0.00024056 | 0.00024056 | 0.00024056 | 0.0 | 0.05
+Output | 0.00034761 | 0.00034761 | 0.00034761 | 0.0 | 0.07
+Modify | 0.00071192 | 0.00071192 | 0.00071192 | 0.0 | 0.14
+Other | | 0.0007269 | | | 0.14
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 247817 ave 247817 max 247817 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
new file mode 100644
index 0000000000..7a22e62bce
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
@@ -0,0 +1,105 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777512 0 272.51604 0.17489112
+ 5 286.36222 -4.382053 0 424.73173 0.26957567
+ 6 481.42206 -4.3095567 0 717.1014 0.4532011
+ 7 488.59167 -3.8685194 0 728.2861 0.45995044
+ 8 497.85287 -3.0417966 0 742.99073 0.46866874
+ 9 499.61615 -3.419003 0 745.2558 0.47032866
+ 10 502.63684 -2.8360961 0 750.36521 0.47317227
+ 11 504.4846 -2.7628105 0 753.20736 0.47491172
+ 12 506.54485 -2.8460356 0 756.21142 0.47685119
+ 13 508.27211 -2.730935 0 758.91482 0.4784772
+ 14 510.57045 -2.6094877 0 762.48033 0.48064081
+ 15 513.14798 -2.7150827 0 766.23717 0.48306726
+ 16 515.78124 -2.3961811 0 770.50201 0.48554615
+ 17 515.70265 -2.2982683 0 770.48215 0.48547216
+ 18 515.7081 -2.1515983 0 770.63699 0.4854773
+ 19 515.74906 -2.0581436 0 770.79182 0.48551586
+ 20 515.70883 -1.8922577 0 770.89742 0.48547798
+Loop time of 0.330519 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 26140.700 tau/day, 60.511 timesteps/s
+99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002749 | 0.00027692 | 0.00027895 | 0.0 | 0.08
+Kspace | 0.21565 | 0.24173 | 0.26782 | 5.3 | 73.14
+Neigh | 0.058644 | 0.084906 | 0.11117 | 9.0 | 25.69
+Comm | 0.002033 | 0.0022832 | 0.0025334 | 0.5 | 0.69
+Output | 0.00035667 | 0.0004549 | 0.00055313 | 0.0 | 0.14
+Modify | 0.0004704 | 0.00050521 | 0.00054002 | 0.0 | 0.15
+Other | | 0.0003613 | | | 0.11
+
+Nlocal: 500 ave 516 max 484 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 456.5 ave 475 max 438 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 123908 ave 172139 max 75678 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
new file mode 100644
index 0000000000..51d0f8c47e
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
@@ -0,0 +1,105 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777512 0 272.51604 0.17489112
+ 5 286.36222 -4.382053 0 424.73173 0.26957567
+ 6 481.42206 -4.3095567 0 717.1014 0.4532011
+ 7 488.59167 -3.8685194 0 728.2861 0.45995044
+ 8 497.85287 -3.0417966 0 742.99073 0.46866874
+ 9 499.61615 -3.419003 0 745.2558 0.47032866
+ 10 502.63684 -2.8360961 0 750.36521 0.47317227
+ 11 504.4846 -2.7628105 0 753.20736 0.47491172
+ 12 506.54485 -2.8460356 0 756.21142 0.47685119
+ 13 508.27211 -2.730935 0 758.91482 0.4784772
+ 14 510.57045 -2.6094877 0 762.48033 0.48064081
+ 15 513.14798 -2.7150827 0 766.23717 0.48306726
+ 16 515.78124 -2.3961811 0 770.50201 0.48554615
+ 17 515.70265 -2.2982683 0 770.48215 0.48547216
+ 18 515.7081 -2.1515983 0 770.63699 0.4854773
+ 19 515.74906 -2.0581436 0 770.79182 0.48551586
+ 20 515.70883 -1.8922577 0 770.89742 0.48547798
+Loop time of 0.197141 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 43826.435 tau/day, 101.450 timesteps/s
+99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002718 | 0.00027621 | 0.00028539 | 0.0 | 0.14
+Kspace | 0.12861 | 0.14654 | 0.16542 | 3.7 | 74.33
+Neigh | 0.027906 | 0.046895 | 0.064943 | 6.6 | 23.79
+Comm | 0.0022087 | 0.0024236 | 0.0026295 | 0.4 | 1.23
+Output | 0.0003252 | 0.00044608 | 0.0006001 | 0.0 | 0.23
+Modify | 0.00016618 | 0.0001756 | 0.00018811 | 0.0 | 0.09
+Other | | 0.0003839 | | | 0.19
+
+Nlocal: 250 ave 259 max 238 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 672.25 ave 683 max 663 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 61954.2 ave 97157 max 25016 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
new file mode 100644
index 0000000000..90119a101b
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
@@ -0,0 +1,105 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777512 0 272.51604 0.17489112
+ 5 286.36222 -4.382053 0 424.73173 0.26957567
+ 6 481.42206 -4.3095567 0 717.1014 0.4532011
+ 7 488.59167 -3.8685194 0 728.2861 0.45995044
+ 8 497.85287 -3.0417966 0 742.99073 0.46866874
+ 9 499.61615 -3.419003 0 745.2558 0.47032866
+ 10 502.63684 -2.8360961 0 750.36521 0.47317227
+ 11 504.4846 -2.7628105 0 753.20736 0.47491172
+ 12 506.54485 -2.8460356 0 756.21142 0.47685119
+ 13 508.27211 -2.730935 0 758.91482 0.4784772
+ 14 510.57045 -2.6094877 0 762.48033 0.48064081
+ 15 513.14798 -2.7150827 0 766.23717 0.48306726
+ 16 515.78124 -2.3961811 0 770.50201 0.48554615
+ 17 515.70265 -2.2982683 0 770.48215 0.48547216
+ 18 515.7081 -2.1515983 0 770.63699 0.4854773
+ 19 515.74906 -2.0581436 0 770.79182 0.48551586
+ 20 515.70883 -1.8922577 0 770.89742 0.48547798
+Loop time of 0.107014 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 80736.875 tau/day, 186.891 timesteps/s
+98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00027704 | 0.00029281 | 0.00035691 | 0.0 | 0.27
+Kspace | 0.069458 | 0.07877 | 0.089146 | 2.5 | 73.61
+Neigh | 0.013525 | 0.024156 | 0.033524 | 4.7 | 22.57
+Comm | 0.002552 | 0.0029828 | 0.0033691 | 0.5 | 2.79
+Output | 0.00037909 | 0.00051123 | 0.00070429 | 0.0 | 0.48
+Modify | 8.9645e-05 | 9.5487e-05 | 0.000103 | 0.0 | 0.09
+Other | | 0.0002059 | | | 0.19
+
+Nlocal: 125 ave 133 max 113 min
+Histogram: 2 0 0 0 0 1 1 0 2 2
+Nghost: 773.625 ave 788 max 764 min
+Histogram: 1 1 2 1 1 0 0 0 1 1
+Neighs: 30977.1 ave 50690 max 10447 min
+Histogram: 1 1 1 0 1 1 0 0 2 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
new file mode 100644
index 0000000000..432ea72b67
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
@@ -0,0 +1,109 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.00141207
+ 1 18.780412 -10.770009 0 17.372438 0.017679504
+ 2 65.294131 -11.084501 0 86.758754 0.06146659
+ 3 121.92555 -7.0612033 0 175.64423 0.11477827
+ 4 185.71165 -5.8781334 0 272.41077 0.17482523
+ 5 286.28339 -4.3800108 0 424.61565 0.26950146
+ 6 481.28097 -4.3052012 0 716.89433 0.45306828
+ 7 487.26022 -3.8672741 0 726.29216 0.45869703
+ 8 493.65478 -3.0242687 0 736.71742 0.46471675
+ 9 495.66203 -3.4336343 0 739.31592 0.46660633
+ 10 498.41831 -2.8837072 0 743.99613 0.46920104
+ 11 499.20944 -2.7724783 0 745.29287 0.46994579
+ 12 500.97345 -2.8281484 0 747.88057 0.4716064
+ 13 507.46412 -2.7752775 0 757.65971 0.47771658
+ 14 525.35729 -2.5749814 0 784.67292 0.49456085
+ 15 563.9578 -2.9982381 0 842.09253 0.5308986
+ 16 645.47602 -2.5519203 0 964.69389 0.60763822
+ 17 647.09276 -2.2568468 0 967.41166 0.60916019
+ 18 647.12596 -2.2791003 0 967.43915 0.60919144
+ 19 647.24862 -2.2495226 0 967.65253 0.60930691
+ 20 647.51175 -2.0239179 0 968.27244 0.60955462
+Loop time of 0.644143 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 13413.173 tau/day, 31.049 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00027657 | 0.00027657 | 0.00027657 | 0.0 | 0.04
+Kspace | 0.4788 | 0.4788 | 0.4788 | 0.0 | 74.33
+Neigh | 0.16279 | 0.16279 | 0.16279 | 0.0 | 25.27
+Comm | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.03
+Output | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.09
+Modify | 0.00075102 | 0.00075102 | 0.00075102 | 0.0 | 0.12
+Other | | 0.000757 | | | 0.12
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 244342 ave 244342 max 244342 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
new file mode 100644
index 0000000000..4d4b1100e3
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
@@ -0,0 +1,109 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.00141207
+ 1 18.780412 -10.770009 0 17.372438 0.017679504
+ 2 65.294131 -11.084501 0 86.758754 0.06146659
+ 3 121.92555 -7.0612033 0 175.64423 0.11477827
+ 4 185.71165 -5.8781334 0 272.41077 0.17482523
+ 5 286.28339 -4.3800108 0 424.61565 0.26950146
+ 6 481.28097 -4.3052012 0 716.89433 0.45306828
+ 7 487.26022 -3.8672741 0 726.29216 0.45869703
+ 8 493.65478 -3.0242687 0 736.71742 0.46471675
+ 9 495.66203 -3.4336343 0 739.31592 0.46660633
+ 10 498.41831 -2.8837072 0 743.99613 0.46920104
+ 11 499.20944 -2.7724783 0 745.29287 0.46994579
+ 12 500.97345 -2.8281484 0 747.88057 0.4716064
+ 13 507.46412 -2.7752775 0 757.65971 0.47771658
+ 14 525.35729 -2.5749814 0 784.67292 0.49456085
+ 15 563.9578 -2.9982381 0 842.09253 0.5308986
+ 16 645.47602 -2.5519203 0 964.69389 0.60763822
+ 17 647.09276 -2.2568468 0 967.41166 0.60916019
+ 18 647.12596 -2.2791003 0 967.43915 0.60919144
+ 19 647.24862 -2.2495226 0 967.65253 0.60930691
+ 20 647.51175 -2.0239179 0 968.27244 0.60955462
+Loop time of 0.563049 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 15345.024 tau/day, 35.521 timesteps/s
+99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00024986 | 0.00026596 | 0.00028205 | 0.0 | 0.05
+Kspace | 0.45103 | 0.47692 | 0.50281 | 3.7 | 84.70
+Neigh | 0.055771 | 0.081813 | 0.10785 | 9.1 | 14.53
+Comm | 0.0022206 | 0.0024507 | 0.0026808 | 0.5 | 0.44
+Output | 0.00050044 | 0.00061882 | 0.00073719 | 0.0 | 0.11
+Modify | 0.00029945 | 0.00044227 | 0.00058508 | 0.0 | 0.08
+Other | | 0.0005381 | | | 0.10
+
+Nlocal: 500 ave 509 max 491 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 455.5 ave 467 max 444 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 122171 ave 171834 max 72508 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
new file mode 100644
index 0000000000..9634a0174b
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
@@ -0,0 +1,109 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.00141207
+ 1 18.780412 -10.770009 0 17.372438 0.017679504
+ 2 65.294131 -11.084501 0 86.758754 0.06146659
+ 3 121.92555 -7.0612033 0 175.64423 0.11477827
+ 4 185.71165 -5.8781334 0 272.41077 0.17482523
+ 5 286.28339 -4.3800108 0 424.61565 0.26950146
+ 6 481.28097 -4.3052012 0 716.89433 0.45306828
+ 7 487.26022 -3.8672741 0 726.29216 0.45869703
+ 8 493.65478 -3.0242687 0 736.71742 0.46471675
+ 9 495.66203 -3.4336343 0 739.31592 0.46660633
+ 10 498.41831 -2.8837072 0 743.99613 0.46920104
+ 11 499.20944 -2.7724783 0 745.29287 0.46994579
+ 12 500.97345 -2.8281484 0 747.88057 0.4716064
+ 13 507.46412 -2.7752775 0 757.65971 0.47771658
+ 14 525.35729 -2.5749814 0 784.67292 0.49456085
+ 15 563.9578 -2.9982381 0 842.09253 0.5308986
+ 16 645.47602 -2.5519203 0 964.69389 0.60763822
+ 17 647.09276 -2.2568468 0 967.41166 0.60916019
+ 18 647.12596 -2.2791003 0 967.43915 0.60919144
+ 19 647.24862 -2.2495226 0 967.65253 0.60930691
+ 20 647.51175 -2.0239179 0 968.27244 0.60955462
+Loop time of 0.508149 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 17002.884 tau/day, 39.359 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00024509 | 0.00026453 | 0.00028753 | 0.0 | 0.05
+Kspace | 0.43933 | 0.45836 | 0.47734 | 2.2 | 90.20
+Neigh | 0.025956 | 0.045068 | 0.064242 | 7.2 | 8.87
+Comm | 0.002799 | 0.0030612 | 0.0033174 | 0.4 | 0.60
+Output | 0.00047231 | 0.00058293 | 0.00076509 | 0.0 | 0.11
+Modify | 0.00016856 | 0.0002442 | 0.00042009 | 0.0 | 0.05
+Other | | 0.0005655 | | | 0.11
+
+Nlocal: 250 ave 259 max 240 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 668.75 ave 679 max 657 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs: 61085.5 ave 95363 max 24964 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
new file mode 100644
index 0000000000..a6a020b031
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
@@ -0,0 +1,109 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...3
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.00141207
+ 1 18.780412 -10.770009 0 17.372438 0.017679504
+ 2 65.294131 -11.084501 0 86.758754 0.06146659
+ 3 121.92555 -7.0612033 0 175.64423 0.11477827
+ 4 185.71165 -5.8781334 0 272.41077 0.17482523
+ 5 286.28339 -4.3800108 0 424.61565 0.26950146
+ 6 481.28097 -4.3052012 0 716.89433 0.45306828
+ 7 487.26022 -3.8672741 0 726.29216 0.45869703
+ 8 493.65478 -3.0242687 0 736.71742 0.46471675
+ 9 495.66203 -3.4336343 0 739.31592 0.46660633
+ 10 498.41831 -2.8837072 0 743.99613 0.46920104
+ 11 499.20944 -2.7724783 0 745.29287 0.46994579
+ 12 500.97345 -2.8281484 0 747.88057 0.4716064
+ 13 507.46412 -2.7752775 0 757.65971 0.47771658
+ 14 525.35729 -2.5749814 0 784.67292 0.49456085
+ 15 563.9578 -2.9982381 0 842.09253 0.5308986
+ 16 645.47602 -2.5519203 0 964.69389 0.60763822
+ 17 647.09276 -2.2568468 0 967.41166 0.60916019
+ 18 647.12596 -2.2791003 0 967.43915 0.60919144
+ 19 647.24862 -2.2495226 0 967.65253 0.60930691
+ 20 647.51175 -2.0239179 0 968.27244 0.60955462
+Loop time of 0.494261 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 17480.630 tau/day, 40.464 timesteps/s
+99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00027752 | 0.00030088 | 0.0003736 | 0.0 | 0.06
+Kspace | 0.45443 | 0.46295 | 0.47316 | 1.0 | 93.67
+Neigh | 0.014408 | 0.02515 | 0.034048 | 4.6 | 5.09
+Comm | 0.0036254 | 0.0041741 | 0.0048032 | 0.6 | 0.84
+Output | 0.00072742 | 0.0009357 | 0.0012984 | 0.0 | 0.19
+Modify | 0.00011778 | 0.00015756 | 0.00019836 | 0.0 | 0.03
+Other | | 0.000589 | | | 0.12
+
+Nlocal: 125 ave 137 max 111 min
+Histogram: 1 1 0 0 0 2 2 1 0 1
+Nghost: 768.875 ave 788 max 761 min
+Histogram: 4 0 2 0 0 0 1 0 0 1
+Neighs: 30542.8 ave 48077 max 10011 min
+Histogram: 1 1 1 0 1 1 0 0 0 3
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
new file mode 100644
index 0000000000..f9192cdfaf
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
@@ -0,0 +1,107 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777511 0 272.51603 0.17489112
+ 5 286.36221 -4.3820531 0 424.73172 0.26957566
+ 6 481.42203 -4.3095567 0 717.10136 0.45320108
+ 7 488.59165 -3.8685193 0 728.28607 0.45995042
+ 8 497.85288 -3.0417938 0 742.99075 0.46866875
+ 9 499.61619 -3.4190063 0 745.25585 0.47032869
+ 10 502.63691 -2.8360951 0 750.36531 0.47317234
+ 11 504.4847 -2.7628089 0 753.20751 0.47491181
+ 12 506.54494 -2.8460319 0 756.21157 0.47685128
+ 13 508.2722 -2.7309328 0 758.91497 0.47847729
+ 14 510.57053 -2.6094792 0 762.48045 0.48064089
+ 15 513.14804 -2.7150819 0 766.23726 0.48306731
+ 16 515.78127 -2.3961749 0 770.50206 0.48554618
+ 17 515.70267 -2.2982581 0 770.48219 0.48547219
+ 18 515.70813 -2.1516075 0 770.63702 0.48547732
+ 19 515.74908 -2.0581483 0 770.79185 0.48551588
+ 20 515.70881 -1.892235 0 770.89742 0.48547797
+Loop time of 1.34132 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 6441.409 tau/day, 14.911 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00028849 | 0.00028849 | 0.00028849 | 0.0 | 0.02
+Kspace | 1.1744 | 1.1744 | 1.1744 | 0.0 | 87.56
+Neigh | 0.16435 | 0.16435 | 0.16435 | 0.0 | 12.25
+Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02
+Output | 0.00051928 | 0.00051928 | 0.00051928 | 0.0 | 0.04
+Modify | 0.00079513 | 0.00079513 | 0.00079513 | 0.0 | 0.06
+Other | | 0.0007439 | | | 0.06
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 247817 ave 247817 max 247817 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
new file mode 100644
index 0000000000..4db3e28dbf
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
@@ -0,0 +1,107 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777511 0 272.51603 0.17489112
+ 5 286.36221 -4.3820531 0 424.73172 0.26957566
+ 6 481.42203 -4.3095567 0 717.10136 0.45320108
+ 7 488.59165 -3.8685193 0 728.28607 0.45995042
+ 8 497.85288 -3.0417938 0 742.99075 0.46866875
+ 9 499.61619 -3.4190063 0 745.25585 0.47032869
+ 10 502.63691 -2.8360951 0 750.36531 0.47317234
+ 11 504.4847 -2.7628089 0 753.20751 0.47491181
+ 12 506.54494 -2.8460319 0 756.21157 0.47685128
+ 13 508.2722 -2.7309328 0 758.91497 0.47847729
+ 14 510.57053 -2.6094792 0 762.48045 0.48064089
+ 15 513.14804 -2.7150819 0 766.23726 0.48306731
+ 16 515.78127 -2.3961749 0 770.50206 0.48554618
+ 17 515.70267 -2.2982581 0 770.48219 0.48547219
+ 18 515.70813 -2.1516075 0 770.63702 0.48547732
+ 19 515.74908 -2.0581483 0 770.79185 0.48551588
+ 20 515.70881 -1.892235 0 770.89742 0.48547797
+Loop time of 0.858675 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 10062.016 tau/day, 23.292 timesteps/s
+100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00026321 | 0.00026667 | 0.00027013 | 0.0 | 0.03
+Kspace | 0.74531 | 0.77182 | 0.79833 | 3.0 | 89.89
+Neigh | 0.055915 | 0.082578 | 0.10924 | 9.3 | 9.62
+Comm | 0.0021703 | 0.002401 | 0.0026317 | 0.5 | 0.28
+Output | 0.00048423 | 0.00061262 | 0.000741 | 0.0 | 0.07
+Modify | 0.00034285 | 0.0004636 | 0.00058436 | 0.0 | 0.05
+Other | | 0.0005329 | | | 0.06
+
+Nlocal: 500 ave 516 max 484 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 456.5 ave 475 max 438 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 123908 ave 172139 max 75678 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
new file mode 100644
index 0000000000..3a2d653106
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
@@ -0,0 +1,107 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777511 0 272.51603 0.17489112
+ 5 286.36221 -4.3820531 0 424.73172 0.26957566
+ 6 481.42203 -4.3095567 0 717.10136 0.45320108
+ 7 488.59165 -3.8685193 0 728.28607 0.45995042
+ 8 497.85288 -3.0417938 0 742.99075 0.46866875
+ 9 499.61619 -3.4190063 0 745.25585 0.47032869
+ 10 502.63691 -2.8360951 0 750.36531 0.47317234
+ 11 504.4847 -2.7628089 0 753.20751 0.47491181
+ 12 506.54494 -2.8460319 0 756.21157 0.47685128
+ 13 508.2722 -2.7309328 0 758.91497 0.47847729
+ 14 510.57053 -2.6094792 0 762.48045 0.48064089
+ 15 513.14804 -2.7150819 0 766.23726 0.48306731
+ 16 515.78127 -2.3961749 0 770.50206 0.48554618
+ 17 515.70267 -2.2982581 0 770.48219 0.48547219
+ 18 515.70813 -2.1516075 0 770.63702 0.48547732
+ 19 515.74908 -2.0581483 0 770.79185 0.48551588
+ 20 515.70881 -1.892235 0 770.89742 0.48547797
+Loop time of 0.540235 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 15993.051 tau/day, 37.021 timesteps/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00025725 | 0.00028253 | 0.00031233 | 0.0 | 0.05
+Kspace | 0.47152 | 0.48989 | 0.50709 | 1.9 | 90.68
+Neigh | 0.028196 | 0.045694 | 0.064338 | 6.3 | 8.46
+Comm | 0.0026579 | 0.003028 | 0.0033965 | 0.5 | 0.56
+Output | 0.00049663 | 0.00064254 | 0.00084853 | 0.0 | 0.12
+Modify | 0.00019264 | 0.0002293 | 0.00030923 | 0.0 | 0.04
+Other | | 0.0004709 | | | 0.09
+
+Nlocal: 250 ave 259 max 238 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 672.25 ave 683 max 663 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 61954.2 ave 97157 max 25016 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
new file mode 100644
index 0000000000..08e68531a9
--- /dev/null
+++ b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
@@ -0,0 +1,107 @@
+LAMMPS (29 Jun 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.00141207
+ 1 18.780041 -10.770002 0 17.371889 0.017679155
+ 2 65.289192 -11.084705 0 86.751149 0.06146194
+ 3 121.92987 -7.0625759 0 175.64933 0.11478234
+ 4 185.78164 -5.8777511 0 272.51603 0.17489112
+ 5 286.36221 -4.3820531 0 424.73172 0.26957566
+ 6 481.42203 -4.3095567 0 717.10136 0.45320108
+ 7 488.59165 -3.8685193 0 728.28607 0.45995042
+ 8 497.85288 -3.0417938 0 742.99075 0.46866875
+ 9 499.61619 -3.4190063 0 745.25585 0.47032869
+ 10 502.63691 -2.8360951 0 750.36531 0.47317234
+ 11 504.4847 -2.7628089 0 753.20751 0.47491181
+ 12 506.54494 -2.8460319 0 756.21157 0.47685128
+ 13 508.2722 -2.7309328 0 758.91497 0.47847729
+ 14 510.57053 -2.6094792 0 762.48045 0.48064089
+ 15 513.14804 -2.7150819 0 766.23726 0.48306731
+ 16 515.78127 -2.3961749 0 770.50206 0.48554618
+ 17 515.70267 -2.2982581 0 770.48219 0.48547219
+ 18 515.70813 -2.1516075 0 770.63702 0.48547732
+ 19 515.74908 -2.0581483 0 770.79185 0.48551588
+ 20 515.70881 -1.892235 0 770.89742 0.48547797
+Loop time of 0.317433 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 27218.342 tau/day, 63.005 timesteps/s
+99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00027013 | 0.00028479 | 0.00029206 | 0.0 | 0.09
+Kspace | 0.27742 | 0.28666 | 0.29702 | 1.4 | 90.31
+Neigh | 0.014795 | 0.025382 | 0.03481 | 4.8 | 8.00
+Comm | 0.0034907 | 0.0038758 | 0.0042439 | 0.5 | 1.22
+Output | 0.00055361 | 0.00073573 | 0.0010755 | 0.0 | 0.23
+Modify | 0.00012279 | 0.00014156 | 0.00016165 | 0.0 | 0.04
+Other | | 0.0003535 | | | 0.11
+
+Nlocal: 125 ave 133 max 113 min
+Histogram: 2 0 0 0 0 1 1 0 2 2
+Nghost: 773.625 ave 788 max 764 min
+Histogram: 1 1 2 1 1 0 0 0 1 1
+Neighs: 30977.1 ave 50690 max 10447 min
+Histogram: 1 1 1 0 1 1 0 0 2 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
--
GitLab
From 1b7af5d93bd77d791a1ae6b3fef6cbb373ea2fcb Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 23 Jul 2018 16:24:16 -0600
Subject: [PATCH 047/332] added the computation of the global virial by
ScaFaCoS
---
src/USER-SCAFACOS/scafacos.cpp | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 352a298b86..e7dbcb4523 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -154,7 +154,11 @@ void Scafacos::compute(int eflag, int vflag)
const double qscale = qqrd2e;
if (eflag || vflag) ev_setup(eflag,vflag);
- else eflag_atom = 0;
+ else
+ {
+ eflag_atom = 0;
+ vflag_global = 0;
+ }
// if simulation box has changed, call fcs_tune()
@@ -175,9 +179,19 @@ void Scafacos::compute(int eflag, int vflag)
}
+ if (vflag_global)
+ {
+ fcs_set_compute_virial(fcs,1);
+ }
+
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
check_result(result);
+ if (vflag_global)
+ {
+ fcs_get_virial(fcs,virial);
+ }
+
// apply Efield to each particle
// accumulate total energy
--
GitLab
From ae2d43031bfd2c7b345478091fe3a2b8879b68f0 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 23 Jul 2018 16:25:02 -0600
Subject: [PATCH 048/332] added pressure output, to compare results with global
virial (with internal PPPM)
---
examples/USER/scafacos/in.scafacos.cw.ewald | 2 +-
examples/USER/scafacos/in.scafacos.cw.fmm | 2 +-
examples/USER/scafacos/in.scafacos.cw.p2nfft | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/examples/USER/scafacos/in.scafacos.cw.ewald b/examples/USER/scafacos/in.scafacos.cw.ewald
index f8444dd01f..55ebd0e7b3 100644
--- a/examples/USER/scafacos/in.scafacos.cw.ewald
+++ b/examples/USER/scafacos/in.scafacos.cw.ewald
@@ -18,7 +18,7 @@ kspace_modify scafacos tolerance field
timestep 0.005
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
diff --git a/examples/USER/scafacos/in.scafacos.cw.fmm b/examples/USER/scafacos/in.scafacos.cw.fmm
index 24a2739581..c63e241d63 100644
--- a/examples/USER/scafacos/in.scafacos.cw.fmm
+++ b/examples/USER/scafacos/in.scafacos.cw.fmm
@@ -24,7 +24,7 @@ kspace_modify scafacos fmm_tuning 1
timestep 0.005
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
diff --git a/examples/USER/scafacos/in.scafacos.cw.p2nfft b/examples/USER/scafacos/in.scafacos.cw.p2nfft
index 7a2391bc77..96be1b7d3c 100644
--- a/examples/USER/scafacos/in.scafacos.cw.p2nfft
+++ b/examples/USER/scafacos/in.scafacos.cw.p2nfft
@@ -18,7 +18,7 @@ kspace_modify scafacos tolerance field
timestep 0.005
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
run_style verlet
--
GitLab
From 8495fb62f400762a881e3d256cdb3dc995df5657 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 24 Jul 2018 10:33:12 -0400
Subject: [PATCH 049/332] Add preliminary cmake support
---
cmake/CMakeLists.txt | 28 +++++++++++++++++++++++++++-
cmake/Modules/FindZMQ.cmake | 8 ++++++++
2 files changed, 35 insertions(+), 1 deletion(-)
create mode 100644 cmake/Modules/FindZMQ.cmake
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index bf57398c71..288b8b2476 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -154,7 +154,7 @@ if(ENABLE_TESTING)
endif(ENABLE_TESTING)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+ KSPACE MANYBODY MC MEAM MISC MOLECULE MESSAGE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -426,6 +426,32 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
+if(PKG_MESSAGE)
+ option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+ add_library(cslib STATIC ${cslib_SOURCES})
+
+ if(BUILD_MPI)
+ target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ else()
+ target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ endif()
+
+ if(MESSAGE_ZMQ)
+ target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+ find_package(ZMQ REQUIRED)
+ target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+ target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+ else()
+ target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+ target_include_directories(cslib PRIVATE ${LAMMPS_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ endif()
+
+ list(APPEND LAMMPS_LINK_LIBS cslib)
+ include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()
+
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake
new file mode 100644
index 0000000000..608ccda777
--- /dev/null
+++ b/cmake/Modules/FindZMQ.cmake
@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
--
GitLab
From 7702114e252d2ab1ab9691668ea400a68b141b38 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 24 Jul 2018 13:11:58 -0400
Subject: [PATCH 050/332] fix typo in pair_atm.txt
---
doc/src/pair_atm.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index e442c32814..afe08c2a9b 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -88,7 +88,7 @@ pair_coeff 2 3 4 0.1 :pre
Note that for a simulation with a single atom type, only a single
entry is required, e.g.
-pair_coeff 1 1 1 0.25 :per
+pair_coeff 1 1 1 0.25 :pre
For a simulation with two atom types, four pair_coeff commands will
specify all possible nu values:
--
GitLab
From b08a2fcd3b997cb3930dfd7fb98d23aa78157a6c Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 11:36:12 -0600
Subject: [PATCH 051/332] mended un-done changes from Git master
---
doc/src/Section_commands.txt | 6 +++++-
doc/src/lammps.book | 7 +++++--
src/domain.cpp | 1 +
3 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index ec0c0dc454..433d761a90 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -681,6 +681,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
@@ -933,7 +935,9 @@ KOKKOS, o = USER-OMP, t = OPT.
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
-"body"_pair_body.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded/polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index a75f2469ca..2d586f195f 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -144,7 +144,7 @@ fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
-fix_box_relax.htmlf
+fix_box_relax.html
fix_client_md.html
fix_cmap.html
fix_colvars.html
@@ -288,6 +288,8 @@ fix_vector.html
fix_viscosity.html
fix_viscous.html
fix_wall.html
+fix_wall_body_polygon.html
+fix_wall_body_polyhedron.html
fix_wall_ees.html
fix_wall_gran.html
fix_wall_gran_region.html
@@ -429,8 +431,9 @@ pair_agni.html
pair_airebo.html
pair_awpmd.html
pair_beck.html
-pair_body.html
+pair_body_nparticle.html
pair_body_rounded_polygon.html
+pair_body_rounded_polyhedron.html
pair_bop.html
pair_born.html
pair_brownian.html
diff --git a/src/domain.cpp b/src/domain.cpp
index c00a716613..053959f937 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1208,6 +1208,7 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
+ called by ServerMD class
------------------------------------------------------------------------- */
void Domain::closest_image(double *xi, double *xj, double *xjimage)
--
GitLab
From c2c654c87b7979dea6af1ee4cdbb2bce70576ef7 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 11:44:15 -0600
Subject: [PATCH 052/332] CMake additions to new MESSAGE package
---
cmake/CMakeLists.txt | 28 +++++++++++++++++++++++++++-
cmake/Modules/FindZMQ.cmake | 8 ++++++++
2 files changed, 35 insertions(+), 1 deletion(-)
create mode 100644 cmake/Modules/FindZMQ.cmake
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index bf57398c71..288b8b2476 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -154,7 +154,7 @@ if(ENABLE_TESTING)
endif(ENABLE_TESTING)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+ KSPACE MANYBODY MC MEAM MISC MOLECULE MESSAGE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -426,6 +426,32 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
+if(PKG_MESSAGE)
+ option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+ add_library(cslib STATIC ${cslib_SOURCES})
+
+ if(BUILD_MPI)
+ target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ else()
+ target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ endif()
+
+ if(MESSAGE_ZMQ)
+ target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+ find_package(ZMQ REQUIRED)
+ target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+ target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+ else()
+ target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+ target_include_directories(cslib PRIVATE ${LAMMPS_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ endif()
+
+ list(APPEND LAMMPS_LINK_LIBS cslib)
+ include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()
+
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake
new file mode 100644
index 0000000000..608ccda777
--- /dev/null
+++ b/cmake/Modules/FindZMQ.cmake
@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
--
GitLab
From ab1cc706cc305ab1bdb54f12efa793a7ba94ae1f Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 11:55:56 -0600
Subject: [PATCH 053/332] change syntax of standard C include files
---
examples/COUPLE/lammps_mc/mc.cpp | 13 ++++++-------
src/MESSAGE/fix_client_md.cpp | 7 ++++---
src/MESSAGE/message.cpp | 2 +-
src/MESSAGE/server.cpp | 2 +-
src/MESSAGE/server_md.cpp | 2 +-
5 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp
index 24bb96641d..e62a786ac8 100644
--- a/examples/COUPLE/lammps_mc/mc.cpp
+++ b/examples/COUPLE/lammps_mc/mc.cpp
@@ -11,17 +11,16 @@
// mode = file, zmq
// modearg = filename for file, localhost:5555 for zmq
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "mc.h"
+#include "random_park.h"
#include "cslib.h"
using namespace CSLIB_NS;
-#include "mc.h"
-#include "random_park.h"
-
void error(const char *);
CSlib *cs_create(char *, char *);
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 20b56e031d..9ca6df4edc 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -14,14 +14,15 @@
#include <cstdio>
#include <cstring>
#include "fix_client_md.h"
-#include "cslib.h"
#include "atom.h"
+#include "comm.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
-#include "comm.h"
-#include "update.h"
+// CSlib interface
+
+#include "cslib.h"
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index 67e0a49046..a6ecf5cd60 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring.h>
#include "message.h"
#include "error.h"
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
index cbf769be74..c8de6de466 100644
--- a/src/MESSAGE/server.cpp
+++ b/src/MESSAGE/server.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring.h>
#include "server.h"
#include "error.h"
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index 88fe1abe5f..9783383553 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstring>
#include "server_md.h"
#include "atom.h"
--
GitLab
From 81abd8bc0a3bc7eec25ce4a1a634e148ea69a05a Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 24 Jul 2018 11:59:44 -0600
Subject: [PATCH 054/332] extended scafacos documentation
---
doc/src/kspace_modify.txt | 34 ++++++++++++++++++++++++++++------
doc/src/kspace_style.txt | 29 ++++++++++++++++++-----------
2 files changed, 46 insertions(+), 17 deletions(-)
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index fbc569306c..d21bb379e7 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -45,6 +45,8 @@ keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto}
{scafacos} values = option value1 value2 ...
option = {tolerance}
value = {energy} or {energy_rel} or {field} or {field_rel} or {potential} or {potential_rel}
+ option = {fmm_tuning}
+ value = {0} or {1}
{slab} value = volfactor or {nozforce}
volfactor = ratio of the total extended volume used in the
2d approximation compared with the volume of the simulation domain
@@ -308,8 +310,6 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU.
:line
-RENE: check this section
-
The {scafacos} keyword is used for settings that are passed to the
ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html.
@@ -324,10 +324,32 @@ field_rel = relative accuracy in electric field
potential = absolute accuracy in total Coulomic potential
potential_rel = relative accuracy in total Coulomic potential
-RENE: which one is closest to what LAMMPS used (see kspace_style
-command) - is it "field"? That's why I set it as the default.
-
-RENE: How is potential different than energy for this ??
+Potential and potential_rel impose a tolerance on a per-atom basis,
+in comparison to the energy and energy_rel tolerance types, where
+the tolerance is computed with regard to the total Coulomic energy
+in the system. In comparison to that, the field and field_rel
+tolerance types set a tolerance for the field values calculated
+within ScaFaCoS. Since the forces are derived from the field
+values, it indirectly sets a tolerance for the forces, comparable
+to other LAMMPS KSpace styles, see "kspace_style"_kspace_modify.html.
+The suffix '_rel' indicates that the tolerance is a relative tolerance,
+whereas the other case imposes an absolute tolerance on the given
+quantity.
+
+What needs to be taken into account is that not all solvers within
+the ScaFaCoS library support all kinds of tolerance types.
+
+fmm = energy and energy_rel
+p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
+ewald = field
+direct = has no tolerance tuning
+
+The {fmm_tuning} option (de-)activates the internal tuning mechanism
+for the fmm solver. Since the internal tuning mechanism is sequential,
+it can be very time-consuming and usually it is not required for
+systems with a homogenous charge distribution. The default of the
+setting there for is {0}, disabling the internal tuning. {1}
+activates the internal tuning.
:line
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index e5333489cc..49fb13ac37 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
{scafacos} values = method accuracy
- method = fmm or p3m or ... RENE
+ method = fmm or p2nfft or ewald or direct
accuracy = desired relative error in forces :pre
:ule
@@ -214,8 +214,6 @@ pressure simulation with MSM will cause the code to run slower.
:line
-RENE: edit this section
-
The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
library"_http://www.scafacos.de which provides a variety of solver
methods which can be used with LAMMPS. The paper by "(Who)"_#Who2012
@@ -255,16 +253,24 @@ the total Coulombic energy (short- and long-range) will be tallied for
The specified {method} determines which ScaFaCoS algorithm is used.
The list of methods shown above are the ScaFaCoS methods currently
-available from LAMMPS.
-
-RENE: explain this accuracy better compared to what
-it means for other LAMMPS methods?
+available from LAMMPS. Currently the following solvers are
+supported for use with LAMMPS: {fmm} (Fast Multi-Pole method),
+{p2nfft} (FFT-based Coulomb solver), {ewald} (Ewald-Summation)
+and {direct} (direct summation). The other ScaFaCoS solvers
+will be supported later on, but for the time being are
+experimental in connection with LAMMPS, e.g. {p3m} (PPPM-method).
+Use unsupported methods at your own discretion. To get an overview
+about the included solvers, refer to "(Sutmann)"_#Sutmann2013
The specified {accuracy} is similar to the accuracy setting for other
LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
-it in different ways for different methods it supports. See the
-"kspace_modify scafacos accuracy"_kspace_modify.html command for
-details.
+it in different ways for different methods it supports.
+Within the ScaFaCoS library the {accuracy} is treated as a tolerance
+level (either absolute or relative) for the chosen quantity, where
+the quantity can be either the Columic field values, the per-atom
+Columic energy or the total Columic energy. Different solver support
+different tolerance types, for more information on that, please
+refer to "kspace_modify scafacos accuracy"_kspace_modify.html.
The "kspace_modify scafacos"_kspace_modify.html command also explains
all the ScaFaCoS options currently exposed to LAMMPS.
@@ -460,7 +466,8 @@ Illinois at Urbana-Champaign, (2006).
[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
(2009).
-RENE:
+:link(Sutmann2013)
+[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
:link(Who2012)
[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
--
GitLab
From 1aa8307fa11c3efd5c6683c400f70d9b2ae3c158 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 12:04:23 -0600
Subject: [PATCH 055/332] change CSlib files to BSD license
---
lib/message/cslib/LICENSE | 533 ++------------------------
lib/message/cslib/README | 14 +-
lib/message/cslib/src/STUBS_MPI/mpi.h | 17 +-
lib/message/cslib/src/STUBS_ZMQ/zmq.h | 17 +-
lib/message/cslib/src/cslib.cpp | 4 +-
lib/message/cslib/src/cslib.h | 4 +-
lib/message/cslib/src/cslib_wrap.cpp | 4 +-
lib/message/cslib/src/cslib_wrap.h | 4 +-
lib/message/cslib/src/msg.cpp | 4 +-
lib/message/cslib/src/msg.h | 4 +-
lib/message/cslib/src/msg_file.cpp | 4 +-
lib/message/cslib/src/msg_file.h | 4 +-
lib/message/cslib/src/msg_mpi_one.cpp | 4 +-
lib/message/cslib/src/msg_mpi_one.h | 4 +-
lib/message/cslib/src/msg_mpi_two.cpp | 4 +-
lib/message/cslib/src/msg_mpi_two.h | 4 +-
lib/message/cslib/src/msg_zmq.cpp | 4 +-
lib/message/cslib/src/msg_zmq.h | 4 +-
18 files changed, 86 insertions(+), 551 deletions(-)
diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE
index 41ba9bbcd0..7a36e21daf 100644
--- a/lib/message/cslib/LICENSE
+++ b/lib/message/cslib/LICENSE
@@ -1,501 +1,32 @@
-GNU LESSER GENERAL PUBLIC LICENSE
-
-Version 2.1, February 1999
-
-Copyright (C) 1991, 1999 Free Software Foundation, Inc.
-51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-
-Everyone is permitted to copy and distribute verbatim copies
-of this license document, but changing it is not allowed.
-
-Preamble
-
-The licenses for most software are designed to take away your freedom
-to share and change it. By contrast, the GNU General Public Licenses
-are intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users.
-
-This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it. You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations
-below.
-
-When we speak of free software, we are referring to freedom of use,
-not price. Our General Public Licenses are designed to make sure that
-you have the freedom to distribute copies of free software (and charge
-for this service if you wish); that you receive source code or can get
-it if you want it; that you can change the software and use pieces of
-it in new free programs; and that you are informed that you can do
-these things.
-
-To protect your rights, we need to make restrictions that forbid
-distributors to deny you these rights or to ask you to surrender these
-rights. These restrictions translate to certain responsibilities for
-you if you distribute copies of the library or if you modify it.
-
-For example, if you distribute copies of the library, whether gratis
-or for a fee, you must give the recipients all the rights that we gave
-you. You must make sure that they, too, receive or can get the source
-code. If you link other code with the library, you must provide
-complete object files to the recipients, so that they can relink them
-with the library after making changes to the library and recompiling
-it. And you must show them these terms so they know their rights.
-
-We protect your rights with a two-step method: (1) we copyright the
-library, and (2) we offer you this license, which gives you legal
-permission to copy, distribute and/or modify the library.
-
-To protect each distributor, we want to make it very clear that there
-is no warranty for the free library. Also, if the library is modified
-by someone else and passed on, the recipients should know that what
-they have is not the original version, so that the original author's
-reputation will not be affected by problems that might be introduced
-by others.
-
-Finally, software patents pose a constant threat to the existence of
-any free program. We wish to make sure that a company cannot
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-ordinary GNU General Public License. This license, the GNU Lesser
-General Public License, applies to certain designated libraries, and
-is quite different from the ordinary General Public License. We use
-this license for certain libraries in order to permit linking those
-libraries into non-free programs.
-
-When a program is linked with a library, whether statically or using a
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-does Less to protect the user's freedom than the ordinary General
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-are the reason we use the ordinary General Public License for many
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-users' freedom, it does ensure that the user of a program that is
-linked with the Library has the freedom and the wherewithal to run
-that program using a modified version of the Library.
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-The precise terms and conditions for copying, distribution and
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-Ty Coon, President of Vice
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-That's all there is to it!
+Program: CSlib client/server coupling library
+
+Copyright 2018 National Technology & Engineering Solutions of Sandia,
+LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
+U.S. Government retains certain rights in this software. This
+software is distributed under the modified Berkeley Software
+Distribution (BSD) License.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+* Neither the name of Sandia Corporation nor the names of contributors
+ to this software may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/lib/message/cslib/README b/lib/message/cslib/README
index 1cc75861c6..37f4a97d54 100644
--- a/lib/message/cslib/README
+++ b/lib/message/cslib/README
@@ -1,7 +1,8 @@
-This is the July 2018 version of the Client/Server messaging library
-(CSlib). Only the source directory and license file are included here
-as part of the LAMMPS distribution. The full CSlib distribution,
-including documentation and test codes, can be found at the website:
+This is the the Client/Server messaging library (CSlib).
+
+Only the source directory and license file are included here as part
+of the LAMMPS distribution. The full CSlib distribution, including
+documentation and test codes, can be found at the website:
http://cslib.sandia.gov (as of Aug 2018).
The contact author is
@@ -11,8 +12,9 @@ Sandia National Laboratories
sjplimp@sandia.gov
http://www.sandia.gov/~sjplimp
-The CSlib is distributed as open-source code under the GNU LGPL
-license. See the accompanying LICENSE file.
+The CSlib is distributed as open-source code under the modified
+Berkeley Software Distribution (BSD) License. See the accompanying
+LICENSE file.
This directory contains the following:
diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h
index fd2dbf8113..2919e4c3a2 100644
--- a/lib/message/cslib/src/STUBS_MPI/mpi.h
+++ b/lib/message/cslib/src/STUBS_MPI/mpi.h
@@ -1,14 +1,15 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
// MPI constants and dummy functions
diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
index af920974cd..2f02eb4035 100644
--- a/lib/message/cslib/src/STUBS_ZMQ/zmq.h
+++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
@@ -1,14 +1,15 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
- See the README file in the top-level LAMMPS directory.
+ See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
// ZMQ constants and dummy functions
diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp
index 8b4d27f134..874333607e 100644
--- a/lib/message/cslib/src/cslib.cpp
+++ b/lib/message/cslib/src/cslib.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h
index 20d82a2469..b4da968026 100644
--- a/lib/message/cslib/src/cslib.h
+++ b/lib/message/cslib/src/cslib.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp
index 453948f783..c2d69eaf0d 100644
--- a/lib/message/cslib/src/cslib_wrap.cpp
+++ b/lib/message/cslib/src/cslib_wrap.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h
index 42d095f452..bf7df029c3 100644
--- a/lib/message/cslib/src/cslib_wrap.h
+++ b/lib/message/cslib/src/cslib_wrap.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp
index 1ba24d2b48..c67e4a5c8c 100644
--- a/lib/message/cslib/src/msg.cpp
+++ b/lib/message/cslib/src/msg.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h
index 48805a0f4f..f75942b027 100644
--- a/lib/message/cslib/src/msg.h
+++ b/lib/message/cslib/src/msg.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp
index 31126b8444..d97e249fad 100644
--- a/lib/message/cslib/src/msg_file.cpp
+++ b/lib/message/cslib/src/msg_file.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h
index 6d7c7017f6..d6bd802607 100644
--- a/lib/message/cslib/src/msg_file.h
+++ b/lib/message/cslib/src/msg_file.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp
index c028961abc..db11735b27 100644
--- a/lib/message/cslib/src/msg_mpi_one.cpp
+++ b/lib/message/cslib/src/msg_mpi_one.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h
index 8f1b781bc6..4b4140a3f7 100644
--- a/lib/message/cslib/src/msg_mpi_one.h
+++ b/lib/message/cslib/src/msg_mpi_one.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp
index 4c8f593939..e9a9e87eeb 100644
--- a/lib/message/cslib/src/msg_mpi_two.cpp
+++ b/lib/message/cslib/src/msg_mpi_two.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h
index 40dd95e7ea..7b31db5a63 100644
--- a/lib/message/cslib/src/msg_mpi_two.h
+++ b/lib/message/cslib/src/msg_mpi_two.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp
index dcbeedaaa0..c2d408f3a5 100644
--- a/lib/message/cslib/src/msg_zmq.cpp
+++ b/lib/message/cslib/src/msg_zmq.cpp
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h
index 5f6dd7f26b..c0621a26ff 100644
--- a/lib/message/cslib/src/msg_zmq.h
+++ b/lib/message/cslib/src/msg_zmq.h
@@ -6,8 +6,8 @@
Copyright 2018 National Technology & Engineering Solutions of
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
NTESS, the U.S. Government retains certain rights in this software.
- This software is distributed under the GNU Lesser General Public
- License (LGPL).
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
--
GitLab
From 655bd10db6279c947fba9a32120ca32077eabef5 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 15:20:37 -0600
Subject: [PATCH 056/332] doc changes to 2 files
---
doc/src/kspace_modify.txt | 75 ++++++++++++++++++++++++++-------------
doc/src/kspace_style.txt | 51 ++++++++++++--------------
2 files changed, 72 insertions(+), 54 deletions(-)
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index d21bb379e7..c41e9a9336 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -313,43 +313,67 @@ or with suffix kspace/pair styles of MSM, like OMP or GPU.
The {scafacos} keyword is used for settings that are passed to the
ScaFaCoS library when using "kspace_style scafacos"_kspace_style.html.
-The {tolerance} option affects how the {accuracy} specified with
-the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS.
+The {tolerance} option affects how the {accuracy} specified with the
+"kspace_style"_kspace_style.html command is interpreted by ScaFaCoS.
The following values may be used:
energy = absolute accuracy in total Coulomic energy
energy_rel = relative accuracy in total Coulomic energy
-field = absolute accuracy in electric field
-field_rel = relative accuracy in electric field
potential = absolute accuracy in total Coulomic potential
potential_rel = relative accuracy in total Coulomic potential
+field = absolute accuracy in electric field
+field_rel = relative accuracy in electric field :ul
-Potential and potential_rel impose a tolerance on a per-atom basis,
-in comparison to the energy and energy_rel tolerance types, where
-the tolerance is computed with regard to the total Coulomic energy
-in the system. In comparison to that, the field and field_rel
-tolerance types set a tolerance for the field values calculated
-within ScaFaCoS. Since the forces are derived from the field
-values, it indirectly sets a tolerance for the forces, comparable
-to other LAMMPS KSpace styles, see "kspace_style"_kspace_modify.html.
-The suffix '_rel' indicates that the tolerance is a relative tolerance,
-whereas the other case imposes an absolute tolerance on the given
+The values with suffix "_rel" indicate the tolerance is a relative
+tolerance; the other values impose an absolute tolerance on the given
quantity.
-What needs to be taken into account is that not all solvers within
-the ScaFaCoS library support all kinds of tolerance types.
+The energy and energy_rel values, set a tolerance based on the total
+Coulomic energy of the system. The potential and potential_rel set a
+tolerance based on the per-atom Coulomic energy. The field and
+field_rel tolerance types set a tolerance based on the electric field
+values computed by ScaFaCoS. Since per-atom forces are derived from
+the per-atom electric field, this effectively sets a tolerance on the
+forces, simimlar to other LAMMPS KSpace styles, as explained on the
+"kspace_style"_kspace_style.html doc page.
+
+RENE: Can you add some explanation of the difference between relative
+and absolute? Something like this (if it's correct). If the total
+Coul energy is computed to be -1000.0, then an absolute tolerance of
+1.0e-3 means the actual energy is between -999.999 and -1000.001.
+Whereas a relative tolerance means it is between -999 and -1001. Thus
+an absolute tolerance is generally much more stringent?
+
+RENE: Also, can you explain more what is the difference between energy
+(total) and potential (per-atom)? Which one is more vs less accurate?
+Does potential mean that the maximum of any atom's energy error is <
+tolerance? I.e. it is a max across all per-atom values? Ditto for
+field, since it is computed on a per-atom basis?
+
+Note that not all ScaFaCoS solvers support all tolerance types.
+These are the allowed values for each method:
fmm = energy and energy_rel
p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
ewald = field
-direct = has no tolerance tuning
+direct = has no tolerance tuning :ul
+
+RENE: I think this means that the default tolerance setting
+is differnet for different methods. If so, it should
+be documented in the above list, i.e. by listing the default
+value first.
+
+RENE: Does the code (LAMMPS or Scafacos) generate an error
+if an unsupported tolerance is specified for a method?
+
+The {fmm_tuning} option is only relevant when using the FMM method.
+It activates (value=1) or deactivates (value=0) an internal tuning
+mechanism for the FMM solver. The tuning operation runs sequentially
+and can be very time-consuming. Usually it is not needed for systems
+with a homogenous charge distribution. The default for this option is
+therefore {0}.
-The {fmm_tuning} option (de-)activates the internal tuning mechanism
-for the fmm solver. Since the internal tuning mechanism is sequential,
-it can be very time-consuming and usually it is not required for
-systems with a homogenous charge distribution. The default of the
-setting there for is {0}, disabling the internal tuning. {1}
-activates the internal tuning.
+RENE: is the tuning a one-time (start-up) operation if enabled?
:line
@@ -405,8 +429,9 @@ gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff =
ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace
= -1.0, split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel,
-order = order/disp = 7. For scafacos settings, scafacos tolerance
-field.
+order = order/disp = 7. For scafacos settings, the scafacos tolerance
+option depends on the method chosen, as documented above. The
+scafacos fmm_tuning default = 0.
:line
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 49fb13ac37..742d71ffb8 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -236,41 +236,34 @@ See details on "this page"_Section_packages.html#USER-SCAFACOS.
NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
Coulombic interactions, both short- and long-range. Thus you should
-NOT use a Coulmbic pair style when using kspace_style scafacos. Thus
-the total Coulombic energy (short- and long-range) will be tallied for
-"thermodynamic output"_thermo_style.html command as part of the
-{elong} keyword; the {ecoul} keyword will be zero.
+NOT use a Coulmbic pair style when using kspace_style scafacos. This
+also means the total Coulombic energy (short- and long-range) will be
+tallied for "thermodynamic output"_thermo_style.html command as part
+of the {elong} keyword; the {ecoul} keyword will be zero.
-NOTE: See the restriction below about use of ScaFaCoS in LAMMPS with
-molecular charged systems or the TIP4P water model.
-
-Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
-Coulombic interactions, both short- and long-range. Thus you should
-NOT use a Coulmbic pair style when using kspace_style scafacos. Thus
-the total Coulombic energy (short- and long-range) will be tallied for
-"thermodynamic output"_thermo_style.html command as part of the
-{elong} keyword; the {ecoul} keyword will be zero.
+NOTE: See the current restriction below about use of ScaFaCoS in
+LAMMPS with molecular charged systems or the TIP4P water model.
The specified {method} determines which ScaFaCoS algorithm is used.
-The list of methods shown above are the ScaFaCoS methods currently
-available from LAMMPS. Currently the following solvers are
-supported for use with LAMMPS: {fmm} (Fast Multi-Pole method),
-{p2nfft} (FFT-based Coulomb solver), {ewald} (Ewald-Summation)
-and {direct} (direct summation). The other ScaFaCoS solvers
-will be supported later on, but for the time being are
-experimental in connection with LAMMPS, e.g. {p3m} (PPPM-method).
-Use unsupported methods at your own discretion. To get an overview
-about the included solvers, refer to "(Sutmann)"_#Sutmann2013
+These are the ScaFaCoS methods currently available from LAMMPS:
+
+{fmm} = Fast Multi-Pole method
+{p2nfft} = FFT-based Coulomb solver
+{ewald} = Ewald summation
+{direct} = direct O(N^2) summation
+
+We plan to support additional ScaFaCoS solvers from LAMMPS in the
+future. For an overview of the included solvers, refer to
+"(Sutmann)"_#Sutmann2013
The specified {accuracy} is similar to the accuracy setting for other
LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
-it in different ways for different methods it supports.
-Within the ScaFaCoS library the {accuracy} is treated as a tolerance
-level (either absolute or relative) for the chosen quantity, where
-the quantity can be either the Columic field values, the per-atom
-Columic energy or the total Columic energy. Different solver support
-different tolerance types, for more information on that, please
-refer to "kspace_modify scafacos accuracy"_kspace_modify.html.
+it in different ways for different methods it supports. Within the
+ScaFaCoS library the {accuracy} is treated as a tolerance level
+(either absolute or relative) for the chosen quantity, where the
+quantity can be either the Columic field values, the per-atom Columic
+energy or the total Columic energy. To select from these options, see
+the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
The "kspace_modify scafacos"_kspace_modify.html command also explains
all the ScaFaCoS options currently exposed to LAMMPS.
--
GitLab
From 8846f97868f24ef75cecf9dd4547640cf8cb06e7 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 24 Jul 2018 15:46:28 -0600
Subject: [PATCH 057/332] explained differences between absolute and relative
tolerance more
---
doc/src/kspace_modify.txt | 25 +++++++++++++------------
1 file changed, 13 insertions(+), 12 deletions(-)
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index c41e9a9336..f552f9b9b6 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -326,7 +326,16 @@ field_rel = relative accuracy in electric field :ul
The values with suffix "_rel" indicate the tolerance is a relative
tolerance; the other values impose an absolute tolerance on the given
-quantity.
+quantity. Absoulte tolerance in this case means, that for a given
+quantity q and a given absolute tolerance of t_a the result should
+be between q-t_a and q+t_a. For a relative tolerance t_r the relative
+error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r.
+As a consequence of this, the tolerance type should be checked, when
+performing computations with a high absolute field / energy. E.g.
+if the total energy in the system is 1000000.0 an absolute tolerance
+of 1e-3 would mean that the result has to be between 999999.999 and
+1000000.001, which would be equivalent to a relative tolerance of
+1e-9.
The energy and energy_rel values, set a tolerance based on the total
Coulomic energy of the system. The potential and potential_rel set a
@@ -337,13 +346,6 @@ the per-atom electric field, this effectively sets a tolerance on the
forces, simimlar to other LAMMPS KSpace styles, as explained on the
"kspace_style"_kspace_style.html doc page.
-RENE: Can you add some explanation of the difference between relative
-and absolute? Something like this (if it's correct). If the total
-Coul energy is computed to be -1000.0, then an absolute tolerance of
-1.0e-3 means the actual energy is between -999.999 and -1000.001.
-Whereas a relative tolerance means it is between -999 and -1001. Thus
-an absolute tolerance is generally much more stringent?
-
RENE: Also, can you explain more what is the difference between energy
(total) and potential (per-atom)? Which one is more vs less accurate?
Does potential mean that the maximum of any atom's energy error is <
@@ -358,10 +360,9 @@ p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
ewald = field
direct = has no tolerance tuning :ul
-RENE: I think this means that the default tolerance setting
-is differnet for different methods. If so, it should
-be documented in the above list, i.e. by listing the default
-value first.
+If the tolerance type is not changed, the default values for the
+tolerance type are the first values in the above list, e.g. energy
+is the default tolerance type for the fmm solver.
RENE: Does the code (LAMMPS or Scafacos) generate an error
if an unsupported tolerance is specified for a method?
--
GitLab
From 37a0a7b49bb54cedeb475772c7f64b3e83b8153c Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 24 Jul 2018 15:55:48 -0600
Subject: [PATCH 058/332] fixed compilation error
---
doc/src/kspace_modify.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index f552f9b9b6..57cff18d7e 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -324,7 +324,7 @@ potential_rel = relative accuracy in total Coulomic potential
field = absolute accuracy in electric field
field_rel = relative accuracy in electric field :ul
-The values with suffix "_rel" indicate the tolerance is a relative
+The values with suffix _rel indicate the tolerance is a relative
tolerance; the other values impose an absolute tolerance on the given
quantity. Absoulte tolerance in this case means, that for a given
quantity q and a given absolute tolerance of t_a the result should
--
GitLab
From a4dbac63d32af5683bf73d49817561c390f6036e Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 17:22:15 -0600
Subject: [PATCH 059/332] more updates to the new MESSAGE package
---
examples/COUPLE/lammps_vasp/OUTCAR | 14953 +++++++++++++++++++++
examples/COUPLE/lammps_vasp/README | 48 +-
examples/COUPLE/lammps_vasp/vasp_wrap.py | 33 +-
lib/message/cslib/src/cslib.py | 4 +-
src/MESSAGE/message.cpp | 2 +-
src/MESSAGE/server.cpp | 2 +-
6 files changed, 15009 insertions(+), 33 deletions(-)
create mode 100644 examples/COUPLE/lammps_vasp/OUTCAR
diff --git a/examples/COUPLE/lammps_vasp/OUTCAR b/examples/COUPLE/lammps_vasp/OUTCAR
new file mode 100644
index 0000000000..6e8ef736cc
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/OUTCAR
@@ -0,0 +1,14953 @@
+ vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Aug 01 2017 10:32:50) complex
+
+ executed on LinuxIFC date 2017.12.19 15:22:45
+ running on 9 total cores
+ distrk: each k-point on 9 cores, 1 groups
+ distr: one band on NCORES_PER_BAND= 1 cores, 9 groups
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ INCAR:
+ POTCAR: PAW_PBE W_sv_GW 23Mar2010
+ POTCAR: PAW_PBE Be_sv_GW 31Mar2010
+
+ -----------------------------------------------------------------------------
+| |
+| W W AA RRRRR N N II N N GGGG !!! |
+| W W A A R R NN N II NN N G G !!! |
+| W W A A R R N N N II N N N G !!! |
+| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
+| WW WW A A R R N NN II N NN G G |
+| W W A A R R N N II N N GGGG !!! |
+| |
+| For optimal performance we recommend to set |
+| NCORE= 4 - approx SQRT( number of cores) |
+| NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). |
+| This setting can greatly improve the performance of VASP for DFT. |
+| The default, NCORE=1 might be grossly inefficient |
+| on modern multi-core architectures or massively parallel machines. |
+| Do your own testing !!!! |
+| Unfortunately you need to use the default for GW and RPA calculations. |
+| (for HF NCORE is supported but not extensively tested yet) |
+| |
+ -----------------------------------------------------------------------------
+
+ POTCAR: PAW_PBE W_sv_GW 23Mar2010
+ VRHFIN =W: 5p6s5d
+ LEXCH = PE
+ EATOM = 1863.8917 eV, 136.9922 Ry
+
+ TITEL = PAW_PBE W_sv_GW 23Mar2010
+ LULTRA = F use ultrasoft PP ?
+ IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
+ RPACOR = 1.500 partial core radius
+ POMASS = 183.850; ZVAL = 14.000 mass and valenz
+ RCORE = 2.300 outmost cutoff radius
+ RWIGS = 2.600; RWIGS = 1.376 wigner-seitz radius (au A)
+ ENMAX = 317.132; ENMIN = 237.849 eV
+ RCLOC = 1.609 cutoff for local pot
+ LCOR = T correct aug charges
+ LPAW = T paw PP
+ EAUG = 807.757
+ DEXC = 0.000
+ RMAX = 2.349 core radius for proj-oper
+ RAUG = 1.300 factor for augmentation sphere
+ RDEP = 2.382 radius for radial grids
+ RDEPT = 1.832 core radius for aug-charge
+
+ Atomic configuration
+ 14 entries
+ n l j E occ.
+ 1 0 0.50 -69464.1497 2.0000
+ 2 0 0.50 -11984.7400 2.0000
+ 2 1 1.50 -10478.3405 6.0000
+ 3 0 0.50 -2757.5605 2.0000
+ 3 1 1.50 -2311.6706 6.0000
+ 3 2 2.50 -1799.5973 10.0000
+ 4 0 0.50 -566.1609 2.0000
+ 4 1 1.50 -419.9482 6.0000
+ 4 2 2.50 -234.8191 10.0000
+ 4 3 3.50 -29.7363 14.0000
+ 5 0 0.50 -75.5905 2.0000
+ 5 1 1.50 -39.9756 6.0000
+ 5 2 2.50 -2.4479 6.0000
+ 5 3 2.50 -1.3606 0.0000
+ Description
+ l E TYP RCUT TYP RCUT
+ 0 -75.5905419 23 1.500
+ 0 -76.9511245 23 1.500
+ 0 108.8466080 23 1.500
+ 1 -39.9756040 23 1.800
+ 1 68.0291300 23 1.800
+ 2 -2.4478587 23 2.150
+ 2 -0.0030619 23 2.150
+ 3 4.0817478 23 2.300
+ local pseudopotential read in
+ partial core-charges read in
+ partial kinetic energy density read in
+ kinetic energy density of atom read in
+ atomic valenz-charges read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 1 read in
+ real space projection operators read in
+ non local Contribution for L= 1 read in
+ real space projection operators read in
+ non local Contribution for L= 2 read in
+ real space projection operators read in
+ non local Contribution for L= 2 read in
+ real space projection operators read in
+ non local Contribution for L= 3 read in
+ real space projection operators read in
+ PAW grid and wavefunctions read in
+
+ number of l-projection operators is LMAX = 8
+ number of lm-projection operators is LMMAX = 26
+
+ POTCAR: PAW_PBE Be_sv_GW 31Mar2010
+ VRHFIN =Be: s2p0
+ LEXCH = PE
+ EATOM = 390.9322 eV, 28.7327 Ry
+
+ TITEL = PAW_PBE Be_sv_GW 31Mar2010
+ LULTRA = F use ultrasoft PP ?
+ IUNSCR = 0 unscreen: 0-lin 1-nonlin 2-no
+ RPACOR = 0.000 partial core radius
+ POMASS = 9.013; ZVAL = 4.000 mass and valenz
+ RCORE = 1.300 outmost cutoff radius
+ RWIGS = 1.600; RWIGS = 0.847 wigner-seitz radius (au A)
+ ENMAX = 537.454; ENMIN = 403.090 eV
+ RCLOC = 1.007 cutoff for local pot
+ LCOR = T correct aug charges
+ LPAW = T paw PP
+ EAUG = 1293.449
+ RMAX = 1.324 core radius for proj-oper
+ RAUG = 1.300 factor for augmentation sphere
+ RDEP = 1.364 radius for radial grids
+ RDEPT = 1.200 core radius for aug-charge
+
+ Atomic configuration
+ 5 entries
+ n l j E occ.
+ 1 0 0.50 -108.8489 2.0000
+ 1 0 0.50 -107.4860 0.0000
+ 2 1 0.50 -2.9389 2.0000
+ 3 2 1.50 -1.3606 0.0000
+ 4 3 2.50 -1.3606 0.0000
+ Description
+ l E TYP RCUT TYP RCUT
+ 0 -108.8489274 23 1.100
+ 0 -107.4860254 23 1.100
+ 0 95.2407820 23 1.100
+ 1 -2.9389331 23 1.300
+ 1 15.5352276 23 1.300
+ 2 54.4233040 23 1.300
+ local pseudopotential read in
+ kinetic energy density of atom read in
+ atomic valenz-charges read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 0 read in
+ real space projection operators read in
+ non local Contribution for L= 1 read in
+ real space projection operators read in
+ non local Contribution for L= 1 read in
+ real space projection operators read in
+ non local Contribution for L= 2 read in
+ real space projection operators read in
+ PAW grid and wavefunctions read in
+
+ number of l-projection operators is LMAX = 6
+ number of lm-projection operators is LMMAX = 14
+
+ PAW_PBE W_sv_GW 23Mar2010 :
+ energy of atom 1 EATOM=-1863.8917
+ kinetic energy error for atom= 0.0147 (will be added to EATOM!!)
+ PAW_PBE Be_sv_GW 31Mar2010 :
+ energy of atom 2 EATOM= -390.9322
+ kinetic energy error for atom= 0.0274 (will be added to EATOM!!)
+
+
+ POSCAR: WBe3 L1_2
+ positions in direct lattice
+ No initial velocities read in
+ exchange correlation table for LEXCH = 8
+ RHO(1)= 0.500 N(1) = 2000
+ RHO(2)= 100.500 N(2) = 4000
+
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ ion position nearest neighbor table
+ 1 0.000 0.000 0.000- 2 2.38 2 2.38 2 2.38 2 2.38 3 2.43 3 2.43 3 2.43 3 2.43
+ 4 2.56 4 2.56 4 2.56 4 2.56
+ 2 0.000 0.500 0.500- 1 2.38 1 2.38 1 2.38 1 2.38
+ 3 0.500 0.000 0.500- 1 2.43 1 2.43 1 2.43 1 2.43
+ 4 0.500 0.500 0.000- 1 2.56 1 2.56 1 2.56 1 2.56
+
+ LATTYP: Found a simple orthorhombic cell.
+ ALAT = 3.1767810000
+ B/A-ratio = 1.1198253830
+ C/A-ratio = 1.1551350250
+
+ Lattice vectors:
+
+ A1 = ( 0.0000000000, 0.0000000000, -3.1767810000)
+ A2 = ( 0.0000000000, -3.5574400000, 0.0000000000)
+ A3 = ( -3.6696110000, 0.0000000000, 0.0000000000)
+
+
+Analysis of symmetry for initial positions (statically):
+=====================================================================
+ Subroutine PRICEL returns:
+ Original cell was already a primitive cell.
+
+
+ Routine SETGRP: Setting up the symmetry group for a
+ simple orthorhombic supercell.
+
+
+ Subroutine GETGRP returns: Found 8 space group operations
+ (whereof 8 operations were pure point group operations)
+ out of a pool of 8 trial point group operations.
+
+
+The static configuration has the point symmetry D_2h.
+
+
+Analysis of symmetry for dynamics (positions and initial velocities):
+=====================================================================
+ Subroutine PRICEL returns:
+ Original cell was already a primitive cell.
+
+
+ Routine SETGRP: Setting up the symmetry group for a
+ simple orthorhombic supercell.
+
+
+ Subroutine GETGRP returns: Found 8 space group operations
+ (whereof 8 operations were pure point group operations)
+ out of a pool of 8 trial point group operations.
+
+
+The dynamic configuration has the point symmetry D_2h.
+
+
+ Subroutine INISYM returns: Found 8 space group operations
+ (whereof 8 operations are pure point group operations),
+ and found 1 'primitive' translations
+
+
+
+ KPOINTS: K-Points
+
+Automatic generation of k-mesh.
+Space group operators:
+ irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z
+ 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ 2 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ 3 1.000000 179.999999 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ 4 -1.000000 179.999999 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ 5 1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000
+ 6 -1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000
+ 7 1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
+ 8 -1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
+
+ Subroutine IBZKPT returns following result:
+ ===========================================
+
+ Found 512 irreducible k-points:
+
+ Following reciprocal coordinates:
+ Coordinates Weight
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+
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+ Dimension of arrays:
+ k-points NKPTS = 512 k-points in BZ NKDIM = 512 number of bands NBANDS= 18
+ number of dos NEDOS = 301 number of ions NIONS = 4
+ non local maximal LDIM = 8 non local SUM 2l+1 LMDIM = 26
+ total plane-waves NPLWV = 11520
+ max r-space proj IRMAX = 1 max aug-charges IRDMAX= 9112
+ dimension x,y,z NGX = 24 NGY = 24 NGZ = 20
+ dimension x,y,z NGXF= 48 NGYF= 48 NGZF= 40
+ support grid NGXF= 48 NGYF= 48 NGZF= 40
+ ions per type = 1 3
+ NGX,Y,Z is equivalent to a cutoff of 10.87, 11.22, 10.47 a.u.
+ NGXF,Y,Z is equivalent to a cutoff of 21.75, 22.43, 20.93 a.u.
+
+ SYSTEM = unknown system
+ POSCAR = WBe3 L1_2
+
+ Startparameter for this run:
+ NWRITE = 2 write-flag & timer
+ PREC = normal normal or accurate (medium, high low for compatibility)
+ ISTART = 0 job : 0-new 1-cont 2-samecut
+ ICHARG = 2 charge: 1-file 2-atom 10-const
+ ISPIN = 1 spin polarized calculation?
+ LNONCOLLINEAR = F non collinear calculations
+ LSORBIT = F spin-orbit coupling
+ INIWAV = 1 electr: 0-lowe 1-rand 2-diag
+ LASPH = F aspherical Exc in radial PAW
+ METAGGA= F non-selfconsistent MetaGGA calc.
+
+ Electronic Relaxation 1
+ ENCUT = 600.0 eV 44.10 Ry 6.64 a.u. 7.33 7.11 6.34*2*pi/ulx,y,z
+ ENINI = 600.0 initial cutoff
+ ENAUG = 1293.4 eV augmentation charge cutoff
+ NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
+ EDIFF = 0.1E-05 stopping-criterion for ELM
+ LREAL = F real-space projection
+ NLSPLINE = F spline interpolate recip. space projectors
+ LCOMPAT= F compatible to vasp.4.4
+ GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6
+ LMAXPAW = -100 max onsite density
+ LMAXMIX = 2 max onsite mixed and CHGCAR
+ VOSKOWN= 0 Vosko Wilk Nusair interpolation
+ ROPT = 0.00000 0.00000
+ Ionic relaxation
+ EDIFFG = 0.1E-02 stopping-criterion for IOM
+ NSW = 0 number of steps for IOM
+ NBLOCK = 1; KBLOCK = 1 inner block; outer block
+ IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG
+ NFREE = 0 steps in history (QN), initial steepest desc. (CG)
+ ISIF = 2 stress and relaxation
+ IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb
+ ISYM = 2 0-nonsym 1-usesym 2-fastsym
+ LCORR = T Harris-Foulkes like correction to forces
+
+ POTIM = 0.5000 time-step for ionic-motion
+ TEIN = 0.0 initial temperature
+ TEBEG = 3500.0; TEEND =3500.0 temperature during run
+ SMASS = -3.00 Nose mass-parameter (am)
+ estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.308E-27a.u.
+ SCALEE = 1.0000 scale energy and forces
+ NPACO = 256; APACO = 16.0 distance and # of slots for P.C.
+ PSTRESS= 0.0 pullay stress
+
+ Mass of Ions in am
+ POMASS = 183.85 9.01
+ Ionic Valenz
+ ZVAL = 14.00 4.00
+ Atomic Wigner-Seitz radii
+ RWIGS = -1.00 -1.00
+ virtual crystal weights
+ VCA = 1.00 1.00
+ NELECT = 26.0000 total number of electrons
+ NUPDOWN= -1.0000 fix difference up-down
+
+ DOS related values:
+ EMIN = 10.00; EMAX =-10.00 energy-range for DOS
+ EFERMI = 0.00
+ ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
+
+ Electronic relaxation 2 (details)
+ IALGO = 48 algorithm
+ LDIAG = T sub-space diagonalisation (order eigenvalues)
+ LSUBROT= F optimize rotation matrix (better conditioning)
+ TURBO = 0 0=normal 1=particle mesh
+ IRESTART = 0 0=no restart 2=restart with 2 vectors
+ NREBOOT = 0 no. of reboots
+ NMIN = 0 reboot dimension
+ EREF = 0.00 reference energy to select bands
+ IMIX = 4 mixing-type and parameters
+ AMIX = 0.40; BMIX = 1.00
+ AMIX_MAG = 1.60; BMIX_MAG = 1.00
+ AMIN = 0.10
+ WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45
+
+ Intra band minimization:
+ WEIMIN = 0.0000 energy-eigenvalue tresh-hold
+ EBREAK = 0.14E-07 absolut break condition
+ DEPER = 0.30 relativ break condition
+
+ TIME = 0.40 timestep for ELM
+
+ volume/ion in A,a.u. = 10.37 69.97
+ Fermi-wavevector in a.u.,A,eV,Ry = 1.401149 2.647788 26.711209 1.963218
+ Thomas-Fermi vector in A = 2.524039
+
+ Write flags
+ LWAVE = T write WAVECAR
+ LDOWNSAMPLE = F k-point downsampling of WAVECAR
+ LCHARG = T write CHGCAR
+ LVTOT = F write LOCPOT, total local potential
+ LVHAR = F write LOCPOT, Hartree potential only
+ LELF = F write electronic localiz. function (ELF)
+ LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes
+
+
+ Dipole corrections
+ LMONO = F monopole corrections only (constant potential shift)
+ LDIPOL = F correct potential (dipole corrections)
+ IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
+ EPSILON= 1.0000000 bulk dielectric constant
+
+ Exchange correlation treatment:
+ GGA = -- GGA type
+ LEXCH = 8 internal setting for exchange type
+ VOSKOWN= 0 Vosko Wilk Nusair interpolation
+ LHFCALC = F Hartree Fock is set to
+ LHFONE = F Hartree Fock one center treatment
+ AEXX = 0.0000 exact exchange contribution
+
+ Linear response parameters
+ LEPSILON= F determine dielectric tensor
+ LRPA = F only Hartree local field effects (RPA)
+ LNABLA = F use nabla operator in PAW spheres
+ LVEL = F velocity operator in full k-point grid
+ LINTERFAST= F fast interpolation
+ KINTER = 0 interpolate to denser k-point grid
+ CSHIFT =0.1000 complex shift for real part using Kramers Kronig
+ OMEGAMAX= -1.0 maximum frequency
+ DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate
+ RTIME = -0.100 relaxation time in fs
+ (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME)
+ DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time
+
+ Orbital magnetization related:
+ ORBITALMAG= F switch on orbital magnetization
+ LCHIMAG = F perturbation theory with respect to B field
+ DQ = 0.001000 dq finite difference perturbation B field
+ LLRAUG = F two centre corrections for induced B field
+
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ Static calculation
+ charge density and potential will be updated during run
+ non-spin polarized calculation
+ RMM-DIIS sequential band-by-band
+ perform sub-space diagonalisation
+ before iterative eigenvector-optimisation
+ modified Broyden-mixing scheme, WC = 100.0
+ initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000
+ Hartree-type preconditioning will be used
+ using additional bands 5
+ reciprocal scheme for non local part
+ use partial core corrections
+ calculate Harris-corrections to forces
+ (improved forces if not selfconsistent)
+ use gradient corrections
+ use of overlap-Matrix (Vanderbilt PP)
+ Gauss-broadening in eV SIGMA = 0.10
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ energy-cutoff : 600.00
+ volume of cell : 41.47
+ direct lattice vectors reciprocal lattice vectors
+ 3.669611000 0.000000000 0.000000000 0.272508448 0.000000000 0.000000000
+ 0.000000000 3.557440000 0.000000000 0.000000000 0.281101016 0.000000000
+ 0.000000000 0.000000000 3.176781000 0.000000000 0.000000000 0.314784053
+
+ length of vectors
+ 3.669611000 3.557440000 3.176781000 0.272508448 0.281101016 0.314784053
+
+
+
+ k-points in units of 2pi/SCALE and weight: K-Points
+ 0.00000000 0.00000000 0.00000000 0.000
+ 0.01816723 0.00000000 0.00000000 0.001
+ 0.03633446 0.00000000 0.00000000 0.001
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+ position of ions in fractional coordinates (direct lattice)
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+
+ position of ions in cartesian coordinates (Angst):
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+ 0.00000000 1.77872000 1.58839050
+ 1.83480550 0.00000000 1.58839050
+ 1.83480550 1.77872000 0.00000000
+
+
+
+--------------------------------------------------------------------------------------------------------
+
+
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+ k-point ** : 0.0667 0.2000 0.4667 plane waves: 1394
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+ k-point ** : 0.0000 0.2667 0.4667 plane waves: 1386
+ k-point ** : 0.0667 0.2667 0.4667 plane waves: 1391
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+ k-point ** : 0.2000 0.2667 0.4667 plane waves: 1385
+ k-point ** : 0.2667 0.2667 0.4667 plane waves: 1382
+ k-point ** : 0.3333 0.2667 0.4667 plane waves: 1381
+ k-point ** : 0.4000 0.2667 0.4667 plane waves: 1387
+ k-point ** : 0.4667 0.2667 0.4667 plane waves: 1390
+ k-point ** : 0.0000 0.3333 0.4667 plane waves: 1386
+ k-point ** : 0.0667 0.3333 0.4667 plane waves: 1382
+ k-point ** : 0.1333 0.3333 0.4667 plane waves: 1378
+ k-point ** : 0.2000 0.3333 0.4667 plane waves: 1385
+ k-point ** : 0.2667 0.3333 0.4667 plane waves: 1386
+ k-point ** : 0.3333 0.3333 0.4667 plane waves: 1386
+ k-point ** : 0.4000 0.3333 0.4667 plane waves: 1389
+ k-point ** : 0.4667 0.3333 0.4667 plane waves: 1392
+ k-point ** : 0.0000 0.4000 0.4667 plane waves: 1387
+ k-point ** : 0.0667 0.4000 0.4667 plane waves: 1390
+ k-point ** : 0.1333 0.4000 0.4667 plane waves: 1383
+ k-point ** : 0.2000 0.4000 0.4667 plane waves: 1378
+ k-point ** : 0.2667 0.4000 0.4667 plane waves: 1382
+ k-point ** : 0.3333 0.4000 0.4667 plane waves: 1385
+ k-point ** : 0.4000 0.4000 0.4667 plane waves: 1389
+ k-point ** : 0.4667 0.4000 0.4667 plane waves: 1393
+ k-point ** : 0.0000 0.4667 0.4667 plane waves: 1380
+ k-point ** : 0.0667 0.4667 0.4667 plane waves: 1390
+ k-point ** : 0.1333 0.4667 0.4667 plane waves: 1386
+ k-point ** : 0.2000 0.4667 0.4667 plane waves: 1386
+ k-point ** : 0.2667 0.4667 0.4667 plane waves: 1381
+ k-point ** : 0.3333 0.4667 0.4667 plane waves: 1383
+ k-point ** : 0.4000 0.4667 0.4667 plane waves: 1388
+ k-point ** : 0.4667 0.4667 0.4667 plane waves: 1390
+
+ maximum and minimum number of plane-waves per node : 1401 1362
+
+ maximum number of plane-waves: 1401
+ maximum index in each direction:
+ IXMAX= 7 IYMAX= 7 IZMAX= 6
+ IXMIN= -7 IYMIN= -7 IZMIN= -6
+
+
+ serial 3D FFT for wavefunctions
+ parallel 3D FFT for charge:
+ minimum data exchange during FFTs selected (reduces bandwidth)
+
+
+ total amount of memory used by VASP MPI-rank0 355020. kBytes
+=======================================================================
+
+ base : 30000. kBytes
+ nonl-proj : 299130. kBytes
+ fftplans : 441. kBytes
+ grid : 1138. kBytes
+ one-center: 129. kBytes
+ wavefun : 24182. kBytes
+
+ INWAV: cpu time 0.0001: real time 0.0007
+ Broyden mixing: mesh for mixing (old mesh)
+ NGX = 15 NGY = 15 NGZ = 13
+ (NGX = 48 NGY = 48 NGZ = 40)
+ gives a total of 2925 points
+
+ initial charge density was supplied:
+ charge density of overlapping atoms calculated
+ number of electron 26.0000000 magnetization
+ keeping initial charge density in first step
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ Maximum index for augmentation-charges 1294 (set IRDMAX)
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ First call to EWALD: gamma= 0.512
+ Maximum number of real-space cells 3x 3x 3
+ Maximum number of reciprocal cells 3x 3x 3
+
+ FEWALD: cpu time 0.0014: real time 0.0014
+
+
+--------------------------------------- Iteration 1( 1) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0000: real time 0.0186
+ SETDIJ: cpu time 0.0023: real time 0.0038
+ EDDIAG: cpu time 0.8664: real time 0.8695
+ RMM-DIIS: cpu time 0.9891: real time 0.9915
+ ORTHCH: cpu time 0.0915: real time 0.0917
+ DOS: cpu time 0.0040: real time 0.0040
+ --------------------------------------------
+ LOOP: cpu time 1.9534: real time 1.9792
+
+ eigenvalue-minimisations : 9216
+ total energy-change (2. order) :-0.5752413E+03 (-0.2415436E+04)
+ number of electron 26.0000000 magnetization
+ augmentation part 26.0000000 magnetization
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -527.41646070
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 35.33916255
+ PAW double counting = 1941.62980019 -1939.43826086
+ entropy T*S EENTRO = -0.00530052
+ eigenvalues EBANDS = -1293.52360327
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -575.24128006 eV
+
+ energy without entropy = -575.23597954 energy(sigma->0) = -575.23862980
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 2) ---------------------------------------
+
+
+ EDDIAG: cpu time 0.8612: real time 0.9058
+ RMM-DIIS: cpu time 1.0247: real time 1.0272
+ ORTHCH: cpu time 0.0935: real time 0.0937
+ DOS: cpu time 0.0037: real time 0.0037
+ --------------------------------------------
+ LOOP: cpu time 1.9831: real time 2.0305
+
+ eigenvalue-minimisations : 9216
+ total energy-change (2. order) : 0.6776269E+03 (-0.4029736E+03)
+ number of electron 26.0000000 magnetization
+ augmentation part 26.0000000 magnetization
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -527.41646070
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 35.33916255
+ PAW double counting = 1941.62980019 -1939.43826086
+ entropy T*S EENTRO = -0.00481541
+ eigenvalues EBANDS = -615.89714414
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = 102.38566418 eV
+
+ energy without entropy = 102.39047960 energy(sigma->0) = 102.38807189
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 3) ---------------------------------------
+
+
+ EDDIAG: cpu time 0.8578: real time 0.8850
+ RMM-DIIS: cpu time 0.9854: real time 0.9876
+ ORTHCH: cpu time 0.0927: real time 0.0950
+ DOS: cpu time 0.0039: real time 0.0038
+ --------------------------------------------
+ LOOP: cpu time 1.9398: real time 1.9715
+
+ eigenvalue-minimisations : 9216
+ total energy-change (2. order) :-0.1313635E+03 (-0.1511722E+03)
+ number of electron 26.0000000 magnetization
+ augmentation part 26.0000000 magnetization
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -527.41646070
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 35.33916255
+ PAW double counting = 1941.62980019 -1939.43826086
+ entropy T*S EENTRO = -0.00684255
+ eigenvalues EBANDS = -747.25860832
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -28.97782713 eV
+
+ energy without entropy = -28.97098459 energy(sigma->0) = -28.97440586
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 4) ---------------------------------------
+
+
+ EDDIAG: cpu time 0.8663: real time 0.8792
+ RMM-DIIS: cpu time 2.9235: real time 2.9296
+ ORTHCH: cpu time 0.0974: real time 0.0994
+ DOS: cpu time 0.0037: real time 0.0037
+ --------------------------------------------
+ LOOP: cpu time 3.8909: real time 3.9119
+
+ eigenvalue-minimisations : 29178
+ total energy-change (2. order) :-0.2071636E+02 (-0.8645846E+02)
+ number of electron 26.0000000 magnetization
+ augmentation part 26.0000000 magnetization
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -527.41646070
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 35.33916255
+ PAW double counting = 1941.62980019 -1939.43826086
+ entropy T*S EENTRO = -0.00577549
+ eigenvalues EBANDS = -767.97603184
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -49.69418359 eV
+
+ energy without entropy = -49.68840810 energy(sigma->0) = -49.69129585
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 5) ---------------------------------------
+
+
+ EDDIAG: cpu time 0.8588: real time 0.8713
+ RMM-DIIS: cpu time 3.2869: real time 3.2931
+ ORTHCH: cpu time 0.0916: real time 0.0917
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2189: real time 0.2195
+ MIXING: cpu time 0.0004: real time 0.0004
+ --------------------------------------------
+ LOOP: cpu time 4.4603: real time 4.4798
+
+ eigenvalue-minimisations : 32343
+ total energy-change (2. order) :-0.2221706E+01 (-0.1791219E+02)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7185645 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.99154E+01 rms(broyden)= 0.99154E+01
+ rms(prec ) = 0.10501E+02
+ weight for this iteration 100.00
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -527.41646070
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 35.33916255
+ PAW double counting = 1941.62980019 -1939.43826086
+ entropy T*S EENTRO = -0.00286525
+ eigenvalues EBANDS = -770.20064788
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -51.91588940 eV
+
+ energy without entropy = -51.91302415 energy(sigma->0) = -51.91445678
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 6) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0063: real time 0.0063
+ SETDIJ: cpu time 0.0030: real time 0.0030
+ EDDIAG: cpu time 0.8572: real time 0.8594
+ RMM-DIIS: cpu time 3.1432: real time 3.1501
+ ORTHCH: cpu time 0.0945: real time 0.0962
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2174: real time 0.2178
+ MIXING: cpu time 0.0010: real time 0.0005
+ --------------------------------------------
+ LOOP: cpu time 4.3263: real time 4.3370
+
+ eigenvalue-minimisations : 32157
+ total energy-change (2. order) : 0.3557072E+01 (-0.5126209E+01)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7344693 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.63965E+01 rms(broyden)= 0.63965E+01
+ rms(prec ) = 0.64289E+01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 2.3193
+ 2.3193
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -478.34595767
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.69314398
+ PAW double counting = 2583.11263522 -2584.59837190
+ entropy T*S EENTRO = -0.00315334
+ eigenvalues EBANDS = -810.39049628
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.35881744 eV
+
+ energy without entropy = -48.35566410 energy(sigma->0) = -48.35724077
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 7) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0086: real time 0.0151
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8614: real time 0.8634
+ RMM-DIIS: cpu time 3.0067: real time 3.0125
+ ORTHCH: cpu time 0.0904: real time 0.0906
+ DOS: cpu time 0.0038: real time 0.0038
+ CHARGE: cpu time 0.2174: real time 0.2189
+ MIXING: cpu time 0.0004: real time 0.0004
+ --------------------------------------------
+ LOOP: cpu time 4.1915: real time 4.2075
+
+ eigenvalue-minimisations : 31891
+ total energy-change (2. order) :-0.1869340E+00 (-0.1169757E+01)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7769450 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.10740E+01 rms(broyden)= 0.10740E+01
+ rms(prec ) = 0.13069E+01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.5887
+ 1.0277 2.1498
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -468.77317788
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.19468253
+ PAW double counting = 3317.64592811 -3318.50891194
+ entropy T*S EENTRO = -0.00279364
+ eigenvalues EBANDS = -820.27486120
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.54575148 eV
+
+ energy without entropy = -48.54295784 energy(sigma->0) = -48.54435466
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 8) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0061: real time 0.0062
+ SETDIJ: cpu time 0.0027: real time 0.0027
+ EDDIAG: cpu time 0.8569: real time 0.8592
+ RMM-DIIS: cpu time 3.1012: real time 3.1079
+ ORTHCH: cpu time 0.0908: real time 0.0928
+ DOS: cpu time 0.0038: real time 0.0038
+ CHARGE: cpu time 0.2182: real time 0.2185
+ MIXING: cpu time 0.0005: real time 0.0005
+ --------------------------------------------
+ LOOP: cpu time 4.2803: real time 4.2918
+
+ eigenvalue-minimisations : 29478
+ total energy-change (2. order) : 0.4696527E+00 (-0.1641795E+00)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7495559 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.94387E+00 rms(broyden)= 0.94387E+00
+ rms(prec ) = 0.94566E+00
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.7834
+ 1.5400 1.9052 1.9052
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -481.10425992
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.50004761
+ PAW double counting = 3311.78596750 -3311.19575724
+ entropy T*S EENTRO = -0.00267424
+ eigenvalues EBANDS = -809.23280508
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07609882 eV
+
+ energy without entropy = -48.07342458 energy(sigma->0) = -48.07476170
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 9) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0065: real time 0.0165
+ SETDIJ: cpu time 0.0029: real time 0.0029
+ EDDIAG: cpu time 0.8609: real time 0.8633
+ RMM-DIIS: cpu time 2.9123: real time 2.9192
+ ORTHCH: cpu time 0.0968: real time 0.0971
+ DOS: cpu time 0.0038: real time 0.0038
+ CHARGE: cpu time 0.2174: real time 0.2179
+ MIXING: cpu time 0.0005: real time 0.0005
+ --------------------------------------------
+ LOOP: cpu time 4.1010: real time 4.1212
+
+ eigenvalue-minimisations : 31189
+ total energy-change (2. order) :-0.4703762E-01 (-0.5300665E-01)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7619850 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.37364E+00 rms(broyden)= 0.37364E+00
+ rms(prec ) = 0.50262E+00
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.8041
+ 2.5350 2.5350 1.0732 1.0732
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -476.54735144
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.37995814
+ PAW double counting = 3192.69887022 -3192.42542193
+ entropy T*S EENTRO = -0.00286656
+ eigenvalues EBANDS = -813.39970742
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.12313644 eV
+
+ energy without entropy = -48.12026988 energy(sigma->0) = -48.12170316
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 10) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0062: real time 0.0062
+ SETDIJ: cpu time 0.0027: real time 0.0027
+ EDDIAG: cpu time 0.8582: real time 0.8613
+ RMM-DIIS: cpu time 3.1267: real time 3.1349
+ ORTHCH: cpu time 0.0904: real time 0.0905
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2194: real time 0.2197
+ MIXING: cpu time 0.0020: real time 0.0015
+ --------------------------------------------
+ LOOP: cpu time 4.3092: real time 4.3205
+
+ eigenvalue-minimisations : 29390
+ total energy-change (2. order) : 0.2966125E-01 (-0.4742700E-01)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7423041 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.31849E+00 rms(broyden)= 0.31849E+00
+ rms(prec ) = 0.35866E+00
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.5899
+ 2.6842 1.6840 1.6840 1.0048 0.8926
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -482.81360439
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.53890578
+ PAW double counting = 3121.35646553 -3120.29858400
+ entropy T*S EENTRO = -0.00297373
+ eigenvalues EBANDS = -808.04706694
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.09347519 eV
+
+ energy without entropy = -48.09050147 energy(sigma->0) = -48.09198833
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 11) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0050: real time 0.0156
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8582: real time 0.8607
+WARNING in EDDRMM: call to ZHEGV failed, returncode = 8 4 2
+ RMM-DIIS: cpu time 3.6274: real time 3.6355
+ ORTHCH: cpu time 0.0911: real time 0.0912
+ DOS: cpu time 0.0038: real time 0.0038
+ CHARGE: cpu time 0.2177: real time 0.2182
+ MIXING: cpu time 0.0005: real time 0.0005
+ --------------------------------------------
+ LOOP: cpu time 4.8065: real time 4.8283
+
+ eigenvalue-minimisations : 29737
+ total energy-change (2. order) : 0.2156037E-01 (-0.5977483E-02)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7466636 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.53781E-01 rms(broyden)= 0.53781E-01
+ rms(prec ) = 0.62072E-01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.3891
+ 2.6733 1.7034 1.7034 1.0132 0.8845 0.3572
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.78216452
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47821903
+ PAW double counting = 3189.30069522 -3188.42317580
+ entropy T*S EENTRO = -0.00299710
+ eigenvalues EBANDS = -809.81587419
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07191482 eV
+
+ energy without entropy = -48.06891772 energy(sigma->0) = -48.07041627
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 12) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0062: real time 0.0062
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8529: real time 0.8567
+WARNING in EDDRMM: call to ZHEGV failed, returncode = 8 4 2
+ RMM-DIIS: cpu time 3.4862: real time 3.4923
+ ORTHCH: cpu time 0.0915: real time 0.0917
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2184: real time 0.2187
+ MIXING: cpu time 0.0006: real time 0.0006
+ --------------------------------------------
+ LOOP: cpu time 4.6622: real time 4.6726
+
+ eigenvalue-minimisations : 30551
+ total energy-change (2. order) : 0.8869093E-03 (-0.8814040E-03)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7475456 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.17327E-01 rms(broyden)= 0.17326E-01
+ rms(prec ) = 0.19640E-01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.3147
+ 2.6706 1.6701 1.6701 1.0021 0.9039 0.6430 0.6430
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.57803071
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47228286
+ PAW double counting = 3197.70507194 -3196.84324057
+ entropy T*S EENTRO = -0.00301416
+ eigenvalues EBANDS = -809.99747983
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07102791 eV
+
+ energy without entropy = -48.06801376 energy(sigma->0) = -48.06952083
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 13) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0063: real time 0.0063
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8539: real time 0.8558
+ RMM-DIIS: cpu time 3.3017: real time 3.3099
+ ORTHCH: cpu time 0.0903: real time 0.0905
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2175: real time 0.2177
+ MIXING: cpu time 0.0006: real time 0.0005
+ --------------------------------------------
+ LOOP: cpu time 4.4767: real time 4.4872
+
+ eigenvalue-minimisations : 27907
+ total energy-change (2. order) :-0.1094469E-03 (-0.1819417E-03)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7473309 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.41060E-01 rms(broyden)= 0.41060E-01
+ rms(prec ) = 0.43597E-01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.5889
+ 2.6762 2.6235 1.8063 1.8063 1.0829 1.0829 0.8167 0.8167
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.71544123
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47703876
+ PAW double counting = 3194.30045733 -3193.42429176
+ entropy T*S EENTRO = -0.00304443
+ eigenvalues EBANDS = -809.87923859
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07113736 eV
+
+ energy without entropy = -48.06809293 energy(sigma->0) = -48.06961515
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 14) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0064: real time 0.0152
+ SETDIJ: cpu time 0.0027: real time 0.0027
+ EDDIAG: cpu time 0.8625: real time 0.8642
+ RMM-DIIS: cpu time 3.4730: real time 3.4807
+ ORTHCH: cpu time 0.0958: real time 0.0960
+ DOS: cpu time 0.0033: real time 0.0033
+ CHARGE: cpu time 0.2181: real time 0.2185
+ MIXING: cpu time 0.0006: real time 0.0006
+ --------------------------------------------
+ LOOP: cpu time 4.6625: real time 4.6814
+
+ eigenvalue-minimisations : 28867
+ total energy-change (2. order) :-0.4802788E-04 (-0.5334102E-04)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7471770 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.11318E-01 rms(broyden)= 0.11318E-01
+ rms(prec ) = 0.20045E-01
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.4879
+ 2.6297 2.6297 1.6936 1.3132 1.1879 1.1879 0.9918 0.8785 0.8785
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.78948024
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47969724
+ PAW double counting = 3200.45165620 -3199.56117304
+ entropy T*S EENTRO = -0.00304439
+ eigenvalues EBANDS = -809.82222371
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07118539 eV
+
+ energy without entropy = -48.06814100 energy(sigma->0) = -48.06966319
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 15) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0062: real time 0.0062
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8568: real time 0.8614
+ RMM-DIIS: cpu time 3.2087: real time 3.2162
+ ORTHCH: cpu time 0.0943: real time 0.0959
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2176: real time 0.2180
+ MIXING: cpu time 0.0006: real time 0.0006
+ --------------------------------------------
+ LOOP: cpu time 4.3907: real time 4.4048
+
+ eigenvalue-minimisations : 27375
+ total energy-change (2. order) : 0.7992486E-04 (-0.8025044E-04)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7478758 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.46851E-02 rms(broyden)= 0.46851E-02
+ rms(prec ) = 0.51870E-02
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.3579
+ 2.7839 2.5249 1.4729 1.4729 1.1537 1.1537 0.9594 0.9133 0.9133 0.2310
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.57031732
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47337481
+ PAW double counting = 3205.37333857 -3204.50053139
+ entropy T*S EENTRO = -0.00305052
+ eigenvalues EBANDS = -810.01730217
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07110546 eV
+
+ energy without entropy = -48.06805494 energy(sigma->0) = -48.06958020
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 16) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0062: real time 0.0169
+ SETDIJ: cpu time 0.0029: real time 0.0029
+ EDDIAG: cpu time 0.8529: real time 0.8553
+ RMM-DIIS: cpu time 2.8952: real time 2.9013
+ ORTHCH: cpu time 0.0905: real time 0.0907
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2153: real time 0.2156
+ MIXING: cpu time 0.0008: real time 0.0008
+ --------------------------------------------
+ LOOP: cpu time 4.0684: real time 4.0872
+
+ eigenvalue-minimisations : 26944
+ total energy-change (2. order) : 0.6773008E-05 (-0.9673818E-05)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7479216 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.39083E-02 rms(broyden)= 0.39083E-02
+ rms(prec ) = 0.48812E-02
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.3253
+ 2.8948 2.4553 1.5944 1.2157 1.2157 1.0656 1.0656 0.9218 0.9218 0.6138
+ 0.6138
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.57208370
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47337122
+ PAW double counting = 3205.24324251 -3204.37022275
+ entropy T*S EENTRO = -0.00304889
+ eigenvalues EBANDS = -810.01573963
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07109869 eV
+
+ energy without entropy = -48.06804980 energy(sigma->0) = -48.06957425
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 17) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0061: real time 0.0061
+ SETDIJ: cpu time 0.0027: real time 0.0027
+ EDDIAG: cpu time 0.8539: real time 0.8561
+ RMM-DIIS: cpu time 2.4896: real time 2.4948
+ ORTHCH: cpu time 0.0919: real time 0.0936
+ DOS: cpu time 0.0037: real time 0.0037
+ CHARGE: cpu time 0.2152: real time 0.2157
+ MIXING: cpu time 0.0007: real time 0.0007
+ --------------------------------------------
+ LOOP: cpu time 3.6630: real time 3.6735
+
+ eigenvalue-minimisations : 21111
+ total energy-change (2. order) :-0.1378648E-06 (-0.3109433E-05)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7479123 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.28181E-02 rms(broyden)= 0.28181E-02
+ rms(prec ) = 0.39149E-02
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.4710
+ 2.9079 2.2924 2.2924 1.6621 1.6621 1.2410 1.2410 0.9431 0.9431 0.9557
+ 0.9062 0.6049
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.57833821
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47347056
+ PAW double counting = 3205.16062297 -3204.28612410
+ entropy T*S EENTRO = -0.00305011
+ eigenvalues EBANDS = -810.01106249
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07109883 eV
+
+ energy without entropy = -48.06804872 energy(sigma->0) = -48.06957377
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 18) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0113: real time 0.0161
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8562: real time 0.8582
+ RMM-DIIS: cpu time 3.0636: real time 3.0697
+ ORTHCH: cpu time 0.0905: real time 0.0907
+ DOS: cpu time 0.0036: real time 0.0037
+ CHARGE: cpu time 0.2153: real time 0.2157
+ MIXING: cpu time 0.0008: real time 0.0008
+ --------------------------------------------
+ LOOP: cpu time 4.2441: real time 4.2575
+
+ eigenvalue-minimisations : 25981
+ total energy-change (2. order) : 0.2551284E-05 (-0.2256845E-05)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7478071 magnetization
+
+ Broyden mixing:
+ rms(total) = 0.71135E-03 rms(broyden)= 0.71134E-03
+ rms(prec ) = 0.91622E-03
+ weight for this iteration 100.00
+
+ eigenvalues of (default mixing * dielectric matrix)
+ average eigenvalue GAMMA= 1.4171
+ 2.6811 2.5386 1.7609 1.7609 1.7689 1.4591 1.4591 0.8833 0.8833 1.0096
+ 0.8463 0.6854 0.6854
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.61644072
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47429532
+ PAW double counting = 3204.55531159 -3203.67482965
+ entropy T*S EENTRO = -0.00304973
+ eigenvalues EBANDS = -809.97976563
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07109628 eV
+
+ energy without entropy = -48.06804655 energy(sigma->0) = -48.06957141
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+
+--------------------------------------- Iteration 1( 19) ---------------------------------------
+
+
+ POTLOK: cpu time 0.0061: real time 0.0061
+ SETDIJ: cpu time 0.0028: real time 0.0028
+ EDDIAG: cpu time 0.8529: real time 0.8552
+ RMM-DIIS: cpu time 2.5286: real time 2.5345
+ ORTHCH: cpu time 0.0907: real time 0.0909
+ DOS: cpu time 0.0037: real time 0.0037
+ --------------------------------------------
+ LOOP: cpu time 3.4848: real time 3.4932
+
+ eigenvalue-minimisations : 18928
+ total energy-change (2. order) : 0.3110167E-06 (-0.2199411E-06)
+ number of electron 26.0000010 magnetization
+ augmentation part 1.7478071 magnetization
+
+ Free energy of the ion-electron system (eV)
+ ---------------------------------------------------
+ alpha Z PSCENC = 131.43308500
+ Ewald energy TEWEN = -1959.85115532
+ -Hartree energ DENC = -480.61520692
+ -exchange EXHF = 0.00000000
+ -V(xc)+E(xc) XCENC = 33.47431066
+ PAW double counting = 3204.45646866 -3203.57677692
+ entropy T*S EENTRO = -0.00304986
+ eigenvalues EBANDS = -809.98022412
+ atomic energy EATOM = 3036.59145287
+ Solvation Ediel_sol = 0.00000000
+ ---------------------------------------------------
+ free energy TOTEN = -48.07109596 eV
+
+ energy without entropy = -48.06804610 energy(sigma->0) = -48.06957103
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+
+--------------------------------------------------------------------------------------------------------
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+ k-point 509 : 0.2667 0.4667 0.4667
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+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ soft charge-density along one line, spin component 1
+ 0 1 2 3 4 5 6 7 8 9
+ total charge-density along one line
+
+ pseudopotential strength for first ion, spin component: 1
+ 29.271 27.905 24.284 -0.000 -0.000 0.000 0.000 0.000
+ 27.905 26.602 23.219 -0.000 -0.000 0.000 0.000 0.000
+ 24.284 23.219 11.179 -0.000 -0.000 0.000 -0.000 -0.000
+ -0.000 -0.000 -0.000 -15.093 -0.000 0.000 -10.182 0.000
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+ total augmentation occupancy for first ion, spin component: 1
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+******* 102.736 -0.592 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.235 0.000 -0.260 0.000 -0.000
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+ 0.000 0.000 0.000 0.000 0.000 2.031 0.000 0.000 0.028 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.029 -0.000 0.000 0.015 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
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+ 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 3.829 0.000 0.000 -0.000 0.000 -1.514 0.000
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+ -1.192 1.235 -0.008 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 3.492 0.000 0.024 0.000 -0.000
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+ 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.695 -0.000 0.000 0.000 0.000 0.735
+ 0.498 -0.524 0.003 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.540 0.000 -0.012 0.000 0.000
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+ 0.000 0.000 0.000 0.000 -0.005 0.000 0.000 -0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 -0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 0.000 0.000 0.000 0.000 0.000 -0.000 0.000 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+
+
+------------------------ aborting loop because EDIFF is reached ----------------------------------------
+
+
+ CHARGE: cpu time 0.2175: real time 0.2179
+ FORLOC: cpu time 0.0005: real time 0.0005
+ FORNL : cpu time 0.5624: real time 0.5636
+ STRESS: cpu time 4.6134: real time 4.6282
+ FORCOR: cpu time 0.0057: real time 0.0064
+ FORHAR: cpu time 0.0014: real time 0.0014
+ MIXING: cpu time 0.0007: real time 0.0007
+ OFIELD: cpu time 0.0000: real time 0.0000
+
+ FORCE on cell =-STRESS in cart. coord. units (eV):
+ Direction XX YY ZZ XY YZ ZX
+ --------------------------------------------------------------------------------------
+ Alpha Z 131.43309 131.43309 131.43309
+ Ewald -692.66714 -666.25642 -600.92887 0.00000 -0.00000 0.00000
+ Hartree 135.39867 151.55448 193.64184 -0.00000 -0.00000 -0.00000
+ E(xc) -140.07087 -140.06544 -140.05539 -0.00000 0.00000 0.00000
+ Local 156.14173 113.44933 3.98511 0.00000 0.00000 0.00000
+ n-local -184.49986 -184.69575 -185.00090 -0.90955 -1.02411 -0.99577
+ augment 2.00968 1.96706 1.78410 0.00000 -0.00000 -0.00000
+ Kinetic 586.69353 589.41039 597.73423 1.78901 -0.65923 -0.20796
+ Fock 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
+ -------------------------------------------------------------------------------------
+ Total -5.56117 -3.20326 2.59322 0.00000 -0.00000 0.00000
+ in kB -214.84834 -123.75353 100.18546 0.00000 -0.00000 0.00000
+ external pressure = -79.47 kB Pullay stress = 0.00 kB
+
+
+ VOLUME and BASIS-vectors are now :
+ -----------------------------------------------------------------------------
+ energy-cutoff : 600.00
+ volume of cell : 41.47
+ direct lattice vectors reciprocal lattice vectors
+ 3.669611000 0.000000000 0.000000000 0.272508448 0.000000000 0.000000000
+ 0.000000000 3.557440000 0.000000000 0.000000000 0.281101016 0.000000000
+ 0.000000000 0.000000000 3.176781000 0.000000000 0.000000000 0.314784053
+
+ length of vectors
+ 3.669611000 3.557440000 3.176781000 0.272508448 0.281101016 0.314784053
+
+
+ FORCES acting on ions
+ electron-ion (+dipol) ewald-force non-local-force convergence-correction
+ -----------------------------------------------------------------------------------------------
+ -.118E-13 -.390E-14 0.138E-13 -.976E-14 -.123E-13 0.429E-14 -.148E-21 -.385E-22 0.214E-22 0.190E-13 0.402E-13 -.748E-13
+ -.203E-14 0.118E-12 -.610E-14 -.126E-14 0.943E-14 -.634E-15 0.135E-24 -.989E-23 -.124E-22 0.125E-13 -.691E-14 0.178E-13
+ 0.122E-12 -.521E-14 -.592E-12 0.654E-14 0.177E-15 -.121E-15 0.864E-23 0.363E-22 -.325E-24 -.105E-13 0.354E-14 0.142E-13
+ 0.123E-12 -.343E-12 -.754E-12 0.496E-14 0.107E-14 0.499E-15 0.583E-22 -.440E-22 0.929E-22 -.164E-13 -.623E-14 -.585E-14
+ -----------------------------------------------------------------------------------------------
+ 0.231E-12 -.235E-12 -.134E-11 0.483E-15 -.166E-14 0.404E-14 -.808E-22 -.560E-22 0.102E-21 0.463E-14 0.306E-13 -.486E-13
+
+
+ POSITION TOTAL-FORCE (eV/Angst)
+ -----------------------------------------------------------------------------------
+ 0.00000 0.00000 0.00000 0.000000 -0.000000 -0.000000
+ 0.00000 1.77872 1.58839 0.000000 -0.000000 -0.000000
+ 1.83481 0.00000 1.58839 -0.000000 -0.000000 0.000000
+ 1.83481 1.77872 0.00000 0.000000 0.000000 0.000000
+ -----------------------------------------------------------------------------------
+ total drift: 0.000000 -0.000000 -0.000000
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+
+ FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)
+ ---------------------------------------------------
+ free energy TOTEN = -48.07109596 eV
+
+ energy without entropy= -48.06804610 energy(sigma->0) = -48.06957103
+
+ SIGMA = 0.10000000
+
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ POTLOK: cpu time 0.0095: real time 0.0103
+
+
+--------------------------------------------------------------------------------------------------------
+
+
+ writing wavefunctions
+ LOOP+: cpu time 80.5972: real time 81.1155
+ 4ORBIT: cpu time 0.0000: real time 0.0000
+
+ total amount of memory used by VASP MPI-rank0 355020. kBytes
+=======================================================================
+
+ base : 30000. kBytes
+ nonl-proj : 299130. kBytes
+ fftplans : 441. kBytes
+ grid : 1138. kBytes
+ one-center: 129. kBytes
+ wavefun : 24182. kBytes
+
+
+
+ General timing and accounting informations for this job:
+ ========================================================
+
+ Total CPU time used (sec): 84.193
+ User time (sec): 82.086
+ System time (sec): 2.107
+ Elapsed time (sec): 85.614
+
+ Maximum memory used (kb): 339860.
+ Average memory used (kb): 0.
+
+ Minor page faults: 520341
+ Major page faults: 0
+ Voluntary context switches: 1787
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
index 3d83ff7dc1..ab347be568 100644
--- a/examples/COUPLE/lammps_vasp/README
+++ b/examples/COUPLE/lammps_vasp/README
@@ -5,7 +5,7 @@ See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
Section_howto.html#howto10 for more details on how client/server
coupling works in LAMMPS.
-In this dir, the vasp_warp.py is a wrapper on the VASP quantum DFT
+In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
code so it can work as a "server" code which LAMMPS drives as a
"client" code to perform ab initio MD. LAMMPS performs the MD
timestepping, sends VASP a current set of coordinates each timestep,
@@ -34,6 +34,40 @@ You can leave off the -z if you do not have ZMQ on your system.
----------------
+Prepare to use VASP and the vasp_wrapper.py script
+
+You can run the vasp_wrap.py script as-is to test that the
+coupling between it and LAMMPS is functional. But the as-is
+version will not attempt to run VASP.
+
+To do this, you must edit the 1st vaspcmd line at the top of
+vasp_wrapper.py to be the launch command needed to run VASP on your
+system. It can be a command to run VASP in serial or in parallel,
+e.g. an mpirun command. Then comment out the 2nd vaspcmd line
+immediately following it.
+
+Insure you have the necessary VASP input files in this
+directory, suitable for the VASP calculation you want to perform:
+
+INCAR
+KPOINTS
+POSCAR_template
+POTCAR
+
+Examples of all but the POTCAR file are provided. As explained below,
+POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
+be used to test the LAMMPS/VASP coupling. The POTCAR file is a
+proprietary VASP file, so use one from your VASP installation.
+
+Note that the POSCAR_template file should be matched to the LAMMPS
+input script (# of atoms and atom types, box size, etc). The provided
+POSCAR_W matches in.client.W.
+
+NOTE: explain how vasp_wrapper.py finds the cslib.py wrapper on the
+CSlib to import.
+
+----------------
+
To run in client/server mode:
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
@@ -76,15 +110,3 @@ ZMQ mode of messaging:
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
% python vasp_wrap.py zmq POSCAR_W
-
---------------
-
-The provided data.W file (for LAMMPS) and POSCAR_W file (for VASP) are
-for a simple 2-atom unit cell of bcc tungsten (W). You could
-replicate this with LAMMPS to create a larger system. The
-vasp_wrap.py script needs to be generalized to create an appropriate
-POSCAR_W file for a larger box.
-
-VASP input file include the sample INCAR and KPOINTS files provided.
-A POTCAR file is also needed, which should come from your VASP package
-installation.
diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py
index 35955b6adb..30d449e31c 100644
--- a/examples/COUPLE/lammps_vasp/vasp_wrap.py
+++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py
@@ -23,13 +23,15 @@
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
-import sys
-import commands
+import sys,subprocess
import xml.etree.ElementTree as ET
from cslib import CSlib
+# comment out 2nd line once 1st line is correct for your system
+
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
+vaspcmd = "touch tmp"
# enums matching FixClientMD class in LAMMPS
@@ -84,18 +86,18 @@ def poscar_write(poscar,natoms,ntypes,types,coords,box):
# header, including box size
- print >>psnew,psold[0],
- print >>psnew,psold[1],
- print >>psnew,"%g 0.0 0.0" % box[0]
- print >>psnew,"0.0 %g 0.0" % box[1]
- print >>psnew,"0.0 0.0 %g" % box[2]
- print >>psnew,psold[5],
- print >>psnew,psold[6],
+ psnew.write(psold[0])
+ psnew.write(psold[1])
+ psnew.write("%g 0.0 0.0\n" % box[0])
+ psnew.write("0.0 %g 0.0\n" % box[1])
+ psnew.write("0.0 0.0 %g\n" % box[2])
+ psnew.write(psold[5])
+ psnew.write(psold[6])
# per-atom coords
# grouped by types
-
- print >>psnew,"Cartesian"
+
+ psnew.write("Cartesian\n")
for itype in range(1,ntypes+1):
for i in range(natoms):
@@ -103,8 +105,8 @@ def poscar_write(poscar,natoms,ntypes,types,coords,box):
x = coords[3*i+0]
y = coords[3*i+1]
z = coords[3*i+2]
- aline = " %g %g %g" % (x,y,z)
- print >>psnew,aline
+ aline = " %g %g %g\n" % (x,y,z)
+ psnew.write(aline)
psnew.close()
@@ -209,10 +211,9 @@ while 1:
# invoke VASP
- print "Launching VASP ..."
+ print "\nLaunching VASP ..."
print vaspcmd
- out = commands.getoutput(vaspcmd)
- print out
+ subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
# process VASP output
diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py
index e2ed78b61b..0ba3516255 100644
--- a/lib/message/cslib/src/cslib.py
+++ b/lib/message/cslib/src/cslib.py
@@ -6,8 +6,8 @@
# Copyright 2018 National Technology & Engineering Solutions of
# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
# NTESS, the U.S. Government retains certain rights in this software.
-# This software is distributed under the GNU Lesser General Public
-# License (LGPL).
+# This software is distributed under the modified Berkeley Software
+# Distribution (BSD) License.
#
# See the README file in the top-level CSlib directory.
# -------------------------------------------------------------------------
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index a6ecf5cd60..329ce1fbd9 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <cstring.h>
+#include <cstring>
#include "message.h"
#include "error.h"
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
index c8de6de466..f587fb76df 100644
--- a/src/MESSAGE/server.cpp
+++ b/src/MESSAGE/server.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <cstring.h>
+#include <cstring>
#include "server.h"
#include "error.h"
--
GitLab
From b2c75cc0b90a8b60565f25fabc91e4a96bbc22a8 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 24 Jul 2018 17:29:52 -0600
Subject: [PATCH 060/332] enable LAMMPS/VASP coupling to work w/out using VASP
---
examples/COUPLE/lammps_vasp/OUTCAR | 14953 ----------------------
examples/COUPLE/lammps_vasp/README | 10 +-
examples/COUPLE/lammps_vasp/vasprun.xml | 12329 ++++++++++++++++++
3 files changed, 12336 insertions(+), 14956 deletions(-)
delete mode 100644 examples/COUPLE/lammps_vasp/OUTCAR
create mode 100644 examples/COUPLE/lammps_vasp/vasprun.xml
diff --git a/examples/COUPLE/lammps_vasp/OUTCAR b/examples/COUPLE/lammps_vasp/OUTCAR
deleted file mode 100644
index 6e8ef736cc..0000000000
--- a/examples/COUPLE/lammps_vasp/OUTCAR
+++ /dev/null
@@ -1,14953 +0,0 @@
- vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Aug 01 2017 10:32:50) complex
-
- executed on LinuxIFC date 2017.12.19 15:22:45
- running on 9 total cores
- distrk: each k-point on 9 cores, 1 groups
- distr: one band on NCORES_PER_BAND= 1 cores, 9 groups
-
-
---------------------------------------------------------------------------------------------------------
-
-
- INCAR:
- POTCAR: PAW_PBE W_sv_GW 23Mar2010
- POTCAR: PAW_PBE Be_sv_GW 31Mar2010
-
- -----------------------------------------------------------------------------
-| |
-| W W AA RRRRR N N II N N GGGG !!! |
-| W W A A R R NN N II NN N G G !!! |
-| W W A A R R N N N II N N N G !!! |
-| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
-| WW WW A A R R N NN II N NN G G |
-| W W A A R R N N II N N GGGG !!! |
-| |
-| For optimal performance we recommend to set |
-| NCORE= 4 - approx SQRT( number of cores) |
-| NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). |
-| This setting can greatly improve the performance of VASP for DFT. |
-| The default, NCORE=1 might be grossly inefficient |
-| on modern multi-core architectures or massively parallel machines. |
-| Do your own testing !!!! |
-| Unfortunately you need to use the default for GW and RPA calculations. |
-| (for HF NCORE is supported but not extensively tested yet) |
-| |
- -----------------------------------------------------------------------------
-
- POTCAR: PAW_PBE W_sv_GW 23Mar2010
- VRHFIN =W: 5p6s5d
- LEXCH = PE
- EATOM = 1863.8917 eV, 136.9922 Ry
-
- TITEL = PAW_PBE W_sv_GW 23Mar2010
- LULTRA = F use ultrasoft PP ?
- IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
- RPACOR = 1.500 partial core radius
- POMASS = 183.850; ZVAL = 14.000 mass and valenz
- RCORE = 2.300 outmost cutoff radius
- RWIGS = 2.600; RWIGS = 1.376 wigner-seitz radius (au A)
- ENMAX = 317.132; ENMIN = 237.849 eV
- RCLOC = 1.609 cutoff for local pot
- LCOR = T correct aug charges
- LPAW = T paw PP
- EAUG = 807.757
- DEXC = 0.000
- RMAX = 2.349 core radius for proj-oper
- RAUG = 1.300 factor for augmentation sphere
- RDEP = 2.382 radius for radial grids
- RDEPT = 1.832 core radius for aug-charge
-
- Atomic configuration
- 14 entries
- n l j E occ.
- 1 0 0.50 -69464.1497 2.0000
- 2 0 0.50 -11984.7400 2.0000
- 2 1 1.50 -10478.3405 6.0000
- 3 0 0.50 -2757.5605 2.0000
- 3 1 1.50 -2311.6706 6.0000
- 3 2 2.50 -1799.5973 10.0000
- 4 0 0.50 -566.1609 2.0000
- 4 1 1.50 -419.9482 6.0000
- 4 2 2.50 -234.8191 10.0000
- 4 3 3.50 -29.7363 14.0000
- 5 0 0.50 -75.5905 2.0000
- 5 1 1.50 -39.9756 6.0000
- 5 2 2.50 -2.4479 6.0000
- 5 3 2.50 -1.3606 0.0000
- Description
- l E TYP RCUT TYP RCUT
- 0 -75.5905419 23 1.500
- 0 -76.9511245 23 1.500
- 0 108.8466080 23 1.500
- 1 -39.9756040 23 1.800
- 1 68.0291300 23 1.800
- 2 -2.4478587 23 2.150
- 2 -0.0030619 23 2.150
- 3 4.0817478 23 2.300
- local pseudopotential read in
- partial core-charges read in
- partial kinetic energy density read in
- kinetic energy density of atom read in
- atomic valenz-charges read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 1 read in
- real space projection operators read in
- non local Contribution for L= 1 read in
- real space projection operators read in
- non local Contribution for L= 2 read in
- real space projection operators read in
- non local Contribution for L= 2 read in
- real space projection operators read in
- non local Contribution for L= 3 read in
- real space projection operators read in
- PAW grid and wavefunctions read in
-
- number of l-projection operators is LMAX = 8
- number of lm-projection operators is LMMAX = 26
-
- POTCAR: PAW_PBE Be_sv_GW 31Mar2010
- VRHFIN =Be: s2p0
- LEXCH = PE
- EATOM = 390.9322 eV, 28.7327 Ry
-
- TITEL = PAW_PBE Be_sv_GW 31Mar2010
- LULTRA = F use ultrasoft PP ?
- IUNSCR = 0 unscreen: 0-lin 1-nonlin 2-no
- RPACOR = 0.000 partial core radius
- POMASS = 9.013; ZVAL = 4.000 mass and valenz
- RCORE = 1.300 outmost cutoff radius
- RWIGS = 1.600; RWIGS = 0.847 wigner-seitz radius (au A)
- ENMAX = 537.454; ENMIN = 403.090 eV
- RCLOC = 1.007 cutoff for local pot
- LCOR = T correct aug charges
- LPAW = T paw PP
- EAUG = 1293.449
- RMAX = 1.324 core radius for proj-oper
- RAUG = 1.300 factor for augmentation sphere
- RDEP = 1.364 radius for radial grids
- RDEPT = 1.200 core radius for aug-charge
-
- Atomic configuration
- 5 entries
- n l j E occ.
- 1 0 0.50 -108.8489 2.0000
- 1 0 0.50 -107.4860 0.0000
- 2 1 0.50 -2.9389 2.0000
- 3 2 1.50 -1.3606 0.0000
- 4 3 2.50 -1.3606 0.0000
- Description
- l E TYP RCUT TYP RCUT
- 0 -108.8489274 23 1.100
- 0 -107.4860254 23 1.100
- 0 95.2407820 23 1.100
- 1 -2.9389331 23 1.300
- 1 15.5352276 23 1.300
- 2 54.4233040 23 1.300
- local pseudopotential read in
- kinetic energy density of atom read in
- atomic valenz-charges read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 0 read in
- real space projection operators read in
- non local Contribution for L= 1 read in
- real space projection operators read in
- non local Contribution for L= 1 read in
- real space projection operators read in
- non local Contribution for L= 2 read in
- real space projection operators read in
- PAW grid and wavefunctions read in
-
- number of l-projection operators is LMAX = 6
- number of lm-projection operators is LMMAX = 14
-
- PAW_PBE W_sv_GW 23Mar2010 :
- energy of atom 1 EATOM=-1863.8917
- kinetic energy error for atom= 0.0147 (will be added to EATOM!!)
- PAW_PBE Be_sv_GW 31Mar2010 :
- energy of atom 2 EATOM= -390.9322
- kinetic energy error for atom= 0.0274 (will be added to EATOM!!)
-
-
- POSCAR: WBe3 L1_2
- positions in direct lattice
- No initial velocities read in
- exchange correlation table for LEXCH = 8
- RHO(1)= 0.500 N(1) = 2000
- RHO(2)= 100.500 N(2) = 4000
-
-
-
---------------------------------------------------------------------------------------------------------
-
-
- ion position nearest neighbor table
- 1 0.000 0.000 0.000- 2 2.38 2 2.38 2 2.38 2 2.38 3 2.43 3 2.43 3 2.43 3 2.43
- 4 2.56 4 2.56 4 2.56 4 2.56
- 2 0.000 0.500 0.500- 1 2.38 1 2.38 1 2.38 1 2.38
- 3 0.500 0.000 0.500- 1 2.43 1 2.43 1 2.43 1 2.43
- 4 0.500 0.500 0.000- 1 2.56 1 2.56 1 2.56 1 2.56
-
- LATTYP: Found a simple orthorhombic cell.
- ALAT = 3.1767810000
- B/A-ratio = 1.1198253830
- C/A-ratio = 1.1551350250
-
- Lattice vectors:
-
- A1 = ( 0.0000000000, 0.0000000000, -3.1767810000)
- A2 = ( 0.0000000000, -3.5574400000, 0.0000000000)
- A3 = ( -3.6696110000, 0.0000000000, 0.0000000000)
-
-
-Analysis of symmetry for initial positions (statically):
-=====================================================================
- Subroutine PRICEL returns:
- Original cell was already a primitive cell.
-
-
- Routine SETGRP: Setting up the symmetry group for a
- simple orthorhombic supercell.
-
-
- Subroutine GETGRP returns: Found 8 space group operations
- (whereof 8 operations were pure point group operations)
- out of a pool of 8 trial point group operations.
-
-
-The static configuration has the point symmetry D_2h.
-
-
-Analysis of symmetry for dynamics (positions and initial velocities):
-=====================================================================
- Subroutine PRICEL returns:
- Original cell was already a primitive cell.
-
-
- Routine SETGRP: Setting up the symmetry group for a
- simple orthorhombic supercell.
-
-
- Subroutine GETGRP returns: Found 8 space group operations
- (whereof 8 operations were pure point group operations)
- out of a pool of 8 trial point group operations.
-
-
-The dynamic configuration has the point symmetry D_2h.
-
-
- Subroutine INISYM returns: Found 8 space group operations
- (whereof 8 operations are pure point group operations),
- and found 1 'primitive' translations
-
-
-
- KPOINTS: K-Points
-
-Automatic generation of k-mesh.
-Space group operators:
- irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z
- 1 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
- 2 -1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
- 3 1.000000 179.999999 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
- 4 -1.000000 179.999999 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
- 5 1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000
- 6 -1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000
- 7 1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
- 8 -1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
-
- Subroutine IBZKPT returns following result:
- ===========================================
-
- Found 512 irreducible k-points:
-
- Following reciprocal coordinates:
- Coordinates Weight
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-
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
- Dimension of arrays:
- k-points NKPTS = 512 k-points in BZ NKDIM = 512 number of bands NBANDS= 18
- number of dos NEDOS = 301 number of ions NIONS = 4
- non local maximal LDIM = 8 non local SUM 2l+1 LMDIM = 26
- total plane-waves NPLWV = 11520
- max r-space proj IRMAX = 1 max aug-charges IRDMAX= 9112
- dimension x,y,z NGX = 24 NGY = 24 NGZ = 20
- dimension x,y,z NGXF= 48 NGYF= 48 NGZF= 40
- support grid NGXF= 48 NGYF= 48 NGZF= 40
- ions per type = 1 3
- NGX,Y,Z is equivalent to a cutoff of 10.87, 11.22, 10.47 a.u.
- NGXF,Y,Z is equivalent to a cutoff of 21.75, 22.43, 20.93 a.u.
-
- SYSTEM = unknown system
- POSCAR = WBe3 L1_2
-
- Startparameter for this run:
- NWRITE = 2 write-flag & timer
- PREC = normal normal or accurate (medium, high low for compatibility)
- ISTART = 0 job : 0-new 1-cont 2-samecut
- ICHARG = 2 charge: 1-file 2-atom 10-const
- ISPIN = 1 spin polarized calculation?
- LNONCOLLINEAR = F non collinear calculations
- LSORBIT = F spin-orbit coupling
- INIWAV = 1 electr: 0-lowe 1-rand 2-diag
- LASPH = F aspherical Exc in radial PAW
- METAGGA= F non-selfconsistent MetaGGA calc.
-
- Electronic Relaxation 1
- ENCUT = 600.0 eV 44.10 Ry 6.64 a.u. 7.33 7.11 6.34*2*pi/ulx,y,z
- ENINI = 600.0 initial cutoff
- ENAUG = 1293.4 eV augmentation charge cutoff
- NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
- EDIFF = 0.1E-05 stopping-criterion for ELM
- LREAL = F real-space projection
- NLSPLINE = F spline interpolate recip. space projectors
- LCOMPAT= F compatible to vasp.4.4
- GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6
- LMAXPAW = -100 max onsite density
- LMAXMIX = 2 max onsite mixed and CHGCAR
- VOSKOWN= 0 Vosko Wilk Nusair interpolation
- ROPT = 0.00000 0.00000
- Ionic relaxation
- EDIFFG = 0.1E-02 stopping-criterion for IOM
- NSW = 0 number of steps for IOM
- NBLOCK = 1; KBLOCK = 1 inner block; outer block
- IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG
- NFREE = 0 steps in history (QN), initial steepest desc. (CG)
- ISIF = 2 stress and relaxation
- IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb
- ISYM = 2 0-nonsym 1-usesym 2-fastsym
- LCORR = T Harris-Foulkes like correction to forces
-
- POTIM = 0.5000 time-step for ionic-motion
- TEIN = 0.0 initial temperature
- TEBEG = 3500.0; TEEND =3500.0 temperature during run
- SMASS = -3.00 Nose mass-parameter (am)
- estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.308E-27a.u.
- SCALEE = 1.0000 scale energy and forces
- NPACO = 256; APACO = 16.0 distance and # of slots for P.C.
- PSTRESS= 0.0 pullay stress
-
- Mass of Ions in am
- POMASS = 183.85 9.01
- Ionic Valenz
- ZVAL = 14.00 4.00
- Atomic Wigner-Seitz radii
- RWIGS = -1.00 -1.00
- virtual crystal weights
- VCA = 1.00 1.00
- NELECT = 26.0000 total number of electrons
- NUPDOWN= -1.0000 fix difference up-down
-
- DOS related values:
- EMIN = 10.00; EMAX =-10.00 energy-range for DOS
- EFERMI = 0.00
- ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
-
- Electronic relaxation 2 (details)
- IALGO = 48 algorithm
- LDIAG = T sub-space diagonalisation (order eigenvalues)
- LSUBROT= F optimize rotation matrix (better conditioning)
- TURBO = 0 0=normal 1=particle mesh
- IRESTART = 0 0=no restart 2=restart with 2 vectors
- NREBOOT = 0 no. of reboots
- NMIN = 0 reboot dimension
- EREF = 0.00 reference energy to select bands
- IMIX = 4 mixing-type and parameters
- AMIX = 0.40; BMIX = 1.00
- AMIX_MAG = 1.60; BMIX_MAG = 1.00
- AMIN = 0.10
- WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45
-
- Intra band minimization:
- WEIMIN = 0.0000 energy-eigenvalue tresh-hold
- EBREAK = 0.14E-07 absolut break condition
- DEPER = 0.30 relativ break condition
-
- TIME = 0.40 timestep for ELM
-
- volume/ion in A,a.u. = 10.37 69.97
- Fermi-wavevector in a.u.,A,eV,Ry = 1.401149 2.647788 26.711209 1.963218
- Thomas-Fermi vector in A = 2.524039
-
- Write flags
- LWAVE = T write WAVECAR
- LDOWNSAMPLE = F k-point downsampling of WAVECAR
- LCHARG = T write CHGCAR
- LVTOT = F write LOCPOT, total local potential
- LVHAR = F write LOCPOT, Hartree potential only
- LELF = F write electronic localiz. function (ELF)
- LORBIT = 0 0 simple, 1 ext, 2 COOP (PROOUT), +10 PAW based schemes
-
-
- Dipole corrections
- LMONO = F monopole corrections only (constant potential shift)
- LDIPOL = F correct potential (dipole corrections)
- IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
- EPSILON= 1.0000000 bulk dielectric constant
-
- Exchange correlation treatment:
- GGA = -- GGA type
- LEXCH = 8 internal setting for exchange type
- VOSKOWN= 0 Vosko Wilk Nusair interpolation
- LHFCALC = F Hartree Fock is set to
- LHFONE = F Hartree Fock one center treatment
- AEXX = 0.0000 exact exchange contribution
-
- Linear response parameters
- LEPSILON= F determine dielectric tensor
- LRPA = F only Hartree local field effects (RPA)
- LNABLA = F use nabla operator in PAW spheres
- LVEL = F velocity operator in full k-point grid
- LINTERFAST= F fast interpolation
- KINTER = 0 interpolate to denser k-point grid
- CSHIFT =0.1000 complex shift for real part using Kramers Kronig
- OMEGAMAX= -1.0 maximum frequency
- DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate
- RTIME = -0.100 relaxation time in fs
- (WPLASMAI= 0.000 imaginary part of plasma frequency in eV, 0.658/RTIME)
- DFIELD = 0.0000000 0.0000000 0.0000000 field for delta impulse in time
-
- Orbital magnetization related:
- ORBITALMAG= F switch on orbital magnetization
- LCHIMAG = F perturbation theory with respect to B field
- DQ = 0.001000 dq finite difference perturbation B field
- LLRAUG = F two centre corrections for induced B field
-
-
-
---------------------------------------------------------------------------------------------------------
-
-
- Static calculation
- charge density and potential will be updated during run
- non-spin polarized calculation
- RMM-DIIS sequential band-by-band
- perform sub-space diagonalisation
- before iterative eigenvector-optimisation
- modified Broyden-mixing scheme, WC = 100.0
- initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000
- Hartree-type preconditioning will be used
- using additional bands 5
- reciprocal scheme for non local part
- use partial core corrections
- calculate Harris-corrections to forces
- (improved forces if not selfconsistent)
- use gradient corrections
- use of overlap-Matrix (Vanderbilt PP)
- Gauss-broadening in eV SIGMA = 0.10
-
-
---------------------------------------------------------------------------------------------------------
-
-
- energy-cutoff : 600.00
- volume of cell : 41.47
- direct lattice vectors reciprocal lattice vectors
- 3.669611000 0.000000000 0.000000000 0.272508448 0.000000000 0.000000000
- 0.000000000 3.557440000 0.000000000 0.000000000 0.281101016 0.000000000
- 0.000000000 0.000000000 3.176781000 0.000000000 0.000000000 0.314784053
-
- length of vectors
- 3.669611000 3.557440000 3.176781000 0.272508448 0.281101016 0.314784053
-
-
-
- k-points in units of 2pi/SCALE and weight: K-Points
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- 0.20000000 0.40000000 0.20000000 0.002
- 0.26666667 0.40000000 0.20000000 0.002
- 0.33333333 0.40000000 0.20000000 0.002
- 0.40000000 0.40000000 0.20000000 0.002
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- 0.46666667 0.26666667 0.26666667 0.002
- 0.00000000 0.33333333 0.26666667 0.001
- 0.06666667 0.33333333 0.26666667 0.002
- 0.13333333 0.33333333 0.26666667 0.002
- 0.20000000 0.33333333 0.26666667 0.002
- 0.26666667 0.33333333 0.26666667 0.002
- 0.33333333 0.33333333 0.26666667 0.002
- 0.40000000 0.33333333 0.26666667 0.002
- 0.46666667 0.33333333 0.26666667 0.002
- 0.00000000 0.40000000 0.26666667 0.001
- 0.06666667 0.40000000 0.26666667 0.002
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- 0.26666667 0.40000000 0.26666667 0.002
- 0.33333333 0.40000000 0.26666667 0.002
- 0.40000000 0.40000000 0.26666667 0.002
- 0.46666667 0.40000000 0.26666667 0.002
- 0.00000000 0.46666667 0.26666667 0.001
- 0.06666667 0.46666667 0.26666667 0.002
- 0.13333333 0.46666667 0.26666667 0.002
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- 0.46666667 0.46666667 0.26666667 0.002
- 0.00000000 0.00000000 0.33333333 0.001
- 0.06666667 0.00000000 0.33333333 0.001
- 0.13333333 0.00000000 0.33333333 0.001
- 0.20000000 0.00000000 0.33333333 0.001
- 0.26666667 0.00000000 0.33333333 0.001
- 0.33333333 0.00000000 0.33333333 0.001
- 0.40000000 0.00000000 0.33333333 0.001
- 0.46666667 0.00000000 0.33333333 0.001
- 0.00000000 0.06666667 0.33333333 0.001
- 0.06666667 0.06666667 0.33333333 0.002
- 0.13333333 0.06666667 0.33333333 0.002
- 0.20000000 0.06666667 0.33333333 0.002
- 0.26666667 0.06666667 0.33333333 0.002
- 0.33333333 0.06666667 0.33333333 0.002
- 0.40000000 0.06666667 0.33333333 0.002
- 0.46666667 0.06666667 0.33333333 0.002
- 0.00000000 0.13333333 0.33333333 0.001
- 0.06666667 0.13333333 0.33333333 0.002
- 0.13333333 0.13333333 0.33333333 0.002
- 0.20000000 0.13333333 0.33333333 0.002
- 0.26666667 0.13333333 0.33333333 0.002
- 0.33333333 0.13333333 0.33333333 0.002
- 0.40000000 0.13333333 0.33333333 0.002
- 0.46666667 0.13333333 0.33333333 0.002
- 0.00000000 0.20000000 0.33333333 0.001
- 0.06666667 0.20000000 0.33333333 0.002
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- 0.26666667 0.20000000 0.33333333 0.002
- 0.33333333 0.20000000 0.33333333 0.002
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- 0.46666667 0.20000000 0.33333333 0.002
- 0.00000000 0.26666667 0.33333333 0.001
- 0.06666667 0.26666667 0.33333333 0.002
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- 0.20000000 0.26666667 0.33333333 0.002
- 0.26666667 0.26666667 0.33333333 0.002
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- 0.00000000 0.33333333 0.33333333 0.001
- 0.06666667 0.33333333 0.33333333 0.002
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- 0.20000000 0.33333333 0.33333333 0.002
- 0.26666667 0.33333333 0.33333333 0.002
- 0.33333333 0.33333333 0.33333333 0.002
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- 0.46666667 0.33333333 0.33333333 0.002
- 0.00000000 0.40000000 0.33333333 0.001
- 0.06666667 0.40000000 0.33333333 0.002
- 0.13333333 0.40000000 0.33333333 0.002
- 0.20000000 0.40000000 0.33333333 0.002
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- 0.33333333 0.40000000 0.33333333 0.002
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- 0.00000000 0.46666667 0.33333333 0.001
- 0.06666667 0.46666667 0.33333333 0.002
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- 0.20000000 0.46666667 0.33333333 0.002
- 0.26666667 0.46666667 0.33333333 0.002
- 0.33333333 0.46666667 0.33333333 0.002
- 0.40000000 0.46666667 0.33333333 0.002
- 0.46666667 0.46666667 0.33333333 0.002
- 0.00000000 0.00000000 0.40000000 0.001
- 0.06666667 0.00000000 0.40000000 0.001
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- 0.26666667 0.00000000 0.40000000 0.001
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- 0.26666667 0.13333333 0.40000000 0.002
- 0.33333333 0.13333333 0.40000000 0.002
- 0.40000000 0.13333333 0.40000000 0.002
- 0.46666667 0.13333333 0.40000000 0.002
- 0.00000000 0.20000000 0.40000000 0.001
- 0.06666667 0.20000000 0.40000000 0.002
- 0.13333333 0.20000000 0.40000000 0.002
- 0.20000000 0.20000000 0.40000000 0.002
- 0.26666667 0.20000000 0.40000000 0.002
- 0.33333333 0.20000000 0.40000000 0.002
- 0.40000000 0.20000000 0.40000000 0.002
- 0.46666667 0.20000000 0.40000000 0.002
- 0.00000000 0.26666667 0.40000000 0.001
- 0.06666667 0.26666667 0.40000000 0.002
- 0.13333333 0.26666667 0.40000000 0.002
- 0.20000000 0.26666667 0.40000000 0.002
- 0.26666667 0.26666667 0.40000000 0.002
- 0.33333333 0.26666667 0.40000000 0.002
- 0.40000000 0.26666667 0.40000000 0.002
- 0.46666667 0.26666667 0.40000000 0.002
- 0.00000000 0.33333333 0.40000000 0.001
- 0.06666667 0.33333333 0.40000000 0.002
- 0.13333333 0.33333333 0.40000000 0.002
- 0.20000000 0.33333333 0.40000000 0.002
- 0.26666667 0.33333333 0.40000000 0.002
- 0.33333333 0.33333333 0.40000000 0.002
- 0.40000000 0.33333333 0.40000000 0.002
- 0.46666667 0.33333333 0.40000000 0.002
- 0.00000000 0.40000000 0.40000000 0.001
- 0.06666667 0.40000000 0.40000000 0.002
- 0.13333333 0.40000000 0.40000000 0.002
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- 0.26666667 0.40000000 0.40000000 0.002
- 0.33333333 0.40000000 0.40000000 0.002
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- 0.20000000 0.46666667 0.40000000 0.002
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- 0.40000000 0.46666667 0.40000000 0.002
- 0.46666667 0.46666667 0.40000000 0.002
- 0.00000000 0.00000000 0.46666667 0.001
- 0.06666667 0.00000000 0.46666667 0.001
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- 0.40000000 0.06666667 0.46666667 0.002
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- 0.00000000 0.13333333 0.46666667 0.001
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- 0.26666667 0.13333333 0.46666667 0.002
- 0.33333333 0.13333333 0.46666667 0.002
- 0.40000000 0.13333333 0.46666667 0.002
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- 0.40000000 0.20000000 0.46666667 0.002
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- 0.13333333 0.26666667 0.46666667 0.002
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- 0.40000000 0.26666667 0.46666667 0.002
- 0.46666667 0.26666667 0.46666667 0.002
- 0.00000000 0.33333333 0.46666667 0.001
- 0.06666667 0.33333333 0.46666667 0.002
- 0.13333333 0.33333333 0.46666667 0.002
- 0.20000000 0.33333333 0.46666667 0.002
- 0.26666667 0.33333333 0.46666667 0.002
- 0.33333333 0.33333333 0.46666667 0.002
- 0.40000000 0.33333333 0.46666667 0.002
- 0.46666667 0.33333333 0.46666667 0.002
- 0.00000000 0.40000000 0.46666667 0.001
- 0.06666667 0.40000000 0.46666667 0.002
- 0.13333333 0.40000000 0.46666667 0.002
- 0.20000000 0.40000000 0.46666667 0.002
- 0.26666667 0.40000000 0.46666667 0.002
- 0.33333333 0.40000000 0.46666667 0.002
- 0.40000000 0.40000000 0.46666667 0.002
- 0.46666667 0.40000000 0.46666667 0.002
- 0.00000000 0.46666667 0.46666667 0.001
- 0.06666667 0.46666667 0.46666667 0.002
- 0.13333333 0.46666667 0.46666667 0.002
- 0.20000000 0.46666667 0.46666667 0.002
- 0.26666667 0.46666667 0.46666667 0.002
- 0.33333333 0.46666667 0.46666667 0.002
- 0.40000000 0.46666667 0.46666667 0.002
- 0.46666667 0.46666667 0.46666667 0.002
-
- position of ions in fractional coordinates (direct lattice)
- 0.00000000 0.00000000 0.00000000
- 0.00000000 0.50000000 0.50000000
- 0.50000000 0.00000000 0.50000000
- 0.50000000 0.50000000 0.00000000
-
- position of ions in cartesian coordinates (Angst):
- 0.00000000 0.00000000 0.00000000
- 0.00000000 1.77872000 1.58839050
- 1.83480550 0.00000000 1.58839050
- 1.83480550 1.77872000 0.00000000
-
-
-
---------------------------------------------------------------------------------------------------------
-
-
- k-point 1 : 0.0000 0.0000 0.0000 plane waves: 1389
- k-point 2 : 0.0667 0.0000 0.0000 plane waves: 1395
- k-point 3 : 0.1333 0.0000 0.0000 plane waves: 1401
- k-point 4 : 0.2000 0.0000 0.0000 plane waves: 1393
- k-point 5 : 0.2667 0.0000 0.0000 plane waves: 1389
- k-point 6 : 0.3333 0.0000 0.0000 plane waves: 1386
- k-point 7 : 0.4000 0.0000 0.0000 plane waves: 1386
- k-point 8 : 0.4667 0.0000 0.0000 plane waves: 1392
- k-point 9 : 0.0000 0.0667 0.0000 plane waves: 1395
- k-point 10 : 0.0667 0.0667 0.0000 plane waves: 1393
- k-point 11 : 0.1333 0.0667 0.0000 plane waves: 1396
- k-point 12 : 0.2000 0.0667 0.0000 plane waves: 1390
- k-point 13 : 0.2667 0.0667 0.0000 plane waves: 1385
- k-point 14 : 0.3333 0.0667 0.0000 plane waves: 1382
- k-point 15 : 0.4000 0.0667 0.0000 plane waves: 1388
- k-point 16 : 0.4667 0.0667 0.0000 plane waves: 1396
- k-point 17 : 0.0000 0.1333 0.0000 plane waves: 1394
- k-point 18 : 0.0667 0.1333 0.0000 plane waves: 1400
- k-point 19 : 0.1333 0.1333 0.0000 plane waves: 1395
- k-point 20 : 0.2000 0.1333 0.0000 plane waves: 1393
- k-point 21 : 0.2667 0.1333 0.0000 plane waves: 1386
- k-point 22 : 0.3333 0.1333 0.0000 plane waves: 1394
- k-point 23 : 0.4000 0.1333 0.0000 plane waves: 1387
- k-point 24 : 0.4667 0.1333 0.0000 plane waves: 1384
- k-point 25 : 0.0000 0.2000 0.0000 plane waves: 1390
- k-point 26 : 0.0667 0.2000 0.0000 plane waves: 1392
- k-point 27 : 0.1333 0.2000 0.0000 plane waves: 1389
- k-point 28 : 0.2000 0.2000 0.0000 plane waves: 1388
- k-point 29 : 0.2667 0.2000 0.0000 plane waves: 1389
- k-point 30 : 0.3333 0.2000 0.0000 plane waves: 1391
- k-point 31 : 0.4000 0.2000 0.0000 plane waves: 1387
- k-point 32 : 0.4667 0.2000 0.0000 plane waves: 1382
- k-point 33 : 0.0000 0.2667 0.0000 plane waves: 1390
- k-point 34 : 0.0667 0.2667 0.0000 plane waves: 1393
- k-point 35 : 0.1333 0.2667 0.0000 plane waves: 1391
- k-point 36 : 0.2000 0.2667 0.0000 plane waves: 1388
- k-point 37 : 0.2667 0.2667 0.0000 plane waves: 1383
- k-point 38 : 0.3333 0.2667 0.0000 plane waves: 1384
- k-point 39 : 0.4000 0.2667 0.0000 plane waves: 1377
- k-point 40 : 0.4667 0.2667 0.0000 plane waves: 1375
- k-point 41 : 0.0000 0.3333 0.0000 plane waves: 1392
- k-point 42 : 0.0667 0.3333 0.0000 plane waves: 1390
- k-point 43 : 0.1333 0.3333 0.0000 plane waves: 1390
- k-point 44 : 0.2000 0.3333 0.0000 plane waves: 1395
- k-point 45 : 0.2667 0.3333 0.0000 plane waves: 1388
- k-point 46 : 0.3333 0.3333 0.0000 plane waves: 1380
- k-point 47 : 0.4000 0.3333 0.0000 plane waves: 1378
- k-point 48 : 0.4667 0.3333 0.0000 plane waves: 1364
- k-point 49 : 0.0000 0.4000 0.0000 plane waves: 1390
- k-point 50 : 0.0667 0.4000 0.0000 plane waves: 1390
- k-point 51 : 0.1333 0.4000 0.0000 plane waves: 1397
- k-point 52 : 0.2000 0.4000 0.0000 plane waves: 1391
- k-point 53 : 0.2667 0.4000 0.0000 plane waves: 1389
- k-point 54 : 0.3333 0.4000 0.0000 plane waves: 1377
- k-point 55 : 0.4000 0.4000 0.0000 plane waves: 1379
- k-point 56 : 0.4667 0.4000 0.0000 plane waves: 1365
- k-point 57 : 0.0000 0.4667 0.0000 plane waves: 1382
- k-point 58 : 0.0667 0.4667 0.0000 plane waves: 1387
- k-point 59 : 0.1333 0.4667 0.0000 plane waves: 1387
- k-point 60 : 0.2000 0.4667 0.0000 plane waves: 1386
- k-point 61 : 0.2667 0.4667 0.0000 plane waves: 1384
- k-point 62 : 0.3333 0.4667 0.0000 plane waves: 1384
- k-point 63 : 0.4000 0.4667 0.0000 plane waves: 1381
- k-point 64 : 0.4667 0.4667 0.0000 plane waves: 1372
- k-point 65 : 0.0000 0.0000 0.0667 plane waves: 1389
- k-point 66 : 0.0667 0.0000 0.0667 plane waves: 1386
- k-point 67 : 0.1333 0.0000 0.0667 plane waves: 1393
- k-point 68 : 0.2000 0.0000 0.0667 plane waves: 1392
- k-point 69 : 0.2667 0.0000 0.0667 plane waves: 1375
- k-point 70 : 0.3333 0.0000 0.0667 plane waves: 1382
- k-point 71 : 0.4000 0.0000 0.0667 plane waves: 1394
- k-point 72 : 0.4667 0.0000 0.0667 plane waves: 1401
- k-point 73 : 0.0000 0.0667 0.0667 plane waves: 1387
- k-point 74 : 0.0667 0.0667 0.0667 plane waves: 1388
- k-point 75 : 0.1333 0.0667 0.0667 plane waves: 1393
- k-point 76 : 0.2000 0.0667 0.0667 plane waves: 1388
- k-point 77 : 0.2667 0.0667 0.0667 plane waves: 1385
- k-point 78 : 0.3333 0.0667 0.0667 plane waves: 1388
- k-point 79 : 0.4000 0.0667 0.0667 plane waves: 1392
- k-point 80 : 0.4667 0.0667 0.0667 plane waves: 1395
- k-point 81 : 0.0000 0.1333 0.0667 plane waves: 1381
- k-point 82 : 0.0667 0.1333 0.0667 plane waves: 1388
- k-point 83 : 0.1333 0.1333 0.0667 plane waves: 1390
- k-point 84 : 0.2000 0.1333 0.0667 plane waves: 1387
- k-point 85 : 0.2667 0.1333 0.0667 plane waves: 1390
- k-point 86 : 0.3333 0.1333 0.0667 plane waves: 1385
- k-point 87 : 0.4000 0.1333 0.0667 plane waves: 1389
- k-point 88 : 0.4667 0.1333 0.0667 plane waves: 1391
- k-point 89 : 0.0000 0.2000 0.0667 plane waves: 1391
- k-point 90 : 0.0667 0.2000 0.0667 plane waves: 1390
- k-point 91 : 0.1333 0.2000 0.0667 plane waves: 1388
- k-point 92 : 0.2000 0.2000 0.0667 plane waves: 1390
- k-point 93 : 0.2667 0.2000 0.0667 plane waves: 1385
- k-point 94 : 0.3333 0.2000 0.0667 plane waves: 1388
- k-point 95 : 0.4000 0.2000 0.0667 plane waves: 1387
- k-point 96 : 0.4667 0.2000 0.0667 plane waves: 1388
- k-point 97 : 0.0000 0.2667 0.0667 plane waves: 1393
- k-point 98 : 0.0667 0.2667 0.0667 plane waves: 1392
- k-point 99 : 0.1333 0.2667 0.0667 plane waves: 1388
- k-point ** : 0.2000 0.2667 0.0667 plane waves: 1387
- k-point ** : 0.2667 0.2667 0.0667 plane waves: 1386
- k-point ** : 0.3333 0.2667 0.0667 plane waves: 1386
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- k-point ** : 0.2000 0.0000 0.4667 plane waves: 1371
- k-point ** : 0.2667 0.0000 0.4667 plane waves: 1369
- k-point ** : 0.3333 0.0000 0.4667 plane waves: 1371
- k-point ** : 0.4000 0.0000 0.4667 plane waves: 1373
- k-point ** : 0.4667 0.0000 0.4667 plane waves: 1372
- k-point ** : 0.0000 0.0667 0.4667 plane waves: 1381
- k-point ** : 0.0667 0.0667 0.4667 plane waves: 1381
- k-point ** : 0.1333 0.0667 0.4667 plane waves: 1371
- k-point ** : 0.2000 0.0667 0.4667 plane waves: 1375
- k-point ** : 0.2667 0.0667 0.4667 plane waves: 1371
- k-point ** : 0.3333 0.0667 0.4667 plane waves: 1372
- k-point ** : 0.4000 0.0667 0.4667 plane waves: 1373
- k-point ** : 0.4667 0.0667 0.4667 plane waves: 1368
- k-point ** : 0.0000 0.1333 0.4667 plane waves: 1392
- k-point ** : 0.0667 0.1333 0.4667 plane waves: 1383
- k-point ** : 0.1333 0.1333 0.4667 plane waves: 1374
- k-point ** : 0.2000 0.1333 0.4667 plane waves: 1376
- k-point ** : 0.2667 0.1333 0.4667 plane waves: 1375
- k-point ** : 0.3333 0.1333 0.4667 plane waves: 1378
- k-point ** : 0.4000 0.1333 0.4667 plane waves: 1378
- k-point ** : 0.4667 0.1333 0.4667 plane waves: 1377
- k-point ** : 0.0000 0.2000 0.4667 plane waves: 1398
- k-point ** : 0.0667 0.2000 0.4667 plane waves: 1394
- k-point ** : 0.1333 0.2000 0.4667 plane waves: 1384
- k-point ** : 0.2000 0.2000 0.4667 plane waves: 1376
- k-point ** : 0.2667 0.2000 0.4667 plane waves: 1377
- k-point ** : 0.3333 0.2000 0.4667 plane waves: 1380
- k-point ** : 0.4000 0.2000 0.4667 plane waves: 1380
- k-point ** : 0.4667 0.2000 0.4667 plane waves: 1381
- k-point ** : 0.0000 0.2667 0.4667 plane waves: 1386
- k-point ** : 0.0667 0.2667 0.4667 plane waves: 1391
- k-point ** : 0.1333 0.2667 0.4667 plane waves: 1383
- k-point ** : 0.2000 0.2667 0.4667 plane waves: 1385
- k-point ** : 0.2667 0.2667 0.4667 plane waves: 1382
- k-point ** : 0.3333 0.2667 0.4667 plane waves: 1381
- k-point ** : 0.4000 0.2667 0.4667 plane waves: 1387
- k-point ** : 0.4667 0.2667 0.4667 plane waves: 1390
- k-point ** : 0.0000 0.3333 0.4667 plane waves: 1386
- k-point ** : 0.0667 0.3333 0.4667 plane waves: 1382
- k-point ** : 0.1333 0.3333 0.4667 plane waves: 1378
- k-point ** : 0.2000 0.3333 0.4667 plane waves: 1385
- k-point ** : 0.2667 0.3333 0.4667 plane waves: 1386
- k-point ** : 0.3333 0.3333 0.4667 plane waves: 1386
- k-point ** : 0.4000 0.3333 0.4667 plane waves: 1389
- k-point ** : 0.4667 0.3333 0.4667 plane waves: 1392
- k-point ** : 0.0000 0.4000 0.4667 plane waves: 1387
- k-point ** : 0.0667 0.4000 0.4667 plane waves: 1390
- k-point ** : 0.1333 0.4000 0.4667 plane waves: 1383
- k-point ** : 0.2000 0.4000 0.4667 plane waves: 1378
- k-point ** : 0.2667 0.4000 0.4667 plane waves: 1382
- k-point ** : 0.3333 0.4000 0.4667 plane waves: 1385
- k-point ** : 0.4000 0.4000 0.4667 plane waves: 1389
- k-point ** : 0.4667 0.4000 0.4667 plane waves: 1393
- k-point ** : 0.0000 0.4667 0.4667 plane waves: 1380
- k-point ** : 0.0667 0.4667 0.4667 plane waves: 1390
- k-point ** : 0.1333 0.4667 0.4667 plane waves: 1386
- k-point ** : 0.2000 0.4667 0.4667 plane waves: 1386
- k-point ** : 0.2667 0.4667 0.4667 plane waves: 1381
- k-point ** : 0.3333 0.4667 0.4667 plane waves: 1383
- k-point ** : 0.4000 0.4667 0.4667 plane waves: 1388
- k-point ** : 0.4667 0.4667 0.4667 plane waves: 1390
-
- maximum and minimum number of plane-waves per node : 1401 1362
-
- maximum number of plane-waves: 1401
- maximum index in each direction:
- IXMAX= 7 IYMAX= 7 IZMAX= 6
- IXMIN= -7 IYMIN= -7 IZMIN= -6
-
-
- serial 3D FFT for wavefunctions
- parallel 3D FFT for charge:
- minimum data exchange during FFTs selected (reduces bandwidth)
-
-
- total amount of memory used by VASP MPI-rank0 355020. kBytes
-=======================================================================
-
- base : 30000. kBytes
- nonl-proj : 299130. kBytes
- fftplans : 441. kBytes
- grid : 1138. kBytes
- one-center: 129. kBytes
- wavefun : 24182. kBytes
-
- INWAV: cpu time 0.0001: real time 0.0007
- Broyden mixing: mesh for mixing (old mesh)
- NGX = 15 NGY = 15 NGZ = 13
- (NGX = 48 NGY = 48 NGZ = 40)
- gives a total of 2925 points
-
- initial charge density was supplied:
- charge density of overlapping atoms calculated
- number of electron 26.0000000 magnetization
- keeping initial charge density in first step
-
-
---------------------------------------------------------------------------------------------------------
-
-
- Maximum index for augmentation-charges 1294 (set IRDMAX)
-
-
---------------------------------------------------------------------------------------------------------
-
-
- First call to EWALD: gamma= 0.512
- Maximum number of real-space cells 3x 3x 3
- Maximum number of reciprocal cells 3x 3x 3
-
- FEWALD: cpu time 0.0014: real time 0.0014
-
-
---------------------------------------- Iteration 1( 1) ---------------------------------------
-
-
- POTLOK: cpu time 0.0000: real time 0.0186
- SETDIJ: cpu time 0.0023: real time 0.0038
- EDDIAG: cpu time 0.8664: real time 0.8695
- RMM-DIIS: cpu time 0.9891: real time 0.9915
- ORTHCH: cpu time 0.0915: real time 0.0917
- DOS: cpu time 0.0040: real time 0.0040
- --------------------------------------------
- LOOP: cpu time 1.9534: real time 1.9792
-
- eigenvalue-minimisations : 9216
- total energy-change (2. order) :-0.5752413E+03 (-0.2415436E+04)
- number of electron 26.0000000 magnetization
- augmentation part 26.0000000 magnetization
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -527.41646070
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 35.33916255
- PAW double counting = 1941.62980019 -1939.43826086
- entropy T*S EENTRO = -0.00530052
- eigenvalues EBANDS = -1293.52360327
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -575.24128006 eV
-
- energy without entropy = -575.23597954 energy(sigma->0) = -575.23862980
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 2) ---------------------------------------
-
-
- EDDIAG: cpu time 0.8612: real time 0.9058
- RMM-DIIS: cpu time 1.0247: real time 1.0272
- ORTHCH: cpu time 0.0935: real time 0.0937
- DOS: cpu time 0.0037: real time 0.0037
- --------------------------------------------
- LOOP: cpu time 1.9831: real time 2.0305
-
- eigenvalue-minimisations : 9216
- total energy-change (2. order) : 0.6776269E+03 (-0.4029736E+03)
- number of electron 26.0000000 magnetization
- augmentation part 26.0000000 magnetization
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -527.41646070
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 35.33916255
- PAW double counting = 1941.62980019 -1939.43826086
- entropy T*S EENTRO = -0.00481541
- eigenvalues EBANDS = -615.89714414
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = 102.38566418 eV
-
- energy without entropy = 102.39047960 energy(sigma->0) = 102.38807189
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 3) ---------------------------------------
-
-
- EDDIAG: cpu time 0.8578: real time 0.8850
- RMM-DIIS: cpu time 0.9854: real time 0.9876
- ORTHCH: cpu time 0.0927: real time 0.0950
- DOS: cpu time 0.0039: real time 0.0038
- --------------------------------------------
- LOOP: cpu time 1.9398: real time 1.9715
-
- eigenvalue-minimisations : 9216
- total energy-change (2. order) :-0.1313635E+03 (-0.1511722E+03)
- number of electron 26.0000000 magnetization
- augmentation part 26.0000000 magnetization
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -527.41646070
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 35.33916255
- PAW double counting = 1941.62980019 -1939.43826086
- entropy T*S EENTRO = -0.00684255
- eigenvalues EBANDS = -747.25860832
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -28.97782713 eV
-
- energy without entropy = -28.97098459 energy(sigma->0) = -28.97440586
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 4) ---------------------------------------
-
-
- EDDIAG: cpu time 0.8663: real time 0.8792
- RMM-DIIS: cpu time 2.9235: real time 2.9296
- ORTHCH: cpu time 0.0974: real time 0.0994
- DOS: cpu time 0.0037: real time 0.0037
- --------------------------------------------
- LOOP: cpu time 3.8909: real time 3.9119
-
- eigenvalue-minimisations : 29178
- total energy-change (2. order) :-0.2071636E+02 (-0.8645846E+02)
- number of electron 26.0000000 magnetization
- augmentation part 26.0000000 magnetization
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -527.41646070
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 35.33916255
- PAW double counting = 1941.62980019 -1939.43826086
- entropy T*S EENTRO = -0.00577549
- eigenvalues EBANDS = -767.97603184
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -49.69418359 eV
-
- energy without entropy = -49.68840810 energy(sigma->0) = -49.69129585
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 5) ---------------------------------------
-
-
- EDDIAG: cpu time 0.8588: real time 0.8713
- RMM-DIIS: cpu time 3.2869: real time 3.2931
- ORTHCH: cpu time 0.0916: real time 0.0917
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2189: real time 0.2195
- MIXING: cpu time 0.0004: real time 0.0004
- --------------------------------------------
- LOOP: cpu time 4.4603: real time 4.4798
-
- eigenvalue-minimisations : 32343
- total energy-change (2. order) :-0.2221706E+01 (-0.1791219E+02)
- number of electron 26.0000010 magnetization
- augmentation part 1.7185645 magnetization
-
- Broyden mixing:
- rms(total) = 0.99154E+01 rms(broyden)= 0.99154E+01
- rms(prec ) = 0.10501E+02
- weight for this iteration 100.00
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -527.41646070
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 35.33916255
- PAW double counting = 1941.62980019 -1939.43826086
- entropy T*S EENTRO = -0.00286525
- eigenvalues EBANDS = -770.20064788
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -51.91588940 eV
-
- energy without entropy = -51.91302415 energy(sigma->0) = -51.91445678
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 6) ---------------------------------------
-
-
- POTLOK: cpu time 0.0063: real time 0.0063
- SETDIJ: cpu time 0.0030: real time 0.0030
- EDDIAG: cpu time 0.8572: real time 0.8594
- RMM-DIIS: cpu time 3.1432: real time 3.1501
- ORTHCH: cpu time 0.0945: real time 0.0962
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2174: real time 0.2178
- MIXING: cpu time 0.0010: real time 0.0005
- --------------------------------------------
- LOOP: cpu time 4.3263: real time 4.3370
-
- eigenvalue-minimisations : 32157
- total energy-change (2. order) : 0.3557072E+01 (-0.5126209E+01)
- number of electron 26.0000010 magnetization
- augmentation part 1.7344693 magnetization
-
- Broyden mixing:
- rms(total) = 0.63965E+01 rms(broyden)= 0.63965E+01
- rms(prec ) = 0.64289E+01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 2.3193
- 2.3193
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -478.34595767
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.69314398
- PAW double counting = 2583.11263522 -2584.59837190
- entropy T*S EENTRO = -0.00315334
- eigenvalues EBANDS = -810.39049628
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.35881744 eV
-
- energy without entropy = -48.35566410 energy(sigma->0) = -48.35724077
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 7) ---------------------------------------
-
-
- POTLOK: cpu time 0.0086: real time 0.0151
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8614: real time 0.8634
- RMM-DIIS: cpu time 3.0067: real time 3.0125
- ORTHCH: cpu time 0.0904: real time 0.0906
- DOS: cpu time 0.0038: real time 0.0038
- CHARGE: cpu time 0.2174: real time 0.2189
- MIXING: cpu time 0.0004: real time 0.0004
- --------------------------------------------
- LOOP: cpu time 4.1915: real time 4.2075
-
- eigenvalue-minimisations : 31891
- total energy-change (2. order) :-0.1869340E+00 (-0.1169757E+01)
- number of electron 26.0000010 magnetization
- augmentation part 1.7769450 magnetization
-
- Broyden mixing:
- rms(total) = 0.10740E+01 rms(broyden)= 0.10740E+01
- rms(prec ) = 0.13069E+01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.5887
- 1.0277 2.1498
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -468.77317788
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.19468253
- PAW double counting = 3317.64592811 -3318.50891194
- entropy T*S EENTRO = -0.00279364
- eigenvalues EBANDS = -820.27486120
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.54575148 eV
-
- energy without entropy = -48.54295784 energy(sigma->0) = -48.54435466
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 8) ---------------------------------------
-
-
- POTLOK: cpu time 0.0061: real time 0.0062
- SETDIJ: cpu time 0.0027: real time 0.0027
- EDDIAG: cpu time 0.8569: real time 0.8592
- RMM-DIIS: cpu time 3.1012: real time 3.1079
- ORTHCH: cpu time 0.0908: real time 0.0928
- DOS: cpu time 0.0038: real time 0.0038
- CHARGE: cpu time 0.2182: real time 0.2185
- MIXING: cpu time 0.0005: real time 0.0005
- --------------------------------------------
- LOOP: cpu time 4.2803: real time 4.2918
-
- eigenvalue-minimisations : 29478
- total energy-change (2. order) : 0.4696527E+00 (-0.1641795E+00)
- number of electron 26.0000010 magnetization
- augmentation part 1.7495559 magnetization
-
- Broyden mixing:
- rms(total) = 0.94387E+00 rms(broyden)= 0.94387E+00
- rms(prec ) = 0.94566E+00
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.7834
- 1.5400 1.9052 1.9052
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -481.10425992
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.50004761
- PAW double counting = 3311.78596750 -3311.19575724
- entropy T*S EENTRO = -0.00267424
- eigenvalues EBANDS = -809.23280508
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07609882 eV
-
- energy without entropy = -48.07342458 energy(sigma->0) = -48.07476170
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 9) ---------------------------------------
-
-
- POTLOK: cpu time 0.0065: real time 0.0165
- SETDIJ: cpu time 0.0029: real time 0.0029
- EDDIAG: cpu time 0.8609: real time 0.8633
- RMM-DIIS: cpu time 2.9123: real time 2.9192
- ORTHCH: cpu time 0.0968: real time 0.0971
- DOS: cpu time 0.0038: real time 0.0038
- CHARGE: cpu time 0.2174: real time 0.2179
- MIXING: cpu time 0.0005: real time 0.0005
- --------------------------------------------
- LOOP: cpu time 4.1010: real time 4.1212
-
- eigenvalue-minimisations : 31189
- total energy-change (2. order) :-0.4703762E-01 (-0.5300665E-01)
- number of electron 26.0000010 magnetization
- augmentation part 1.7619850 magnetization
-
- Broyden mixing:
- rms(total) = 0.37364E+00 rms(broyden)= 0.37364E+00
- rms(prec ) = 0.50262E+00
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.8041
- 2.5350 2.5350 1.0732 1.0732
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -476.54735144
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.37995814
- PAW double counting = 3192.69887022 -3192.42542193
- entropy T*S EENTRO = -0.00286656
- eigenvalues EBANDS = -813.39970742
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.12313644 eV
-
- energy without entropy = -48.12026988 energy(sigma->0) = -48.12170316
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 10) ---------------------------------------
-
-
- POTLOK: cpu time 0.0062: real time 0.0062
- SETDIJ: cpu time 0.0027: real time 0.0027
- EDDIAG: cpu time 0.8582: real time 0.8613
- RMM-DIIS: cpu time 3.1267: real time 3.1349
- ORTHCH: cpu time 0.0904: real time 0.0905
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2194: real time 0.2197
- MIXING: cpu time 0.0020: real time 0.0015
- --------------------------------------------
- LOOP: cpu time 4.3092: real time 4.3205
-
- eigenvalue-minimisations : 29390
- total energy-change (2. order) : 0.2966125E-01 (-0.4742700E-01)
- number of electron 26.0000010 magnetization
- augmentation part 1.7423041 magnetization
-
- Broyden mixing:
- rms(total) = 0.31849E+00 rms(broyden)= 0.31849E+00
- rms(prec ) = 0.35866E+00
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.5899
- 2.6842 1.6840 1.6840 1.0048 0.8926
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -482.81360439
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.53890578
- PAW double counting = 3121.35646553 -3120.29858400
- entropy T*S EENTRO = -0.00297373
- eigenvalues EBANDS = -808.04706694
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.09347519 eV
-
- energy without entropy = -48.09050147 energy(sigma->0) = -48.09198833
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 11) ---------------------------------------
-
-
- POTLOK: cpu time 0.0050: real time 0.0156
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8582: real time 0.8607
-WARNING in EDDRMM: call to ZHEGV failed, returncode = 8 4 2
- RMM-DIIS: cpu time 3.6274: real time 3.6355
- ORTHCH: cpu time 0.0911: real time 0.0912
- DOS: cpu time 0.0038: real time 0.0038
- CHARGE: cpu time 0.2177: real time 0.2182
- MIXING: cpu time 0.0005: real time 0.0005
- --------------------------------------------
- LOOP: cpu time 4.8065: real time 4.8283
-
- eigenvalue-minimisations : 29737
- total energy-change (2. order) : 0.2156037E-01 (-0.5977483E-02)
- number of electron 26.0000010 magnetization
- augmentation part 1.7466636 magnetization
-
- Broyden mixing:
- rms(total) = 0.53781E-01 rms(broyden)= 0.53781E-01
- rms(prec ) = 0.62072E-01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.3891
- 2.6733 1.7034 1.7034 1.0132 0.8845 0.3572
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.78216452
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47821903
- PAW double counting = 3189.30069522 -3188.42317580
- entropy T*S EENTRO = -0.00299710
- eigenvalues EBANDS = -809.81587419
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07191482 eV
-
- energy without entropy = -48.06891772 energy(sigma->0) = -48.07041627
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 12) ---------------------------------------
-
-
- POTLOK: cpu time 0.0062: real time 0.0062
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8529: real time 0.8567
-WARNING in EDDRMM: call to ZHEGV failed, returncode = 8 4 2
- RMM-DIIS: cpu time 3.4862: real time 3.4923
- ORTHCH: cpu time 0.0915: real time 0.0917
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2184: real time 0.2187
- MIXING: cpu time 0.0006: real time 0.0006
- --------------------------------------------
- LOOP: cpu time 4.6622: real time 4.6726
-
- eigenvalue-minimisations : 30551
- total energy-change (2. order) : 0.8869093E-03 (-0.8814040E-03)
- number of electron 26.0000010 magnetization
- augmentation part 1.7475456 magnetization
-
- Broyden mixing:
- rms(total) = 0.17327E-01 rms(broyden)= 0.17326E-01
- rms(prec ) = 0.19640E-01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.3147
- 2.6706 1.6701 1.6701 1.0021 0.9039 0.6430 0.6430
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.57803071
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47228286
- PAW double counting = 3197.70507194 -3196.84324057
- entropy T*S EENTRO = -0.00301416
- eigenvalues EBANDS = -809.99747983
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07102791 eV
-
- energy without entropy = -48.06801376 energy(sigma->0) = -48.06952083
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 13) ---------------------------------------
-
-
- POTLOK: cpu time 0.0063: real time 0.0063
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8539: real time 0.8558
- RMM-DIIS: cpu time 3.3017: real time 3.3099
- ORTHCH: cpu time 0.0903: real time 0.0905
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2175: real time 0.2177
- MIXING: cpu time 0.0006: real time 0.0005
- --------------------------------------------
- LOOP: cpu time 4.4767: real time 4.4872
-
- eigenvalue-minimisations : 27907
- total energy-change (2. order) :-0.1094469E-03 (-0.1819417E-03)
- number of electron 26.0000010 magnetization
- augmentation part 1.7473309 magnetization
-
- Broyden mixing:
- rms(total) = 0.41060E-01 rms(broyden)= 0.41060E-01
- rms(prec ) = 0.43597E-01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.5889
- 2.6762 2.6235 1.8063 1.8063 1.0829 1.0829 0.8167 0.8167
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.71544123
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47703876
- PAW double counting = 3194.30045733 -3193.42429176
- entropy T*S EENTRO = -0.00304443
- eigenvalues EBANDS = -809.87923859
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07113736 eV
-
- energy without entropy = -48.06809293 energy(sigma->0) = -48.06961515
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 14) ---------------------------------------
-
-
- POTLOK: cpu time 0.0064: real time 0.0152
- SETDIJ: cpu time 0.0027: real time 0.0027
- EDDIAG: cpu time 0.8625: real time 0.8642
- RMM-DIIS: cpu time 3.4730: real time 3.4807
- ORTHCH: cpu time 0.0958: real time 0.0960
- DOS: cpu time 0.0033: real time 0.0033
- CHARGE: cpu time 0.2181: real time 0.2185
- MIXING: cpu time 0.0006: real time 0.0006
- --------------------------------------------
- LOOP: cpu time 4.6625: real time 4.6814
-
- eigenvalue-minimisations : 28867
- total energy-change (2. order) :-0.4802788E-04 (-0.5334102E-04)
- number of electron 26.0000010 magnetization
- augmentation part 1.7471770 magnetization
-
- Broyden mixing:
- rms(total) = 0.11318E-01 rms(broyden)= 0.11318E-01
- rms(prec ) = 0.20045E-01
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.4879
- 2.6297 2.6297 1.6936 1.3132 1.1879 1.1879 0.9918 0.8785 0.8785
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.78948024
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47969724
- PAW double counting = 3200.45165620 -3199.56117304
- entropy T*S EENTRO = -0.00304439
- eigenvalues EBANDS = -809.82222371
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07118539 eV
-
- energy without entropy = -48.06814100 energy(sigma->0) = -48.06966319
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 15) ---------------------------------------
-
-
- POTLOK: cpu time 0.0062: real time 0.0062
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8568: real time 0.8614
- RMM-DIIS: cpu time 3.2087: real time 3.2162
- ORTHCH: cpu time 0.0943: real time 0.0959
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2176: real time 0.2180
- MIXING: cpu time 0.0006: real time 0.0006
- --------------------------------------------
- LOOP: cpu time 4.3907: real time 4.4048
-
- eigenvalue-minimisations : 27375
- total energy-change (2. order) : 0.7992486E-04 (-0.8025044E-04)
- number of electron 26.0000010 magnetization
- augmentation part 1.7478758 magnetization
-
- Broyden mixing:
- rms(total) = 0.46851E-02 rms(broyden)= 0.46851E-02
- rms(prec ) = 0.51870E-02
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.3579
- 2.7839 2.5249 1.4729 1.4729 1.1537 1.1537 0.9594 0.9133 0.9133 0.2310
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.57031732
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47337481
- PAW double counting = 3205.37333857 -3204.50053139
- entropy T*S EENTRO = -0.00305052
- eigenvalues EBANDS = -810.01730217
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07110546 eV
-
- energy without entropy = -48.06805494 energy(sigma->0) = -48.06958020
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 16) ---------------------------------------
-
-
- POTLOK: cpu time 0.0062: real time 0.0169
- SETDIJ: cpu time 0.0029: real time 0.0029
- EDDIAG: cpu time 0.8529: real time 0.8553
- RMM-DIIS: cpu time 2.8952: real time 2.9013
- ORTHCH: cpu time 0.0905: real time 0.0907
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2153: real time 0.2156
- MIXING: cpu time 0.0008: real time 0.0008
- --------------------------------------------
- LOOP: cpu time 4.0684: real time 4.0872
-
- eigenvalue-minimisations : 26944
- total energy-change (2. order) : 0.6773008E-05 (-0.9673818E-05)
- number of electron 26.0000010 magnetization
- augmentation part 1.7479216 magnetization
-
- Broyden mixing:
- rms(total) = 0.39083E-02 rms(broyden)= 0.39083E-02
- rms(prec ) = 0.48812E-02
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.3253
- 2.8948 2.4553 1.5944 1.2157 1.2157 1.0656 1.0656 0.9218 0.9218 0.6138
- 0.6138
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.57208370
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47337122
- PAW double counting = 3205.24324251 -3204.37022275
- entropy T*S EENTRO = -0.00304889
- eigenvalues EBANDS = -810.01573963
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07109869 eV
-
- energy without entropy = -48.06804980 energy(sigma->0) = -48.06957425
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 17) ---------------------------------------
-
-
- POTLOK: cpu time 0.0061: real time 0.0061
- SETDIJ: cpu time 0.0027: real time 0.0027
- EDDIAG: cpu time 0.8539: real time 0.8561
- RMM-DIIS: cpu time 2.4896: real time 2.4948
- ORTHCH: cpu time 0.0919: real time 0.0936
- DOS: cpu time 0.0037: real time 0.0037
- CHARGE: cpu time 0.2152: real time 0.2157
- MIXING: cpu time 0.0007: real time 0.0007
- --------------------------------------------
- LOOP: cpu time 3.6630: real time 3.6735
-
- eigenvalue-minimisations : 21111
- total energy-change (2. order) :-0.1378648E-06 (-0.3109433E-05)
- number of electron 26.0000010 magnetization
- augmentation part 1.7479123 magnetization
-
- Broyden mixing:
- rms(total) = 0.28181E-02 rms(broyden)= 0.28181E-02
- rms(prec ) = 0.39149E-02
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.4710
- 2.9079 2.2924 2.2924 1.6621 1.6621 1.2410 1.2410 0.9431 0.9431 0.9557
- 0.9062 0.6049
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.57833821
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47347056
- PAW double counting = 3205.16062297 -3204.28612410
- entropy T*S EENTRO = -0.00305011
- eigenvalues EBANDS = -810.01106249
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07109883 eV
-
- energy without entropy = -48.06804872 energy(sigma->0) = -48.06957377
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 18) ---------------------------------------
-
-
- POTLOK: cpu time 0.0113: real time 0.0161
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8562: real time 0.8582
- RMM-DIIS: cpu time 3.0636: real time 3.0697
- ORTHCH: cpu time 0.0905: real time 0.0907
- DOS: cpu time 0.0036: real time 0.0037
- CHARGE: cpu time 0.2153: real time 0.2157
- MIXING: cpu time 0.0008: real time 0.0008
- --------------------------------------------
- LOOP: cpu time 4.2441: real time 4.2575
-
- eigenvalue-minimisations : 25981
- total energy-change (2. order) : 0.2551284E-05 (-0.2256845E-05)
- number of electron 26.0000010 magnetization
- augmentation part 1.7478071 magnetization
-
- Broyden mixing:
- rms(total) = 0.71135E-03 rms(broyden)= 0.71134E-03
- rms(prec ) = 0.91622E-03
- weight for this iteration 100.00
-
- eigenvalues of (default mixing * dielectric matrix)
- average eigenvalue GAMMA= 1.4171
- 2.6811 2.5386 1.7609 1.7609 1.7689 1.4591 1.4591 0.8833 0.8833 1.0096
- 0.8463 0.6854 0.6854
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.61644072
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47429532
- PAW double counting = 3204.55531159 -3203.67482965
- entropy T*S EENTRO = -0.00304973
- eigenvalues EBANDS = -809.97976563
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07109628 eV
-
- energy without entropy = -48.06804655 energy(sigma->0) = -48.06957141
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
---------------------------------------- Iteration 1( 19) ---------------------------------------
-
-
- POTLOK: cpu time 0.0061: real time 0.0061
- SETDIJ: cpu time 0.0028: real time 0.0028
- EDDIAG: cpu time 0.8529: real time 0.8552
- RMM-DIIS: cpu time 2.5286: real time 2.5345
- ORTHCH: cpu time 0.0907: real time 0.0909
- DOS: cpu time 0.0037: real time 0.0037
- --------------------------------------------
- LOOP: cpu time 3.4848: real time 3.4932
-
- eigenvalue-minimisations : 18928
- total energy-change (2. order) : 0.3110167E-06 (-0.2199411E-06)
- number of electron 26.0000010 magnetization
- augmentation part 1.7478071 magnetization
-
- Free energy of the ion-electron system (eV)
- ---------------------------------------------------
- alpha Z PSCENC = 131.43308500
- Ewald energy TEWEN = -1959.85115532
- -Hartree energ DENC = -480.61520692
- -exchange EXHF = 0.00000000
- -V(xc)+E(xc) XCENC = 33.47431066
- PAW double counting = 3204.45646866 -3203.57677692
- entropy T*S EENTRO = -0.00304986
- eigenvalues EBANDS = -809.98022412
- atomic energy EATOM = 3036.59145287
- Solvation Ediel_sol = 0.00000000
- ---------------------------------------------------
- free energy TOTEN = -48.07109596 eV
-
- energy without entropy = -48.06804610 energy(sigma->0) = -48.06957103
-
-
---------------------------------------------------------------------------------------------------------
-
-
-
-
- average (electrostatic) potential at core
- the test charge radii are 0.9757 0.6353
- (the norm of the test charge is 1.0000)
- 1 -88.4748 2 -52.0480 3 -52.1785 4 -52.6183
-
-
-
- E-fermi : 7.8828 XC(G=0): -12.0496 alpha+bet :-19.6080
-
-
- k-point 1 : 0.0000 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8804 2.00000
- 2 -91.4252 2.00000
- 3 -91.2902 2.00000
- 4 -65.7478 2.00000
- 5 -30.0216 2.00000
- 6 -29.9884 2.00000
- 7 -29.8113 2.00000
- 8 -2.0041 2.00000
- 9 4.4237 2.00000
- 10 4.8277 2.00000
- 11 6.4981 2.00000
- 12 6.9617 2.00000
- 13 8.1586 0.00010
- 14 8.8821 0.00000
- 15 8.9648 0.00000
- 16 9.0855 0.00000
- 17 13.1593 0.00000
- 18 14.6689 0.00000
-
- k-point 2 : 0.0667 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8808 2.00000
- 2 -91.4256 2.00000
- 3 -91.2906 2.00000
- 4 -65.7478 2.00000
- 5 -30.0237 2.00000
- 6 -29.9882 2.00000
- 7 -29.8111 2.00000
- 8 -1.9535 2.00000
- 9 4.3336 2.00000
- 10 4.8001 2.00000
- 11 6.5232 2.00000
- 12 6.7555 2.00000
- 13 8.3862 0.00000
- 14 8.4025 0.00000
- 15 8.9705 0.00000
- 16 9.5855 0.00000
- 17 13.3605 0.00000
- 18 14.6572 0.00000
-
- k-point 3 : 0.1333 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8814 2.00000
- 2 -91.4262 2.00000
- 3 -91.2911 2.00000
- 4 -65.7477 2.00000
- 5 -30.0297 2.00000
- 6 -29.9877 2.00000
- 7 -29.8105 2.00000
- 8 -1.8058 2.00000
- 9 4.0326 2.00000
- 10 4.7589 2.00000
- 11 6.3613 2.00000
- 12 6.6323 2.00000
- 13 7.8755 1.08202
- 14 8.8446 0.00000
- 15 8.9868 0.00000
- 16 10.1754 0.00000
- 17 14.0117 0.00000
- 18 14.7252 0.00000
-
- k-point 4 : 0.2000 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8809 2.00000
- 2 -91.4258 2.00000
- 3 -91.2907 2.00000
- 4 -65.7475 2.00000
- 5 -30.0383 2.00000
- 6 -29.9868 2.00000
- 7 -29.8096 2.00000
- 8 -1.5620 2.00000
- 9 3.5407 2.00000
- 10 4.7314 2.00000
- 11 5.9618 2.00000
- 12 6.8672 2.00000
- 13 7.4063 2.00000
- 14 9.0110 0.00000
- 15 9.3490 0.00000
- 16 10.7563 0.00000
- 17 14.0913 0.00000
- 18 15.1642 0.00000
-
- k-point 5 : 0.2667 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8806 2.00000
- 2 -91.4255 2.00000
- 3 -91.2905 2.00000
- 4 -65.7473 2.00000
- 5 -30.0481 2.00000
- 6 -29.9858 2.00000
- 7 -29.8086 2.00000
- 8 -1.2340 2.00000
- 9 2.9354 2.00000
- 10 4.7102 2.00000
- 11 5.6128 2.00000
- 12 7.0130 2.00000
- 13 7.2261 2.00000
- 14 9.0390 0.00000
- 15 9.8394 0.00000
- 16 11.3191 0.00000
- 17 14.0352 0.00000
- 18 15.4144 0.00000
-
- k-point 6 : 0.3333 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8804 2.00000
- 2 -91.4253 2.00000
- 3 -91.2903 2.00000
- 4 -65.7471 2.00000
- 5 -30.0576 2.00000
- 6 -29.9848 2.00000
- 7 -29.8076 2.00000
- 8 -0.8326 2.00000
- 9 2.2914 2.00000
- 10 4.6917 2.00000
- 11 5.3376 2.00000
- 12 6.7081 2.00000
- 13 7.6717 1.99716
- 14 9.0662 0.00000
- 15 10.2804 0.00000
- 16 11.8535 0.00000
- 17 13.4527 0.00000
- 18 14.9300 0.00000
-
- k-point 7 : 0.4000 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8804 2.00000
- 2 -91.4254 2.00000
- 3 -91.2904 2.00000
- 4 -65.7470 2.00000
- 5 -30.0651 2.00000
- 6 -29.9841 2.00000
- 7 -29.8068 2.00000
- 8 -0.3829 2.00000
- 9 1.6674 2.00000
- 10 4.6772 2.00000
- 11 5.1483 2.00000
- 12 6.5003 2.00000
- 13 8.1260 0.00058
- 14 9.0876 0.00000
- 15 10.6305 0.00000
- 16 12.3305 0.00000
- 17 12.9072 0.00000
- 18 15.1709 0.00000
-
- k-point 8 : 0.4667 0.0000 0.0000
- band No. band energies occupation
- 1 -91.8810 2.00000
- 2 -91.4260 2.00000
- 3 -91.2910 2.00000
- 4 -65.7470 2.00000
- 5 -30.0692 2.00000
- 6 -29.9837 2.00000
- 7 -29.8064 2.00000
- 8 0.0259 2.00000
- 9 1.1640 2.00000
- 10 4.6691 2.00000
- 11 5.0521 2.00000
- 12 6.3951 2.00000
- 13 8.4419 0.00000
- 14 9.0994 0.00000
- 15 10.8329 0.00000
- 16 12.5866 0.00000
- 17 12.7497 0.00000
- 18 15.0542 0.00000
-
- k-point 9 : 0.0000 0.0667 0.0000
- band No. band energies occupation
- 1 -91.8808 2.00000
- 2 -91.4256 2.00000
- 3 -91.2906 2.00000
- 4 -65.7478 2.00000
- 5 -30.0213 2.00000
- 6 -29.9915 2.00000
- 7 -29.8110 2.00000
- 8 -1.9529 2.00000
- 9 4.3901 2.00000
- 10 4.7755 2.00000
- 11 6.3415 2.00000
- 12 6.9388 2.00000
- 13 8.3265 0.00000
- 14 8.4311 0.00000
- 15 8.8898 0.00000
- 16 9.6264 0.00000
- 17 13.5937 0.00000
- 18 14.7192 0.00000
-
- k-point 10 : 0.0667 0.0667 0.0000
- band No. band energies occupation
- 1 -91.8807 2.00000
- 2 -91.4256 2.00000
- 3 -91.2905 2.00000
- 4 -65.7477 2.00000
- 5 -30.0234 2.00000
- 6 -29.9912 2.00000
- 7 -29.8108 2.00000
- 8 -1.9023 2.00000
- 9 4.3246 2.00000
- 10 4.7293 2.00000
- 11 6.2087 2.00000
- 12 6.9819 2.00000
- 13 8.2546 0.00000
- 14 8.4565 0.00000
- 15 8.8007 0.00000
- 16 9.9214 0.00000
- 17 13.6485 0.00000
- 18 14.6504 0.00000
-
- k-point 11 : 0.1333 0.0667 0.0000
- band No. band energies occupation
- 1 -91.8811 2.00000
- 2 -91.4259 2.00000
- 3 -91.2909 2.00000
- 4 -65.7476 2.00000
- 5 -30.0294 2.00000
- 6 -29.9906 2.00000
- 7 -29.8102 2.00000
- 8 -1.7528 2.00000
- 9 4.0516 2.00000
- 10 4.6663 2.00000
- 11 5.9785 2.00000
- 12 7.0276 2.00000
- 13 7.8427 1.42889
- 14 8.7719 0.00000
- 15 8.8056 0.00000
- 16 10.4508 0.00000
- 17 14.3989 0.00000
- 18 15.1127 0.00000
-
- k-point 12 : 0.2000 0.0667 0.0000
- band No. band energies occupation
- 1 -91.8807 2.00000
- 2 -91.4256 2.00000
- 3 -91.2906 2.00000
- 4 -65.7474 2.00000
- 5 -30.0379 2.00000
- 6 -29.9898 2.00000
- 7 -29.8093 2.00000
- 8 -1.5097 2.00000
- 9 3.5587 2.00000
- 10 4.6450 2.00000
- 11 5.7408 2.00000
- 12 7.1387 2.00000
- 13 7.4085 2.00000
- 14 8.7921 0.00000
- 15 9.2640 0.00000
- 16 11.0130 0.00000
- 17 14.0760 0.00000
- 18 15.2142 0.00000
-
- k-point 13 : 0.2667 0.0667 0.0000
- band No. band energies occupation
- 1 -91.8804 2.00000
- 2 -91.4252 2.00000
- 3 -91.2903 2.00000
- 4 -65.7472 2.00000
- 5 -30.0478 2.00000
- 6 -29.9888 2.00000
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diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
index ab347be568..91a85975e6 100644
--- a/examples/COUPLE/lammps_vasp/README
+++ b/examples/COUPLE/lammps_vasp/README
@@ -36,9 +36,11 @@ You can leave off the -z if you do not have ZMQ on your system.
Prepare to use VASP and the vasp_wrapper.py script
-You can run the vasp_wrap.py script as-is to test that the
-coupling between it and LAMMPS is functional. But the as-is
-version will not attempt to run VASP.
+You can run the vasp_wrap.py script as-is to test that the coupling
+between it and LAMMPS is functional. This will use the included
+vasprun.xml file output by a previous VASP run.
+
+But the as-is version of vasp_wrap.py will not attempt to run VASP.
To do this, you must edit the 1st vaspcmd line at the top of
vasp_wrapper.py to be the launch command needed to run VASP on your
@@ -63,6 +65,8 @@ Note that the POSCAR_template file should be matched to the LAMMPS
input script (# of atoms and atom types, box size, etc). The provided
POSCAR_W matches in.client.W.
+Once you run VASP yourself, the vasprun.xml file will be overwritten.
+
NOTE: explain how vasp_wrapper.py finds the cslib.py wrapper on the
CSlib to import.
diff --git a/examples/COUPLE/lammps_vasp/vasprun.xml b/examples/COUPLE/lammps_vasp/vasprun.xml
new file mode 100644
index 0000000000..0f15c871b4
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasprun.xml
@@ -0,0 +1,12329 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<modeling>
+ <generator>
+ <i name="program" type="string">vasp </i>
+ <i name="version" type="string">5.4.4.18Apr17-6-g9f103f2a35 </i>
+ <i name="subversion" type="string">(build Aug 01 2017 10:32:50) complex parallel </i>
+ <i name="platform" type="string">LinuxIFC </i>
+ <i name="date" type="string">2017 12 19 </i>
+ <i name="time" type="string">15:22:45 </i>
+ </generator>
+ <incar>
+ <i type="int" name="ISTART"> 0</i>
+ <i type="string" name="PREC">normal normal or accurate (medium, h</i>
+ <i type="int" name="IALGO"> 48</i>
+ <i type="logical" name="LSORBIT"> F </i>
+ <i type="int" name="ISPIN"> 1</i>
+ <i type="int" name="ICHARG"> 2</i>
+ <i type="int" name="INIWAV"> 1</i>
+ <i type="int" name="NELM"> 100</i>
+ <i type="int" name="NELMDL"> -5</i>
+ <i type="int" name="NELMIN"> 2</i>
+ <i type="int" name="IBRION"> -1</i>
+ <i type="int" name="NFREE"> 0</i>
+ <i name="EDIFF"> 0.00000100</i>
+ <i name="EDIFFG"> 0.00100000</i>
+ <i type="int" name="NSW"> 0</i>
+ <i type="int" name="ISIF"> 2</i>
+ <i type="int" name="IWAVPR"> 10</i>
+ <i type="int" name="NBLOCK"> 1</i>
+ <i type="int" name="KBLOCK"> 1</i>
+ <i name="ENCUT"> 600.00000000</i>
+ <i name="ENINI"> 600.00000000</i>
+ <i name="POTIM"> 0.50000000</i>
+ <i name="TEBEG"> 3500.00000000</i>
+ <i name="TEEND"> 3500.00000000</i>
+ <i name="SMASS"> -3.00000000</i>
+ <i name="EMIN"> 10.00000000</i>
+ <i name="EMAX"> -10.00000000</i>
+ <i name="EFERMI"> 0.00000000</i>
+ <i type="int" name="ISMEAR"> 0</i>
+ <i name="SIGMA"> 0.10000000</i>
+ <i type="int" name="NWRITE"> 2</i>
+ <i name="PSTRESS"> 0.00000000</i>
+ <i type="logical" name="LWAVE"> T </i>
+ <i type="logical" name="LCHARG"> T </i>
+ <i type="logical" name="LVTOT"> F </i>
+ <i type="logical" name="LVHAR"> F </i>
+ <i type="logical" name="LELF"> F </i>
+ <v type="int" name="KPOINT_BSE"> -1 0 0 0</v>
+ <i type="int" name="NELM"> 100</i>
+ <i type="string" name="GGA"> -- GGA type</i>
+ <i type="logical" name="LDIPOL"> F </i>
+ <i type="logical" name="LMONO"> F </i>
+ <i type="int" name="IDIPOL"> 0</i>
+ <i name="EPSILON"> 1.00000000</i>
+ </incar>
+ <structure name="primitive_cell" >
+ <crystal>
+ <varray name="basis" >
+ <v> 3.66961100 0.00000000 0.00000000 </v>
+ <v> 0.00000000 3.55744000 0.00000000 </v>
+ <v> 0.00000000 0.00000000 3.17678100 </v>
+ </varray>
+ <i name="volume"> 41.47103646 </i>
+ <varray name="rec_basis" >
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+ <v> 0.00000000 0.28110102 0.00000000 </v>
+ <v> 0.00000000 0.00000000 0.31478405 </v>
+ </varray>
+ </crystal>
+ <varray name="positions" >
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+ <v> 0.00000000 -0.50000000 -0.50000000 </v>
+ <v> -0.50000000 0.00000000 -0.50000000 </v>
+ <v> -0.50000000 -0.50000000 0.00000000 </v>
+ </varray>
+ </structure>
+ <varray name="primitive_index" >
+ <v type="int" > 1 </v>
+ <v type="int" > 2 </v>
+ <v type="int" > 3 </v>
+ <v type="int" > 4 </v>
+ </varray>
+ <kpoints>
+ <generation param="Monkhorst-Pack">
+ <v type="int" name="divisions"> 15 15 15 </v>
+ <v name="usershift"> 0.00000000 0.00000000 0.00000000 </v>
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+ <v name="genvec3"> 0.00000000 0.00000000 0.06666667 </v>
+ <v name="shift"> 0.00000000 0.00000000 0.00000000 </v>
+ </generation>
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+ <r> 35.7163 0.0223 35.9437 </r>
+ <r> 36.2199 0.0077 35.9475 </r>
+ <r> 36.7236 0.0030 35.9490 </r>
+ <r> 37.2272 0.0047 35.9514 </r>
+ <r> 37.7308 0.0088 35.9558 </r>
+ <r> 38.2344 0.0020 35.9568 </r>
+ <r> 38.7380 0.0269 35.9704 </r>
+ <r> 39.2416 0.0102 35.9755 </r>
+ <r> 39.7453 0.0015 35.9763 </r>
+ <r> 40.2489 0.0000 35.9763 </r>
+ <r> 40.7525 0.0047 35.9787 </r>
+ <r> 41.2561 0.0000 35.9787 </r>
+ <r> 41.7597 0.0178 35.9876 </r>
+ <r> 42.2633 0.0114 35.9934 </r>
+ <r> 42.7670 0.0038 35.9953 </r>
+ <r> 43.2706 0.0000 35.9953 </r>
+ <r> 43.7742 0.0000 35.9953 </r>
+ <r> 44.2778 0.0000 35.9953 </r>
+ <r> 44.7814 0.0000 35.9953 </r>
+ <r> 45.2850 0.0000 35.9953 </r>
+ <r> 45.7886 0.0094 36.0000 </r>
+ <r> 46.2923 0.0000 36.0000 </r>
+ <r> 46.7959 0.0000 36.0000 </r>
+ <r> 47.2995 0.0000 36.0000 </r>
+ <r> 47.8031 0.0000 36.0000 </r>
+ <r> 48.3067 0.0000 36.0000 </r>
+ <r> 48.8103 0.0000 36.0000 </r>
+ <r> 49.3140 0.0000 36.0000 </r>
+ <r> 49.8176 0.0000 36.0000 </r>
+ <r> 50.3212 0.0000 36.0000 </r>
+ <r> 50.8248 0.0000 36.0000 </r>
+ <r> 51.3284 0.0000 36.0000 </r>
+ <r> 51.8320 0.0000 36.0000 </r>
+ <r> 52.3357 0.0000 36.0000 </r>
+ </set>
+ </set>
+ </array>
+ </total>
+ </dos>
+ </calculation>
+ <structure name="finalpos" >
+ <crystal>
+ <varray name="basis" >
+ <v> 3.66961100 0.00000000 0.00000000 </v>
+ <v> 0.00000000 3.55744000 0.00000000 </v>
+ <v> 0.00000000 0.00000000 3.17678100 </v>
+ </varray>
+ <i name="volume"> 41.47103646 </i>
+ <varray name="rec_basis" >
+ <v> 0.27250845 0.00000000 0.00000000 </v>
+ <v> 0.00000000 0.28110102 0.00000000 </v>
+ <v> 0.00000000 0.00000000 0.31478405 </v>
+ </varray>
+ </crystal>
+ <varray name="positions" >
+ <v> 0.00000000 0.00000000 0.00000000 </v>
+ <v> 0.00000000 0.50000000 0.50000000 </v>
+ <v> 0.50000000 0.00000000 0.50000000 </v>
+ <v> 0.50000000 0.50000000 0.00000000 </v>
+ </varray>
+ </structure>
+</modeling>
--
GitLab
From a2303e5a15b27a40bf82b03bb1d5bf9f0c3c2b69 Mon Sep 17 00:00:00 2001
From: sergeylishchuk <sergey.lishchuk@gmail.com>
Date: Thu, 26 Jul 2018 11:54:04 +0100
Subject: [PATCH 061/332] more changes to ATM source and doc file
---
doc/src/pair_atm.txt | 14 +++++++-------
src/MANYBODY/pair_atm.cpp | 40 +++++++++++++++++++++++++++++++--------
src/MANYBODY/pair_atm.h | 5 +++++
3 files changed, 44 insertions(+), 15 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index e442c32814..6453b02bf8 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -41,17 +41,17 @@ gamma3 are as shown in this diagram:
Note that for the interaction between a triplet of atoms I,J,K, there
is no "central" atom. The interaction is symmetric with respect to
-permutation of the three atoms. In fact, it is computed 3 times by
-the code with each of I,J,K being atom 1. Thus the nu value must be
-the same for all those permutations of the atom types of I,J,K as
-discussed below.
+permutation of the three atoms. Thus the nu value is
+the same for all those permutations of the atom types of I,J,K
+and needs to be specified only once, as discussed below.
The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-The potential for a triplet of atom is calculated only if all 3
-distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
+The potential is calculated if atoms J and K are in the
+"neighbor list"_neighbor.html of atom I
+and the distances between atoms satisfy rIJ rJK rKI > cutoff^3.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@@ -88,7 +88,7 @@ pair_coeff 2 3 4 0.1 :pre
Note that for a simulation with a single atom type, only a single
entry is required, e.g.
-pair_coeff 1 1 1 0.25 :per
+pair_coeff 1 1 1 0.25 :pre
For a simulation with two atom types, four pair_coeff commands will
specify all possible nu values:
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 2ba8912899..090a8352d5 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -91,8 +91,8 @@ void PairATM::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
- double cutoffsq = cut_global*cut_global;
-
+ double cutoff_sixth = cut_global*cut_global;
+ cutoff_sixth = cutoff_sixth*cutoff_sixth*cutoff_sixth;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -112,26 +112,32 @@ void PairATM::compute(int eflag, int vflag)
j = jlist[jj];
j &= NEIGHMASK;
rij[0] = x[j][0] - xi;
+ if (rij[0] < 0.0) continue;
rij[1] = x[j][1] - yi;
+ if (rij[0] == 0.0 and rij[1] < 0.0) continue;
rij[2] = x[j][2] - zi;
+ if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
- rik[0] = x[k][0] - xi;
- rik[1] = x[k][1] - yi;
- rik[2] = x[k][2] - zi;
- rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
-
rjk[0] = x[k][0] - x[j][0];
+ if (rjk[0] < 0.0) continue;
rjk[1] = x[k][1] - x[j][1];
+ if (rjk[0] == 0.0 and rjk[1] < 0.0) continue;
rjk[2] = x[k][2] - x[j][2];
+ if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ rik[0] = x[k][0] - xi;
+ rik[1] = x[k][1] - yi;
+ rik[2] = x[k][2] - zi;
+ rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
+
r6 = rij2*rik2*rjk2;
- if (r6 > cutoffsq) continue;
+ if (r6 > cutoff_sixth) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
@@ -228,6 +234,9 @@ void PairATM::coeff(int narg, char **arg)
void PairATM::init_style()
{
+ if (force->newton_pair == 0)
+ error->all(FLERR,"Pair style ATM requires newton pair on");
+
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
@@ -258,6 +267,21 @@ double PairATM::init_one(int i, int j)
proc 0 writes to restart file
------------------------------------------------------------------------- */
+//
+// PLEASE HELP!
+//
+// From the pair_hybrid documentation:
+//
+// "For the hybrid pair styles, the list of sub-styles and their respective
+// settings are written to binary restart files, so a pair_style command
+// does not need to specified in an input script that reads a restart file.
+// However, the coefficient information is not stored in the restart file.
+// Thus, pair_coeff commands need to be re-specified in the restart input
+// script."
+//
+// As a result, the function "PairATM::write_restart" is not called from
+// "pair_hybrid.cpp". What is the best way to deal with this problem?
+//
void PairATM::write_restart(FILE *fp)
{
write_restart_settings(fp);
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 45a6cda344..210351cfad 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -64,6 +64,11 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
+E: Pair style ATM requires newton pair on
+
+See the newton command. This is a restriction to use the ATM
+potential.
+
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
--
GitLab
From 649d0167c800fa0c88e9f3d344577471e1a29a40 Mon Sep 17 00:00:00 2001
From: sergeylishchuk <sergey.lishchuk@gmail.com>
Date: Fri, 27 Jul 2018 10:41:01 +0100
Subject: [PATCH 062/332] sorted out restart
---
doc/src/pair_atm.txt | 4 ++++
src/MANYBODY/pair_atm.cpp | 15 ---------------
2 files changed, 4 insertions(+), 15 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index 6453b02bf8..b798f7d128 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -130,6 +130,10 @@ mix, shift, table, and tail options.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
+However, if the {atm} potential is used in combination with other
+potentials using the "pair_style hybrid/overlay"_pair_hybrid.html
+command then pair_coeff commands need to be re-specified
+in the restart input script.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 090a8352d5..92d9338dc8 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -267,21 +267,6 @@ double PairATM::init_one(int i, int j)
proc 0 writes to restart file
------------------------------------------------------------------------- */
-//
-// PLEASE HELP!
-//
-// From the pair_hybrid documentation:
-//
-// "For the hybrid pair styles, the list of sub-styles and their respective
-// settings are written to binary restart files, so a pair_style command
-// does not need to specified in an input script that reads a restart file.
-// However, the coefficient information is not stored in the restart file.
-// Thus, pair_coeff commands need to be re-specified in the restart input
-// script."
-//
-// As a result, the function "PairATM::write_restart" is not called from
-// "pair_hybrid.cpp". What is the best way to deal with this problem?
-//
void PairATM::write_restart(FILE *fp)
{
write_restart_settings(fp);
--
GitLab
From ae04fd0beaba1c3561cd17354d2c1fa05bde79ae Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 31 Jul 2018 09:48:59 -0600
Subject: [PATCH 063/332] fixed error: if no particles are on a process, the
arrays for efield and epot were not allocated, leading to segfaults; shifted
the parameter output to after the tuning step, so if the values are changed,
the changed values are displayed
---
src/USER-SCAFACOS/scafacos.cpp | 26 +++++++++++++++++++++-----
1 file changed, 21 insertions(+), 5 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index e7dbcb4523..21e46f76ad 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -121,7 +121,6 @@ void Scafacos::init()
result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
check_result(result);
}
- if (me == 0) fcs_print_parameters(fcs);
double **x = atom->x;
double *q = atom->q;
@@ -130,11 +129,15 @@ void Scafacos::init()
if (strcmp(method,"fmm") == 0)
{
if (fmm_tuning_flag == 1)
- fcs_fmm_set_internal_tuning(fcs,fmm_tuning_flag);
+ fcs_fmm_set_internal_tuning(fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
+ else
+ fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
}
result = fcs_tune(fcs,nlocal,&x[0][0],q);
check_result(result);
+ // more useful here, since the parameters should be tuned now
+ if (me == 0) fcs_print_parameters(fcs);
}
initialized = 1;
}
@@ -170,13 +173,20 @@ void Scafacos::compute(int eflag, int vflag)
// grow epot & efield if necessary
+ if (nlocal == 0 && maxatom == 0) {
+ memory->destroy(epot);
+ memory->destroy(efield);
+ maxatom = 1;
+ memory->create(epot,maxatom,"scafacos:epot");
+ memory->create(efield,maxatom,3,"scafacos:efield");
+ }
+
if (nlocal > maxatom) {
memory->destroy(epot);
memory->destroy(efield);
maxatom = atom->nmax;
memory->create(epot,maxatom,"scafacos:epot");
memory->create(efield,maxatom,3,"scafacos:efield");
-
}
if (vflag_global)
@@ -184,6 +194,12 @@ void Scafacos::compute(int eflag, int vflag)
fcs_set_compute_virial(fcs,1);
}
+ if (strcmp(method,"p3m")==0)
+ {
+ result = fcs_tune(fcs,nlocal,&x[0][0],q);
+ check_result(result);
+ }
+
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
check_result(result);
@@ -252,8 +268,8 @@ int Scafacos::modify_param(int narg, char **arg)
// 1 -> inhomogenous system (more internal tuning is provided (sequential!))
if (strcmp(arg[1],"fmm_tuning") == 0)
{
- if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg);
- if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...%d\n", narg);
+ if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...\n");
+ if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...\n");
if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)");
fmm_tuning_flag = atoi(arg[2]);
return 3;
--
GitLab
From ac0ab4ba346e951e17cb7ad85bd5cd8a5867e666 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 31 Jul 2018 13:31:50 -0600
Subject: [PATCH 064/332] changed CMake file to require pkg_config for ScaFaCoS
and removed Fortran/C dependencies
---
cmake/CMakeLists.txt | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index afb93b9d1b..bfaf9243b1 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -185,11 +185,11 @@ pkg_depends(CORESHELL KSPACE)
######################################################
# packages with special compiler needs or external libs
######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
enable_language(Fortran)
endif()
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
enable_language(C)
endif()
@@ -349,7 +349,7 @@ if(PKG_LATTE)
endif()
if(PKG_USER-SCAFACOS)
- FIND_PACKAGE(PkgConfig)
+ FIND_PACKAGE(PkgConfig REQUIRED)
PKG_CHECK_MODULES(SCAFACOS scafacos)
include_directories(${SCAFACOS_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
--
GitLab
From a8f0200fe9636afeccf464f08b0bf242bf2992fe Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 31 Jul 2018 13:33:10 -0600
Subject: [PATCH 065/332] Install.py works on dummy tar-ball
---
lib/scafacos/Install.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
index 1b39335511..c478589144 100644
--- a/lib/scafacos/Install.py
+++ b/lib/scafacos/Install.py
@@ -29,8 +29,9 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation
# settings
-version = "scafacos-1.0"
-#url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
+version = "scafacos-0.9"
+url = "https://gigamove.rz.rwth-aachen.de/d/id/fTmrTm4EUAUSAp/dd/100"
+#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version
# print error message or help
@@ -75,6 +76,7 @@ def geturl(url,fname):
if not success and which('wget') != None:
cmd = 'wget -O "%s" %s' % (fname,url)
+ print("Wget command: %s" % cmd)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
success = True
@@ -92,7 +94,7 @@ nargs = len(args)
homepath = "."
-buildflag = False
+buildflag = True
pathflag = False
linkflag = True
@@ -145,7 +147,7 @@ if buildflag:
if buildflag:
print("Building Scafacos ...")
- cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir
+ cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j 4; make install' % homedir
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
@@ -157,7 +159,7 @@ if linkflag:
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
- cmd = 'ln -s "%s/include" includelink' % homedir
+ cmd = 'ln -s "%s/build/include" includelink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
- cmd = 'ln -s "%s/lib" liblink' % homedir
+ cmd = 'ln -s "%s/build/lib" liblink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
--
GitLab
From efaebe0eb02d9970c6a03c0e20bca077885ae3d2 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Thu, 2 Aug 2018 13:44:12 -0600
Subject: [PATCH 066/332] READMEs for USER-SCAFACOS completed
---
lib/scafacos/README | 79 +++++++++++++++++++++++++++++++++++++---
src/USER-SCAFACOS/README | 28 ++++++++++++--
2 files changed, 98 insertions(+), 9 deletions(-)
diff --git a/lib/scafacos/README b/lib/scafacos/README
index bdf167aef1..e5f1ecd92c 100644
--- a/lib/scafacos/README
+++ b/lib/scafacos/README
@@ -1,7 +1,76 @@
-RENE - there needs to be a README like the one
-for lib/voronoi/README, explaining how
-to grab the correct version of Scafacos.
+This directory contains links to the ScaFaCoS library which
+is required to use the KSPACE scafacos and its kspace_style
+scafacos command in a LAMMPS input script.
-And how to build, either via traditional make
-and the Install.py script, or via CMake
+The ScaFaCoS library is available at http://scafacos.de or
+on github at https://github.com/scafacos, the libary was
+developed by a consortium of different universities in
+Germany (Bonn, Chemnitz, Stuttgart, Wuppertal) and
+the Research Centre Juelich (Juelich Supercomputing Centre).
+-----------------
+
+Instructions:
+
+1.) Download ScaFaCoS at http://scafacos.de or directly from github
+ https://github.com/scafacos where you can either clone the
+ repository or download the latest stable release.
+ NOTE: For the P2NFFT solver, you require an installation of the
+ GNU Scientific Library (GSL). Also to ensure the correct
+ linker-flags are used, ScaFaCoS employs the pkg-config
+ tool, which is also required.
+ If you cloned the repository, please refer to 2.), else continue
+ with 3.)
+
+2.) If you cloned the git repository, you require autotools to setup
+ the library. For that the following packages are required:
+ m4
+ autotools
+ automake
+ libtools
+ In the build_aux folder of the scafacos folder, you can find the
+ get_autotools.sh script, that downloads and installs the tools
+ to ${HOME}/local. To change the target folder, please change the
+ value of 'myprefix' in that script.
+ To start the auto-configuration process, please run the './bootstrap'
+ command in the scafacos base-folder.
+
+3.) If you downloaded the library as a tarball, please extract the file
+ to somewhere in your file system, or if you finished running
+ './bootstrap', please run './configure' in the base folder.
+ Important flags for './configure' are:
+ --prefix=<install_dir>: sets the directory the compiled files will
+ be installed to [default: /usr/local]
+ --fcs-enable-solvers=<list>: sets the list of solvers that are going to
+ be built. By default all solvers will be
+ built. Currently supported by the kspace in LAMMPS
+ are: direct, ewald, fmm, p2nfft
+ The other solvers might work, but support
+ is purely experimental at the moment. To
+ give a list of solvers, use a comma seperated
+ list.
+ --fcs-disable-doc: disables the compilation of the documentation,
+ e.g. if no Latex is available on the system.
+
+4.) To build the library after configuration, run 'make' from the base folder.
+
+5.) To install the libray in the designated installation folder, run 'make install'.
+ Installation is required, as ScaFaCoS does not support an in-source build!
+
+6.) Create two soft links to this directory (lib/scafacos) to where the libary
+ is installed. E.g. if you built ScaFaCoS in the default install directory:
+ % ln -s /usr/local/include includelink
+ % ln -s /usr/local/lib liblink
+ for any custom directory <custom_dir>:
+ % ln -s <custom_dir>/include includelink
+ % ln -s <custom_dir>/lib liblink
+
+7.) ScaFaCoS uses the pkg-config tool to supply the correct, so you need to setup your
+ PKG_CONFIG_PATH environment variable to include the lib/pkgconfig folder in the
+ installation directory.
+ Depending on the shell you use, this can be done either by:
+ % export PKG_CONFIG_PATH=<custom_dir>/lib/pkgconfig:${PKG_CONFIG_PATH}
+ or
+ % setenv PKG_CONFIG_PATH=<custom_dir>/lib/pkgconfig:${PKG_CONFIG_PATH}
+
+-----------------
diff --git a/src/USER-SCAFACOS/README b/src/USER-SCAFACOS/README
index 30534499e4..42d2e2c0f7 100644
--- a/src/USER-SCAFACOS/README
+++ b/src/USER-SCAFACOS/README
@@ -1,5 +1,25 @@
-RENE: need a short README file - see other examples in the
-USER package dirs within src
+This package provides a kspace style which is a wrapper for the
+ScaFaCoS long-range Coulomb solver library. The library provides
+a selection of different long-range Coulomb solvers, which can be
+used to calculate the Coloumic forces between charged particles.
+More information about the ScaFaCoS library can be found on this
+web site: http://scafacos.de. ScaFaCoS was designed and implemented
+by a consortium of German universities (Bonn, Chemnitz, Stuttgart,
+Wuppertal and others) and the Juelich Supercomputing Centre
+(Forschungszentrum Juelich).
-give short background on ScaFaCos, authors, contact info
-for LAMMPS users to have if needed, citation
+The use of the scafacos kspace requires the download and installation
+of the library on the system. This can be done in lib/scafacos or
+elsewhere in your system. Details of the download and build process
+for ScaFaCoS are given in the lib/scafacos/README file and it can also
+be done via the make lib-user-scafacos command from the LAMMPS
+source directory.
+
+Once you have successfully built LAMMPS with this package and the
+ScaFaCoS library, you can test it using an input file from the
+examples scafacos dir, e.g.:
+
+lmp_serial -in lammps/examples/USER/scafacos/in.scafacos.fmm
+
+For questions about ScaFaCoS, please contact:
+r.halver@fz-juelich.de or g.sutmann@fz-juelich.de
--
GitLab
From b2d1332d461c066cbab1066f5961913d48fce8ca Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Thu, 2 Aug 2018 14:47:20 -0600
Subject: [PATCH 067/332] change proc count to color for MPI_Comm_split
---
doc/src/Section_start.txt | 31 +++++++++++++++++--------------
examples/message/README | 9 ++++-----
src/lammps.cpp | 26 +++++++++++---------------
3 files changed, 32 insertions(+), 34 deletions(-)
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index f38339661b..80f6b0ffc4 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1352,24 +1352,27 @@ specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
--mpi P :pre
+-mpi color :pre
If used, this must be the first command-line argument after the LAMMPS
-executable name. It is only used when running LAMMPS in client/server
-mode with the "mpi/one" mode of messaging provided by the
-"message"_message.html command and the CSlib library LAMMPS links with
-from the lib/message directory. See the "message"_message.html
-command for more details
-
-In the mpi/one mode of messaging, both executables (the client and the
-server) are launched by one mpirun command. P should be specified as
-the number of processors (MPI tasks) the first executable is running
-on (could be the client or the server code).
-
-This information is required so that both codes can shrink the
-MPI_COMM_WORLD communicator they are part of to the subset of
+executable name. It is only used when LAMMPS is launched by an mpirun
+command which also launches another executable(s) (the other
+executable could be LAMMPS as well) at the same time. The color is an
+integer value which should be different for each executable (another
+application may set this value in a different way). LAMMPS and the
+other executable(s) perform an MPI_Comm_split() with their own colors
+to shrink the MPI_COMM_WORLD communication to be the subset of
processors they are actually running on.
+Currently, this is only used in LAMMPS to perform client/server
+messaging with another application. LAMMPS can act as either a client
+or server (or both).
+
+Specifically, this refers to the "mpi/one" mode of messaging provided
+by the "message"_message.html command and the CSlib library LAMMPS
+links with from the lib/message directory. See the
+"message"_message.html command for more details.
+
-nocite :pre
Disable writing the log.cite file which is normally written to list
diff --git a/examples/message/README b/examples/message/README
index 213dbbde51..63055177a4 100644
--- a/examples/message/README
+++ b/examples/message/README
@@ -91,12 +91,11 @@ Mpi/one mode of messaging:
Launch LAMMPS twice in a single mpirun command:
-mpirun -np 2 lmp_mpi -mpi 2 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 2 -in in.message.server -v mode mpione -log log.server
+mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.server
The two -np values determine how many procs the client and the server
run on.
-A LAMMPS executable run in this manner must use the -mpi P
-command-line option as their first option, where P is the number of
-processors the first code in the mpirun command (client or server) is
-running on.
+A LAMMPS executable run in this manner must use the -mpi color
+command-line option as their first option, where color is set to
+one integer value for the 1st app, and another value for the 2nd app.
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 282250c642..dec4a57186 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -86,17 +86,17 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
// check if -mpi is first arg
// if so, then 2 apps were launched with one mpirun command
// this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
- // e.g. for client/server coupling with another code
- // communicator needs to shrink to be just LAMMPS
- // syntax: -mpi P1 means P1 procs for one app, P-P1 procs for second app
- // LAMMPS could be either app, based on proc IDs
+ // e.g. for client/server coupling with another code
+ // in the future LAMMPS might leverage this in other ways
+ // universe communicator needs to shrink to be just LAMMPS
+ // syntax: -mpi color
+ // color = integer for this app, different than other app(s)
// do the following:
// perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
- // NOTE: assuming other app is doing the same thing, else will hang!
+ // NOTE: this assumes other app(s) does same thing, else will hang!
// re-create universe with subcomm
- // store full two-app comm in cscomm
+ // store full multi-app comm in cscomm
// cscomm is used by CSLIB package to exchange messages w/ other app
- // eventually should extend to N > 2 apps launched with one mpirun command
int iarg = 1;
if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
@@ -104,13 +104,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int me,nprocs;
MPI_Comm_rank(communicator,&me);
MPI_Comm_size(communicator,&nprocs);
- int p1 = atoi(arg[iarg+1]);
- if (p1 <= 0 || p1 >= nprocs)
- error->universe_all(FLERR,"Invalid command-line argument");
- int which = 0;
- if (me >= p1) which = 1;
+ int color = atoi(arg[iarg+1]);
MPI_Comm subcomm;
- MPI_Comm_split(communicator,which,me,&subcomm);
+ MPI_Comm_split(communicator,color,me,&subcomm);
cscomm = communicator;
communicator = subcomm;
delete universe;
@@ -656,8 +652,8 @@ LAMMPS::~LAMMPS()
delete [] suffix;
delete [] suffix2;
- // free the MPI comm created by -mpi command-line arg
- // it was passed to universe as if origianl universe world
+ // free the MPI comm created by -mpi command-line arg processed in constructor
+ // it was passed to universe as if original universe world
// may have been split later by partitions, universe will free the splits
// free a copy of uorig here, so check in universe destructor will still work
--
GitLab
From e8774dce9792d3289bcb2fbd8f722796af3ec675 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 3 Aug 2018 11:31:11 -0600
Subject: [PATCH 068/332] removed thread restriction on make command, should
make the building process faster
---
lib/scafacos/Install.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
index c478589144..df82780438 100644
--- a/lib/scafacos/Install.py
+++ b/lib/scafacos/Install.py
@@ -147,7 +147,7 @@ if buildflag:
if buildflag:
print("Building Scafacos ...")
- cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j 4; make install' % homedir
+ cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j; make install' % homedir
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
--
GitLab
From 94bf221258af6fa48fe568a21171c492148ccf71 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Fri, 3 Aug 2018 11:31:50 -0600
Subject: [PATCH 069/332] implemented checks for unsupported solvers
---
src/USER-SCAFACOS/scafacos.cpp | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 21e46f76ad..d4b106b26c 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -47,14 +47,26 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
// optional ScaFaCoS library setting defaults
// choose the correct default tolerance type for chosen method
- // TODO: needs to be expanded for all solvers, currently mainly used ones
+ // throw an error if a not yet supported solver is chosen
if (strcmp(method,"fmm") == 0)
{
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
fmm_tuning_flag = 0;
}
- else if (strcmp(method,"p3m") == 0 || strcmp(method,"p2nfft") == 0)
+ else if (strcmp(method,"p3m") == 0 ||
+ strcmp(method,"p2nfft") == 0 ||
+ strcmp(method,"ewald") == 0)
+ {
tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
+ }
+ else if (strcmp(method,"direct") == 0)
+ {
+ // direct summation has no tolerance type
+ }
+ else
+ {
+ error->all(FLERR,"Unsupported ScaFaCoS method");
+ }
// initializations
@@ -194,11 +206,13 @@ void Scafacos::compute(int eflag, int vflag)
fcs_set_compute_virial(fcs,1);
}
+ /*
if (strcmp(method,"p3m")==0)
{
result = fcs_tune(fcs,nlocal,&x[0][0],q);
check_result(result);
}
+ */
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
check_result(result);
--
GitLab
From 446a8da8e7a0129875840bde675bbe77b3a22a4b Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Mon, 6 Aug 2018 10:25:12 -0400
Subject: [PATCH 070/332] Commit before merge.
---
src/lammps.cpp | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 56af95767b..d25d5473e8 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -249,7 +249,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
helpflag = 1;
citeflag = 0;
iarg += 1;
- } else error->universe_all(FLERR,"Invalid command-line argument");
+ } else {
+ char msg[2048];
+ sprintf( msg, "Invalid command-line argument \"%s\"\n", arg[iarg] );
+ error->universe_all(FLERR,msg);
+ }
}
// if no partition command-line switch, universe is one world with all procs
--
GitLab
From 4d75d2d6115ef9350a57d9a8847b555ca953ba96 Mon Sep 17 00:00:00 2001
From: sergeylishchuk <sergey.lishchuk@gmail.com>
Date: Mon, 6 Aug 2018 20:49:05 +0100
Subject: [PATCH 071/332] more changes to ATM source and doc file
---
.github/CODEOWNERS | 2 +
cmake/CMakeLists.txt | 155 +-
cmake/README.md | 10 +
cmake/etc/profile.d/lammps.csh.in | 2 +
cmake/etc/profile.d/lammps.sh.in | 2 +
doc/Makefile | 2 +-
doc/src/Commands.txt | 51 +
doc/src/Commands_all.txt | 128 +
doc/src/Commands_bond.txt | 124 +
doc/src/Commands_category.txt | 141 +
doc/src/Commands_compute.txt | 153 +
doc/src/Commands_fix.txt | 229 ++
doc/src/Commands_input.txt | 60 +
doc/src/Commands_kspace.txt | 36 +
doc/src/Commands_pair.txt | 231 ++
doc/src/Commands_parse.txt | 136 +
doc/src/Commands_structure.txt | 95 +
doc/src/Eqs/pair_spin_dmi_forces.jpg | Bin 0 -> 13431 bytes
doc/src/Eqs/pair_spin_dmi_forces.tex | 14 +
doc/src/Eqs/pair_spin_dmi_interaction.jpg | Bin 6316 -> 7891 bytes
doc/src/Eqs/pair_spin_dmi_interaction.tex | 2 +-
doc/src/Eqs/pair_spin_exchange_forces.jpg | Bin 13720 -> 13255 bytes
doc/src/Eqs/pair_spin_exchange_forces.tex | 10 +-
.../Eqs/pair_spin_exchange_interaction.jpg | Bin 6661 -> 5940 bytes
.../Eqs/pair_spin_exchange_interaction.tex | 2 +-
doc/src/Errors.txt | 4 +-
doc/src/Errors_bugs.txt | 2 +-
doc/src/Errors_common.txt | 2 +-
doc/src/Errors_messages.txt | 8 +-
doc/src/Errors_warnings.txt | 8 +-
doc/src/Examples.txt | 10 +-
doc/src/Howto.txt | 128 +
doc/src/Howto_2d.txt | 48 +
doc/src/Howto_barostat.txt | 75 +
...ial_bash_on_windows.txt => Howto_bash.txt} | 3 +-
doc/src/Howto_bioFF.txt | 101 +
doc/src/{body.txt => Howto_body.txt} | 18 +-
doc/src/Howto_chunk.txt | 166 +
doc/src/Howto_coreshell.txt | 253 ++
doc/src/Howto_couple.txt | 105 +
doc/src/Howto_diffusion.txt | 31 +
doc/src/Howto_dispersion.txt | 108 +
doc/src/Howto_drude.txt | 77 +
.../{tutorial_drude.txt => Howto_drude2.txt} | 2 +-
doc/src/Howto_elastic.txt | 47 +
.../{tutorial_github.txt => Howto_github.txt} | 12 +-
doc/src/Howto_granular.txt | 57 +
doc/src/Howto_kappa.txt | 90 +
doc/src/Howto_library.txt | 208 ++
doc/src/{manifolds.txt => Howto_manifold.txt} | 4 +-
doc/src/Howto_multiple.txt | 95 +
doc/src/Howto_nemd.txt | 48 +
doc/src/Howto_output.txt | 307 ++
doc/src/Howto_polarizable.txt | 81 +
...torial_pylammps.txt => Howto_pylammps.txt} | 23 +-
doc/src/Howto_replica.txt | 61 +
doc/src/Howto_restart.txt | 97 +
doc/src/Howto_spc.txt | 54 +
doc/src/Howto_spherical.txt | 243 ++
doc/src/Howto_spins.txt | 59 +
doc/src/Howto_temperature.txt | 40 +
doc/src/Howto_thermostat.txt | 89 +
doc/src/Howto_tip3p.txt | 69 +
doc/src/Howto_tip4p.txt | 112 +
doc/src/Howto_triclinic.txt | 213 ++
doc/src/Howto_viscosity.txt | 133 +
doc/src/Howto_viz.txt | 40 +
doc/src/Howto_walls.txt | 80 +
doc/src/Intro.txt | 37 +
doc/src/Intro_authors.txt | 379 +++
doc/src/Intro_features.txt | 202 ++
doc/src/Intro_nonfeatures.txt | 83 +
doc/src/Intro_opensource.txt | 44 +
doc/src/Intro_overview.txt | 58 +
doc/src/Intro_website.txt | 42 +
doc/src/Manual.txt | 224 +-
doc/src/Manual_version.txt | 33 +
doc/src/Modify.txt | 2 +-
doc/src/Modify_atom.txt | 2 +-
doc/src/Modify_body.txt | 9 +-
doc/src/Modify_bond.txt | 2 +-
doc/src/Modify_command.txt | 2 +-
doc/src/Modify_compute.txt | 2 +-
doc/src/Modify_contribute.txt | 23 +-
doc/src/Modify_dump.txt | 2 +-
doc/src/Modify_fix.txt | 2 +-
doc/src/Modify_kspace.txt | 2 +-
doc/src/Modify_min.txt | 2 +-
doc/src/Modify_overview.txt | 2 +-
doc/src/Modify_pair.txt | 2 +-
doc/src/Modify_region.txt | 2 +-
doc/src/Modify_thermo.txt | 2 +-
doc/src/Modify_variable.txt | 2 +-
doc/src/Packages.txt | 39 +
...tion_packages.txt => Packages_details.txt} | 379 +--
doc/src/Packages_standard.txt | 65 +
doc/src/Packages_user.txt | 74 +
doc/src/Python.txt | 2 +-
doc/src/Python_call.txt | 2 +-
doc/src/Python_examples.txt | 2 +-
doc/src/Python_install.txt | 2 +-
doc/src/Python_library.txt | 16 +-
doc/src/Python_mpi.txt | 2 +-
doc/src/Python_pylammps.txt | 6 +-
doc/src/Python_run.txt | 2 +-
doc/src/Python_shlib.txt | 2 +-
doc/src/Python_test.txt | 2 +-
doc/src/Section_accelerate.txt | 391 ---
doc/src/Section_commands.txt | 1293 -------
doc/src/Section_history.txt | 135 -
doc/src/Section_howto.txt | 3011 -----------------
doc/src/Section_intro.txt | 550 ---
doc/src/Section_start.txt | 164 +-
doc/src/Speed.txt | 64 +
doc/src/{Section_perf.txt => Speed_bench.txt} | 21 +-
doc/src/Speed_compare.txt | 73 +
doc/src/{accelerate_gpu.txt => Speed_gpu.txt} | 17 +-
.../{accelerate_intel.txt => Speed_intel.txt} | 24 +-
...accelerate_kokkos.txt => Speed_kokkos.txt} | 337 +-
doc/src/Speed_measure.txt | 55 +
doc/src/{accelerate_omp.txt => Speed_omp.txt} | 15 +-
doc/src/{accelerate_opt.txt => Speed_opt.txt} | 13 +-
doc/src/Speed_packages.txt | 192 ++
doc/src/Speed_tips.txt | 63 +
doc/src/Tools.txt | 14 +-
doc/src/angle_charmm.txt | 13 +-
doc/src/angle_class2.txt | 13 +-
doc/src/angle_coeff.txt | 8 +-
doc/src/angle_cosine.txt | 13 +-
doc/src/angle_cosine_buck6d.txt | 2 +-
doc/src/angle_cosine_delta.txt | 13 +-
doc/src/angle_cosine_periodic.txt | 21 +-
doc/src/angle_cosine_shift.txt | 13 +-
doc/src/angle_cosine_shift_exp.txt | 13 +-
doc/src/angle_cosine_squared.txt | 13 +-
doc/src/angle_dipole.txt | 13 +-
doc/src/angle_fourier.txt | 13 +-
doc/src/angle_fourier_simple.txt | 13 +-
doc/src/angle_harmonic.txt | 13 +-
doc/src/angle_hybrid.txt | 2 +-
doc/src/angle_none.txt | 2 +-
doc/src/angle_quartic.txt | 13 +-
doc/src/angle_sdk.txt | 2 +-
doc/src/angle_style.txt | 8 +-
doc/src/angle_table.txt | 13 +-
doc/src/angle_zero.txt | 2 +-
doc/src/atom_modify.txt | 2 +-
doc/src/atom_style.txt | 35 +-
doc/src/balance.txt | 2 +-
doc/src/bond_class2.txt | 13 +-
doc/src/bond_coeff.txt | 7 +-
doc/src/bond_fene.txt | 13 +-
doc/src/bond_fene_expand.txt | 13 +-
doc/src/bond_gromos.txt | 13 +-
doc/src/bond_harmonic.txt | 13 +-
doc/src/bond_harmonic_shift.txt | 13 +-
doc/src/bond_harmonic_shift_cut.txt | 13 +-
doc/src/bond_hybrid.txt | 2 +-
doc/src/bond_morse.txt | 13 +-
doc/src/bond_none.txt | 2 +-
doc/src/bond_nonlinear.txt | 13 +-
doc/src/bond_oxdna.txt | 2 +-
doc/src/bond_quartic.txt | 13 +-
doc/src/bond_style.txt | 7 +-
doc/src/bond_table.txt | 13 +-
doc/src/bond_write.txt | 2 +-
doc/src/bond_zero.txt | 2 +-
doc/src/boundary.txt | 8 +-
doc/src/box.txt | 8 +-
doc/src/change_box.txt | 20 +-
doc/src/clear.txt | 2 +-
doc/src/comm_modify.txt | 2 +-
doc/src/comm_style.txt | 2 +-
doc/src/compute.txt | 30 +-
doc/src/compute_ackland_atom.txt | 4 +-
doc/src/compute_angle.txt | 6 +-
doc/src/compute_angle_local.txt | 6 +-
doc/src/compute_angmom_chunk.txt | 13 +-
doc/src/compute_basal_atom.txt | 7 +-
doc/src/compute_body_local.txt | 17 +-
doc/src/compute_bond.txt | 6 +-
doc/src/compute_bond_local.txt | 6 +-
doc/src/compute_centro_atom.txt | 6 +-
doc/src/compute_chunk_atom.txt | 27 +-
doc/src/compute_cluster_atom.txt | 4 +-
doc/src/compute_cna_atom.txt | 4 +-
doc/src/compute_cnp_atom.txt | 4 +-
doc/src/compute_com.txt | 7 +-
doc/src/compute_com_chunk.txt | 14 +-
doc/src/compute_contact_atom.txt | 4 +-
doc/src/compute_coord_atom.txt | 7 +-
doc/src/compute_damage_atom.txt | 4 +-
doc/src/compute_dihedral.txt | 6 +-
doc/src/compute_dihedral_local.txt | 6 +-
doc/src/compute_dilatation_atom.txt | 7 +-
doc/src/compute_dipole_chunk.txt | 13 +-
doc/src/compute_displace_atom.txt | 7 +-
doc/src/compute_dpd.txt | 8 +-
doc/src/compute_dpd_atom.txt | 8 +-
doc/src/compute_edpd_temp_atom.txt | 8 +-
doc/src/compute_entropy_atom.txt | 6 +-
doc/src/compute_erotate_asphere.txt | 4 +-
doc/src/compute_erotate_rigid.txt | 8 +-
doc/src/compute_erotate_sphere.txt | 4 +-
doc/src/compute_erotate_sphere_atom.txt | 4 +-
doc/src/compute_event_displace.txt | 4 +-
doc/src/compute_fep.txt | 6 +-
doc/src/compute_global_atom.txt | 6 +-
doc/src/compute_group_group.txt | 6 +-
doc/src/compute_gyration.txt | 6 +-
doc/src/compute_gyration_chunk.txt | 13 +-
doc/src/compute_heat_flux.txt | 12 +-
doc/src/compute_hexorder_atom.txt | 9 +-
doc/src/compute_improper.txt | 6 +-
doc/src/compute_improper_local.txt | 6 +-
doc/src/compute_inertia_chunk.txt | 13 +-
doc/src/compute_ke.txt | 4 +-
doc/src/compute_ke_atom.txt | 4 +-
doc/src/compute_ke_atom_eff.txt | 8 +-
doc/src/compute_ke_eff.txt | 4 +-
doc/src/compute_ke_rigid.txt | 6 +-
doc/src/compute_meso_e_atom.txt | 4 +-
doc/src/compute_meso_rho_atom.txt | 4 +-
doc/src/compute_meso_t_atom.txt | 4 +-
doc/src/compute_modify.txt | 2 +-
doc/src/compute_msd.txt | 7 +-
doc/src/compute_msd_chunk.txt | 11 +-
doc/src/compute_msd_nongauss.txt | 7 +-
doc/src/compute_omega_chunk.txt | 13 +-
doc/src/compute_orientorder_atom.txt | 9 +-
doc/src/compute_pair.txt | 7 +-
doc/src/compute_pair_local.txt | 6 +-
doc/src/compute_pe.txt | 7 +-
doc/src/compute_pe_atom.txt | 4 +-
doc/src/compute_plasticity_atom.txt | 7 +-
doc/src/compute_pressure.txt | 17 +-
doc/src/compute_pressure_uef.txt | 2 +-
doc/src/compute_property_atom.txt | 16 +-
doc/src/compute_property_chunk.txt | 17 +-
doc/src/compute_property_local.txt | 14 +-
doc/src/compute_rdf.txt | 4 +-
doc/src/compute_reduce.txt | 4 +-
doc/src/compute_rigid_local.txt | 12 +-
doc/src/compute_saed.txt | 9 +-
doc/src/compute_slice.txt | 6 +-
doc/src/compute_smd_contact_radius.txt | 8 +-
doc/src/compute_smd_damage.txt | 10 +-
doc/src/compute_smd_hourglass_error.txt | 10 +-
doc/src/compute_smd_internal_energy.txt | 6 +-
doc/src/compute_smd_plastic_strain.txt | 6 +-
doc/src/compute_smd_plastic_strain_rate.txt | 6 +-
doc/src/compute_smd_rho.txt | 6 +-
doc/src/compute_smd_tlsph_defgrad.txt | 7 +-
doc/src/compute_smd_tlsph_dt.txt | 6 +-
doc/src/compute_smd_tlsph_num_neighs.txt | 6 +-
doc/src/compute_smd_tlsph_shape.txt | 7 +-
doc/src/compute_smd_tlsph_strain.txt | 7 +-
doc/src/compute_smd_tlsph_strain_rate.txt | 7 +-
doc/src/compute_smd_tlsph_stress.txt | 11 +-
.../compute_smd_triangle_mesh_vertices.txt | 8 +-
doc/src/compute_smd_ulsph_num_neighs.txt | 4 +-
doc/src/compute_smd_ulsph_strain.txt | 4 +-
doc/src/compute_smd_ulsph_strain_rate.txt | 7 +-
doc/src/compute_smd_ulsph_stress.txt | 7 +-
doc/src/compute_smd_vol.txt | 6 +-
doc/src/compute_sna_atom.txt | 7 +-
doc/src/compute_spin.txt | 2 +-
doc/src/compute_stress_atom.txt | 7 +-
doc/src/compute_tally.txt | 2 +-
doc/src/compute_tdpd_cc_atom.txt | 8 +-
doc/src/compute_temp.txt | 21 +-
doc/src/compute_temp_asphere.txt | 10 +-
doc/src/compute_temp_body.txt | 10 +-
doc/src/compute_temp_chunk.txt | 18 +-
doc/src/compute_temp_com.txt | 10 +-
doc/src/compute_temp_cs.txt | 13 +-
doc/src/compute_temp_deform.txt | 10 +-
doc/src/compute_temp_deform_eff.txt | 6 +-
doc/src/compute_temp_drude.txt | 14 +-
doc/src/compute_temp_eff.txt | 6 +-
doc/src/compute_temp_partial.txt | 21 +-
doc/src/compute_temp_profile.txt | 10 +-
doc/src/compute_temp_ramp.txt | 10 +-
doc/src/compute_temp_region.txt | 10 +-
doc/src/compute_temp_region_eff.txt | 6 +-
doc/src/compute_temp_rotate.txt | 10 +-
doc/src/compute_temp_sphere.txt | 10 +-
doc/src/compute_temp_uef.txt | 2 +-
doc/src/compute_ti.txt | 7 +-
doc/src/compute_torque_chunk.txt | 11 +-
doc/src/compute_vacf.txt | 7 +-
doc/src/compute_vcm_chunk.txt | 13 +-
doc/src/compute_voronoi_atom.txt | 28 +-
doc/src/compute_xrd.txt | 4 +-
doc/src/create_atoms.txt | 2 +-
doc/src/create_bonds.txt | 2 +-
doc/src/create_box.txt | 8 +-
doc/src/delete_atoms.txt | 2 +-
doc/src/delete_bonds.txt | 2 +-
doc/src/dielectric.txt | 2 +-
doc/src/dihedral_charmm.txt | 13 +-
doc/src/dihedral_class2.txt | 13 +-
doc/src/dihedral_coeff.txt | 8 +-
doc/src/dihedral_cosine_shift_exp.txt | 13 +-
doc/src/dihedral_fourier.txt | 13 +-
doc/src/dihedral_harmonic.txt | 13 +-
doc/src/dihedral_helix.txt | 13 +-
doc/src/dihedral_hybrid.txt | 2 +-
doc/src/dihedral_multi_harmonic.txt | 13 +-
doc/src/dihedral_nharmonic.txt | 13 +-
doc/src/dihedral_none.txt | 2 +-
doc/src/dihedral_opls.txt | 13 +-
doc/src/dihedral_quadratic.txt | 13 +-
doc/src/dihedral_spherical.txt | 2 +-
doc/src/dihedral_style.txt | 8 +-
doc/src/dihedral_table.txt | 13 +-
doc/src/dihedral_table_cut.txt | 2 +-
doc/src/dihedral_zero.txt | 2 +-
doc/src/dimension.txt | 4 +-
doc/src/displace_atoms.txt | 2 +-
doc/src/dump.txt | 16 +-
doc/src/dump_cfg_uef.txt | 2 +-
doc/src/dump_h5md.txt | 2 +-
doc/src/dump_image.txt | 16 +-
doc/src/dump_modify.txt | 2 +-
doc/src/dump_molfile.txt | 2 +-
doc/src/dump_netcdf.txt | 2 +-
doc/src/dump_vtk.txt | 2 +-
doc/src/echo.txt | 2 +-
doc/src/fix.txt | 24 +-
doc/src/fix_adapt.txt | 10 +-
doc/src/fix_adapt_fep.txt | 10 +-
doc/src/fix_addforce.txt | 28 +-
doc/src/fix_addtorque.txt | 12 +-
doc/src/fix_append_atoms.txt | 10 +-
doc/src/fix_atc.txt | 10 +-
doc/src/fix_atom_swap.txt | 6 +-
doc/src/fix_ave_atom.txt | 16 +-
doc/src/fix_ave_chunk.txt | 35 +-
doc/src/fix_ave_correlate.txt | 23 +-
doc/src/fix_ave_correlate_long.txt | 2 +-
doc/src/fix_ave_histo.txt | 17 +-
doc/src/fix_ave_time.txt | 11 +-
doc/src/fix_aveforce.txt | 26 +-
doc/src/fix_balance.txt | 6 +-
doc/src/fix_bocs.txt | 2 +-
doc/src/fix_bond_break.txt | 6 +-
doc/src/fix_bond_create.txt | 6 +-
doc/src/fix_bond_react.txt | 7 +-
doc/src/fix_bond_swap.txt | 16 +-
doc/src/fix_box_relax.txt | 22 +-
doc/src/fix_cmap.txt | 8 +-
doc/src/fix_colvars.txt | 8 +-
doc/src/fix_controller.txt | 8 +-
doc/src/fix_deform.txt | 22 +-
doc/src/fix_deposit.txt | 12 +-
doc/src/fix_dpd_energy.txt | 13 +-
doc/src/fix_dpd_source.txt | 10 +-
doc/src/fix_drag.txt | 8 +-
doc/src/fix_drude.txt | 10 +-
doc/src/fix_drude_transform.txt | 6 +-
doc/src/fix_dt_reset.txt | 6 +-
doc/src/fix_efield.txt | 11 +-
doc/src/fix_ehex.txt | 2 +-
doc/src/fix_enforce2d.txt | 19 +-
doc/src/fix_eos_cv.txt | 2 +-
doc/src/fix_eos_table.txt | 2 +-
doc/src/fix_eos_table_rx.txt | 13 +-
doc/src/fix_evaporate.txt | 8 +-
doc/src/fix_external.txt | 15 +-
doc/src/fix_filter_corotate.txt | 9 +-
doc/src/fix_flow_gauss.txt | 12 +-
doc/src/fix_freeze.txt | 26 +-
doc/src/fix_gcmc.txt | 6 +-
doc/src/fix_gld.txt | 4 +-
doc/src/fix_gle.txt | 8 +-
doc/src/fix_gravity.txt | 23 +-
doc/src/fix_grem.txt | 2 +-
doc/src/fix_halt.txt | 10 +-
doc/src/fix_heat.txt | 13 +-
doc/src/fix_imd.txt | 8 +-
doc/src/fix_indent.txt | 6 +-
doc/src/fix_ipi.txt | 2 +-
doc/src/fix_langevin.txt | 23 +-
doc/src/fix_langevin_drude.txt | 11 +-
doc/src/fix_langevin_eff.txt | 10 +-
doc/src/fix_langevin_spin.txt | 2 +-
doc/src/fix_latte.txt | 8 +-
doc/src/fix_lb_fluid.txt | 8 +-
doc/src/fix_lb_momentum.txt | 10 +-
doc/src/fix_lb_pc.txt | 10 +-
doc/src/fix_lb_rigid_pc_sphere.txt | 36 +-
doc/src/fix_lb_viscous.txt | 8 +-
doc/src/fix_lineforce.txt | 8 +-
doc/src/fix_manifoldforce.txt | 10 +-
doc/src/fix_meso.txt | 10 +-
doc/src/fix_meso_stationary.txt | 10 +-
doc/src/fix_modify.txt | 2 +-
doc/src/fix_momentum.txt | 21 +-
doc/src/fix_move.txt | 9 +-
doc/src/fix_mscg.txt | 2 +-
doc/src/fix_msst.txt | 6 +-
doc/src/fix_mvv_dpd.txt | 10 +-
doc/src/fix_neb.txt | 14 +-
doc/src/fix_nh.txt | 26 +-
doc/src/fix_nh_eff.txt | 2 +-
doc/src/fix_nh_uef.txt | 2 +-
doc/src/fix_nph_asphere.txt | 13 +-
doc/src/fix_nph_body.txt | 13 +-
doc/src/fix_nph_sphere.txt | 13 +-
doc/src/fix_nphug.txt | 19 +-
doc/src/fix_npt_asphere.txt | 13 +-
doc/src/fix_npt_body.txt | 13 +-
doc/src/fix_npt_sphere.txt | 13 +-
doc/src/fix_nve.txt | 21 +-
doc/src/fix_nve_asphere.txt | 21 +-
doc/src/fix_nve_asphere_noforce.txt | 10 +-
doc/src/fix_nve_body.txt | 16 +-
doc/src/fix_nve_dot.txt | 2 +-
doc/src/fix_nve_dotc_langevin.txt | 2 +-
doc/src/fix_nve_eff.txt | 10 +-
doc/src/fix_nve_limit.txt | 18 +-
doc/src/fix_nve_line.txt | 16 +-
doc/src/fix_nve_manifold_rattle.txt | 12 +-
doc/src/fix_nve_noforce.txt | 10 +-
doc/src/fix_nve_sphere.txt | 21 +-
doc/src/fix_nve_spin.txt | 2 +-
doc/src/fix_nve_tri.txt | 18 +-
doc/src/fix_nvk.txt | 10 +-
doc/src/fix_nvt_asphere.txt | 13 +-
doc/src/fix_nvt_body.txt | 13 +-
doc/src/fix_nvt_manifold_rattle.txt | 20 +-
doc/src/fix_nvt_sllod.txt | 13 +-
doc/src/fix_nvt_sllod_eff.txt | 2 +-
doc/src/fix_nvt_sphere.txt | 13 +-
doc/src/fix_oneway.txt | 10 +-
doc/src/fix_orient.txt | 14 +-
doc/src/fix_phonon.txt | 4 +-
doc/src/fix_pimd.txt | 17 +-
doc/src/fix_planeforce.txt | 8 +-
doc/src/fix_poems.txt | 8 +-
doc/src/fix_pour.txt | 8 +-
doc/src/fix_precession_spin.txt | 6 +-
doc/src/fix_press_berendsen.txt | 9 +-
doc/src/fix_print.txt | 10 +-
doc/src/fix_property_atom.txt | 29 +-
doc/src/fix_python_invoke.txt | 2 +-
doc/src/fix_python_move.txt | 10 +-
doc/src/fix_qbmsst.txt | 10 +-
doc/src/fix_qeq.txt | 7 +-
doc/src/fix_qeq_comb.txt | 19 +-
doc/src/fix_qeq_reax.txt | 17 +-
doc/src/fix_qmmm.txt | 8 +-
doc/src/fix_qtb.txt | 2 +-
doc/src/fix_reax_bonds.txt | 14 +-
doc/src/fix_reaxc_species.txt | 10 +-
doc/src/fix_recenter.txt | 12 +-
doc/src/fix_restrain.txt | 6 +-
doc/src/fix_rhok.txt | 2 +-
doc/src/fix_rigid.txt | 49 +-
doc/src/fix_rx.txt | 13 +-
doc/src/fix_saed_vtk.txt | 2 +-
doc/src/fix_setforce.txt | 26 +-
doc/src/fix_shake.txt | 25 +-
doc/src/fix_shardlow.txt | 13 +-
doc/src/fix_smd.txt | 14 +-
doc/src/fix_smd_adjust_dt.txt | 2 +-
doc/src/fix_smd_integrate_tlsph.txt | 2 +-
doc/src/fix_smd_integrate_ulsph.txt | 2 +-
doc/src/fix_smd_move_triangulated_surface.txt | 2 +-
doc/src/fix_smd_setvel.txt | 8 +-
doc/src/fix_smd_wall_surface.txt | 2 +-
doc/src/fix_spring.txt | 24 +-
doc/src/fix_spring_chunk.txt | 6 +-
doc/src/fix_spring_rg.txt | 10 +-
doc/src/fix_spring_self.txt | 10 +-
doc/src/fix_srd.txt | 12 +-
doc/src/fix_store_force.txt | 10 +-
doc/src/fix_store_state.txt | 10 +-
doc/src/fix_surface_global.txt | 2 +-
doc/src/fix_temp_berendsen.txt | 12 +-
doc/src/fix_temp_csvr.txt | 12 +-
doc/src/fix_temp_rescale.txt | 12 +-
doc/src/fix_temp_rescale_eff.txt | 8 +-
doc/src/fix_tfmc.txt | 2 +-
doc/src/fix_thermal_conductivity.txt | 8 +-
doc/src/fix_ti_spring.txt | 15 +-
doc/src/fix_tmd.txt | 5 +-
doc/src/fix_ttm.txt | 25 +-
doc/src/fix_tune_kspace.txt | 2 +-
doc/src/fix_vector.txt | 9 +-
doc/src/fix_viscosity.txt | 29 +-
doc/src/fix_viscous.txt | 8 +-
doc/src/fix_wall.txt | 29 +-
doc/src/fix_wall_body_polygon.txt | 12 +-
doc/src/fix_wall_body_polyhedron.txt | 12 +-
doc/src/fix_wall_ees.txt | 2 +-
doc/src/fix_wall_gran.txt | 8 +-
doc/src/fix_wall_gran_region.txt | 8 +-
doc/src/fix_wall_piston.txt | 10 +-
doc/src/fix_wall_reflect.txt | 21 +-
doc/src/fix_wall_region.txt | 13 +-
doc/src/fix_wall_srd.txt | 8 +-
doc/src/fixes.txt | 2 +
doc/src/group.txt | 2 +-
doc/src/group2ndx.txt | 2 +-
doc/src/if.txt | 8 +-
doc/src/improper_class2.txt | 13 +-
doc/src/improper_coeff.txt | 8 +-
doc/src/improper_cossq.txt | 13 +-
doc/src/improper_cvff.txt | 13 +-
doc/src/improper_distance.txt | 2 +-
doc/src/improper_fourier.txt | 13 +-
doc/src/improper_harmonic.txt | 13 +-
doc/src/improper_hybrid.txt | 2 +-
doc/src/improper_inversion_harmonic.txt | 2 +-
doc/src/improper_none.txt | 2 +-
doc/src/improper_ring.txt | 13 +-
doc/src/improper_style.txt | 8 +-
doc/src/improper_umbrella.txt | 15 +-
doc/src/improper_zero.txt | 2 +-
doc/src/include.txt | 2 +-
doc/src/info.txt | 2 +-
doc/src/jump.txt | 2 +-
doc/src/kspace_modify.txt | 20 +-
doc/src/kspace_style.txt | 32 +-
doc/src/label.txt | 2 +-
doc/src/lammps.book | 92 +-
doc/src/lammps_support.txt | 7 -
doc/src/lammps_tutorials.txt | 6 -
doc/src/lattice.txt | 2 +-
doc/src/log.txt | 2 +-
doc/src/mass.txt | 2 +-
doc/src/min_modify.txt | 2 +-
doc/src/min_style.txt | 2 +-
doc/src/minimize.txt | 2 +-
doc/src/molecule.txt | 7 +-
doc/src/neb.txt | 7 +-
doc/src/neigh_modify.txt | 2 +-
doc/src/neighbor.txt | 2 +-
doc/src/newton.txt | 2 +-
doc/src/next.txt | 2 +-
doc/src/package.txt | 8 +-
doc/src/pair_adp.txt | 13 +-
doc/src/pair_agni.txt | 16 +-
doc/src/pair_airebo.txt | 13 +-
doc/src/pair_atm.txt | 5 +-
doc/src/pair_awpmd.txt | 2 +-
doc/src/pair_beck.txt | 13 +-
doc/src/pair_body_nparticle.txt | 13 +-
doc/src/pair_body_rounded_polygon.txt | 7 +-
doc/src/pair_body_rounded_polyhedron.txt | 7 +-
doc/src/pair_bop.txt | 2 +-
doc/src/pair_born.txt | 21 +-
doc/src/pair_brownian.txt | 6 +-
doc/src/pair_buck.txt | 18 +-
doc/src/pair_buck6d_coul_gauss.txt | 2 +-
doc/src/pair_buck_long.txt | 13 +-
doc/src/pair_charmm.txt | 13 +-
doc/src/pair_class2.txt | 13 +-
doc/src/pair_coeff.txt | 19 +-
doc/src/pair_colloid.txt | 13 +-
doc/src/pair_comb.txt | 13 +-
doc/src/pair_coul.txt | 39 +-
doc/src/pair_coul_diel.txt | 2 +-
doc/src/pair_coul_shield.txt | 2 +-
doc/src/pair_cs.txt | 6 +-
doc/src/pair_dipole.txt | 13 +-
doc/src/pair_dpd.txt | 13 +-
doc/src/pair_dpd_fdt.txt | 13 +-
doc/src/pair_dsmc.txt | 2 +-
doc/src/pair_eam.txt | 20 +-
doc/src/pair_edip.txt | 13 +-
doc/src/pair_eff.txt | 2 +-
doc/src/pair_eim.txt | 13 +-
doc/src/pair_exp6_rx.txt | 13 +-
doc/src/pair_extep.txt | 2 +-
doc/src/pair_gauss.txt | 13 +-
doc/src/pair_gayberne.txt | 13 +-
doc/src/pair_gran.txt | 13 +-
doc/src/pair_gromacs.txt | 13 +-
doc/src/pair_gw.txt | 2 +-
doc/src/pair_hbond_dreiding.txt | 21 +-
doc/src/pair_hybrid.txt | 10 +-
doc/src/pair_ilp_graphene_hbn.txt | 2 +-
doc/src/pair_kim.txt | 6 +-
doc/src/pair_kolmogorov_crespi_full.txt | 2 +-
doc/src/pair_kolmogorov_crespi_z.txt | 2 +-
doc/src/pair_lcbop.txt | 2 +-
doc/src/pair_line_lj.txt | 2 +-
doc/src/pair_list.txt | 2 +-
doc/src/pair_lj.txt | 39 +-
doc/src/pair_lj96.txt | 13 +-
doc/src/pair_lj_cubic.txt | 13 +-
doc/src/pair_lj_expand.txt | 13 +-
doc/src/pair_lj_long.txt | 15 +-
doc/src/pair_lj_smooth.txt | 13 +-
doc/src/pair_lj_smooth_linear.txt | 13 +-
doc/src/pair_lj_soft.txt | 13 +-
doc/src/pair_lubricate.txt | 6 +-
doc/src/pair_lubricateU.txt | 2 +-
doc/src/pair_mdf.txt | 2 +-
doc/src/pair_meam.txt | 2 +-
doc/src/pair_meam_spline.txt | 13 +-
doc/src/pair_meam_sw_spline.txt | 2 +-
doc/src/pair_meso.txt | 2 +-
doc/src/pair_mgpt.txt | 2 +-
doc/src/pair_mie.txt | 2 +-
doc/src/pair_modify.txt | 2 +-
doc/src/pair_momb.txt | 2 +-
doc/src/pair_morse.txt | 13 +-
doc/src/pair_multi_lucy.txt | 2 +-
doc/src/pair_multi_lucy_rx.txt | 13 +-
doc/src/pair_nb3b_harmonic.txt | 13 +-
doc/src/pair_nm.txt | 13 +-
doc/src/pair_none.txt | 2 +-
doc/src/pair_oxdna.txt | 2 +-
doc/src/pair_oxdna2.txt | 2 +-
doc/src/pair_peri.txt | 13 +-
doc/src/pair_polymorphic.txt | 2 +-
doc/src/pair_python.txt | 2 +-
doc/src/pair_quip.txt | 2 +-
doc/src/pair_reax.txt | 2 +-
doc/src/pair_reaxc.txt | 23 +-
doc/src/pair_resquared.txt | 13 +-
doc/src/pair_sdk.txt | 13 +-
doc/src/pair_smd_hertz.txt | 2 +-
doc/src/pair_smd_tlsph.txt | 2 +-
doc/src/pair_smd_triangulated_surface.txt | 2 +-
doc/src/pair_smd_ulsph.txt | 2 +-
doc/src/pair_smtbq.txt | 2 +-
doc/src/pair_snap.txt | 13 +-
doc/src/pair_soft.txt | 13 +-
doc/src/pair_sph_heatconduction.txt | 2 +-
doc/src/pair_sph_idealgas.txt | 2 +-
doc/src/pair_sph_lj.txt | 2 +-
doc/src/pair_sph_rhosum.txt | 2 +-
doc/src/pair_sph_taitwater.txt | 2 +-
doc/src/pair_sph_taitwater_morris.txt | 2 +-
doc/src/pair_spin_dmi.txt | 43 +-
doc/src/pair_spin_exchange.txt | 30 +-
doc/src/pair_spin_magelec.txt | 2 +-
doc/src/pair_spin_neel.txt | 2 +-
doc/src/pair_srp.txt | 2 +-
doc/src/pair_style.txt | 20 +-
doc/src/pair_sw.txt | 13 +-
doc/src/pair_table.txt | 13 +-
doc/src/pair_table_rx.txt | 13 +-
doc/src/pair_tersoff.txt | 13 +-
doc/src/pair_tersoff_mod.txt | 13 +-
doc/src/pair_tersoff_zbl.txt | 13 +-
doc/src/pair_thole.txt | 17 +-
doc/src/pair_tri_lj.txt | 2 +-
doc/src/pair_ufm.txt | 13 +-
doc/src/pair_vashishta.txt | 13 +-
doc/src/pair_write.txt | 2 +-
doc/src/pair_yukawa.txt | 13 +-
doc/src/pair_yukawa_colloid.txt | 13 +-
doc/src/pair_zbl.txt | 13 +-
doc/src/pair_zero.txt | 2 +-
doc/src/pairs.txt | 3 +-
doc/src/partition.txt | 2 +-
doc/src/prd.txt | 6 +-
doc/src/print.txt | 2 +-
doc/src/processors.txt | 2 +-
doc/src/python.txt | 8 +-
doc/src/quit.txt | 2 +-
doc/src/read_data.txt | 14 +-
doc/src/read_dump.txt | 2 +-
doc/src/read_restart.txt | 2 +-
doc/src/region.txt | 24 +-
doc/src/replicate.txt | 2 +-
doc/src/rerun.txt | 2 +-
doc/src/reset_ids.txt | 2 +-
doc/src/reset_timestep.txt | 2 +-
doc/src/restart.txt | 2 +-
doc/src/run.txt | 8 +-
doc/src/run_style.txt | 32 +-
doc/src/set.txt | 2 +-
doc/src/shell.txt | 2 +-
doc/src/special_bonds.txt | 2 +-
doc/src/suffix.txt | 2 +-
doc/src/tad.txt | 7 +-
doc/src/temper.txt | 17 +-
doc/src/temper_grem.txt | 2 +-
doc/src/temper_npt.txt | 2 +-
doc/src/thermo.txt | 2 +-
doc/src/thermo_modify.txt | 2 +-
doc/src/thermo_style.txt | 12 +-
doc/src/timer.txt | 2 +-
doc/src/timestep.txt | 2 +-
doc/src/tutorials.txt | 15 -
doc/src/uncompute.txt | 2 +-
doc/src/undump.txt | 2 +-
doc/src/unfix.txt | 2 +-
doc/src/units.txt | 2 +-
doc/src/variable.txt | 42 +-
doc/src/velocity.txt | 19 +-
doc/src/write_coeff.txt | 2 +-
doc/src/write_data.txt | 2 +-
doc/src/write_dump.txt | 2 +-
doc/src/write_restart.txt | 2 +-
doc/utils/converters/lammpsdoc/txt2html.py | 12 +-
doc/utils/converters/lammpsdoc/txt2rst.py | 2 +
doc/utils/requirements.txt | 1 +
examples/DIFFUSE/README | 4 +-
examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 | 245 --
examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 | 251 ++
...vacf.2d.g++.8 => log.3Aug18.vacf.2d.g++.8} | 54 +-
examples/SPIN/bfo/in.spin.bfo | 11 +-
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp | 10 +-
examples/USER/diffraction/BulkNi.in | 2 +-
src/BODY/fix_wall_body_polygon.cpp | 5 +-
src/BODY/pair_body_rounded_polyhedron.cpp | 7 +-
src/KOKKOS/fix_nh_kokkos.cpp | 2 +-
src/MANYBODY/pair_atm.cpp | 18 +-
src/MANYBODY/pair_atm.h | 4 +-
src/MANYBODY/pair_eam_cd.cpp | 677 ++++
.../pair_cdeam.h => MANYBODY/pair_eam_cd.h} | 22 +-
src/Purge.list | 3 +
src/SPIN/atom_vec_spin.cpp | 6 +-
src/SPIN/compute_spin.cpp | 20 +-
src/SPIN/pair_spin_dmi.cpp | 116 +-
src/SPIN/pair_spin_dmi.h | 15 +-
src/SPIN/pair_spin_exchange.cpp | 52 +-
src/SPIN/pair_spin_magelec.cpp | 88 +-
src/SPIN/pair_spin_neel.cpp | 12 +-
src/SPIN/pair_spin_neel.h | 4 +-
src/USER-BOCS/fix_bocs.cpp | 41 +-
src/USER-MISC/Install.sh | 40 -
src/USER-MISC/README | 1 -
src/USER-MISC/pair_cdeam.cpp | 644 ----
src/fix_nh.cpp | 36 +-
src/variable.cpp | 189 +-
src/version.h | 2 +-
tools/emacs/README.md | 82 +
tools/emacs/README.txt | 23 -
tools/emacs/{lammps.el => lammps-mode.el} | 59 +-
738 files changed, 11127 insertions(+), 10210 deletions(-)
create mode 100644 cmake/etc/profile.d/lammps.csh.in
create mode 100644 cmake/etc/profile.d/lammps.sh.in
create mode 100644 doc/src/Commands.txt
create mode 100644 doc/src/Commands_all.txt
create mode 100644 doc/src/Commands_bond.txt
create mode 100644 doc/src/Commands_category.txt
create mode 100644 doc/src/Commands_compute.txt
create mode 100644 doc/src/Commands_fix.txt
create mode 100644 doc/src/Commands_input.txt
create mode 100644 doc/src/Commands_kspace.txt
create mode 100644 doc/src/Commands_pair.txt
create mode 100644 doc/src/Commands_parse.txt
create mode 100644 doc/src/Commands_structure.txt
create mode 100644 doc/src/Eqs/pair_spin_dmi_forces.jpg
create mode 100644 doc/src/Eqs/pair_spin_dmi_forces.tex
create mode 100644 doc/src/Howto.txt
create mode 100644 doc/src/Howto_2d.txt
create mode 100644 doc/src/Howto_barostat.txt
rename doc/src/{tutorial_bash_on_windows.txt => Howto_bash.txt} (99%)
mode change 100644 => 100755
create mode 100644 doc/src/Howto_bioFF.txt
rename doc/src/{body.txt => Howto_body.txt} (96%)
create mode 100644 doc/src/Howto_chunk.txt
create mode 100644 doc/src/Howto_coreshell.txt
create mode 100644 doc/src/Howto_couple.txt
create mode 100644 doc/src/Howto_diffusion.txt
create mode 100644 doc/src/Howto_dispersion.txt
create mode 100644 doc/src/Howto_drude.txt
rename doc/src/{tutorial_drude.txt => Howto_drude2.txt} (99%)
create mode 100644 doc/src/Howto_elastic.txt
rename doc/src/{tutorial_github.txt => Howto_github.txt} (98%)
create mode 100644 doc/src/Howto_granular.txt
create mode 100644 doc/src/Howto_kappa.txt
create mode 100644 doc/src/Howto_library.txt
rename doc/src/{manifolds.txt => Howto_manifold.txt} (97%)
create mode 100644 doc/src/Howto_multiple.txt
create mode 100644 doc/src/Howto_nemd.txt
create mode 100644 doc/src/Howto_output.txt
create mode 100644 doc/src/Howto_polarizable.txt
rename doc/src/{tutorial_pylammps.txt => Howto_pylammps.txt} (95%)
create mode 100644 doc/src/Howto_replica.txt
create mode 100644 doc/src/Howto_restart.txt
create mode 100644 doc/src/Howto_spc.txt
create mode 100644 doc/src/Howto_spherical.txt
create mode 100644 doc/src/Howto_spins.txt
create mode 100644 doc/src/Howto_temperature.txt
create mode 100644 doc/src/Howto_thermostat.txt
create mode 100644 doc/src/Howto_tip3p.txt
create mode 100644 doc/src/Howto_tip4p.txt
create mode 100644 doc/src/Howto_triclinic.txt
create mode 100644 doc/src/Howto_viscosity.txt
create mode 100644 doc/src/Howto_viz.txt
create mode 100644 doc/src/Howto_walls.txt
create mode 100644 doc/src/Intro.txt
create mode 100644 doc/src/Intro_authors.txt
create mode 100644 doc/src/Intro_features.txt
create mode 100644 doc/src/Intro_nonfeatures.txt
create mode 100644 doc/src/Intro_opensource.txt
create mode 100644 doc/src/Intro_overview.txt
create mode 100644 doc/src/Intro_website.txt
create mode 100644 doc/src/Manual_version.txt
create mode 100644 doc/src/Packages.txt
rename doc/src/{Section_packages.txt => Packages_details.txt} (85%)
create mode 100644 doc/src/Packages_standard.txt
create mode 100644 doc/src/Packages_user.txt
delete mode 100644 doc/src/Section_accelerate.txt
delete mode 100644 doc/src/Section_commands.txt
delete mode 100644 doc/src/Section_history.txt
delete mode 100644 doc/src/Section_howto.txt
delete mode 100644 doc/src/Section_intro.txt
create mode 100644 doc/src/Speed.txt
rename doc/src/{Section_perf.txt => Speed_bench.txt} (86%)
create mode 100644 doc/src/Speed_compare.txt
rename doc/src/{accelerate_gpu.txt => Speed_gpu.txt} (96%)
rename doc/src/{accelerate_intel.txt => Speed_intel.txt} (97%)
rename doc/src/{accelerate_kokkos.txt => Speed_kokkos.txt} (59%)
create mode 100644 doc/src/Speed_measure.txt
rename doc/src/{accelerate_omp.txt => Speed_omp.txt} (95%)
rename doc/src/{accelerate_opt.txt => Speed_opt.txt} (85%)
create mode 100644 doc/src/Speed_packages.txt
create mode 100644 doc/src/Speed_tips.txt
delete mode 100644 doc/src/lammps_support.txt
delete mode 100644 doc/src/lammps_tutorials.txt
delete mode 100644 doc/src/tutorials.txt
create mode 100644 doc/utils/requirements.txt
delete mode 100644 examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
create mode 100644 examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
rename examples/DIFFUSE/{log.13Oct16.vacf.2d.g++.8 => log.3Aug18.vacf.2d.g++.8} (84%)
create mode 100644 src/MANYBODY/pair_eam_cd.cpp
rename src/{USER-MISC/pair_cdeam.h => MANYBODY/pair_eam_cd.h} (93%)
delete mode 100755 src/USER-MISC/Install.sh
delete mode 100644 src/USER-MISC/pair_cdeam.cpp
create mode 100644 tools/emacs/README.md
delete mode 100644 tools/emacs/README.txt
rename tools/emacs/{lammps.el => lammps-mode.el} (73%)
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 75b79443c3..b91e58a83f 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -17,6 +17,7 @@ src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
+src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
@@ -44,6 +45,7 @@ src/USER-MISC/*_grem.* @dstelter92
# tools
tools/msi2lmp/* @akohlmey
+tools/emacs/* @HaoZeke
# cmake
cmake/* @junghans @rbberger
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 60a0f5d48f..f4d3cac5d2 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -9,6 +9,7 @@ set(SOVERSION 0)
get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
+get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
# To avoid conflicts with the conventional Makefile build system, we build everything here
@@ -137,8 +138,11 @@ set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIG
add_definitions(-D${LAMMPS_SIZE_LIMIT})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
-set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
-add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+# posix_memalign is not available on Windows
+if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+ set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
+ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
+endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
if(LAMMPS_EXCEPTIONS)
@@ -153,14 +157,15 @@ if(ENABLE_TESTING)
enable_testing()
endif(ENABLE_TESTING)
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
+ KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
@@ -174,13 +179,12 @@ macro(pkg_depends PKG1 PKG2)
endif()
endmacro()
+# "hard" dependencies between packages resulting
+# in an error instead of skipping over files
pkg_depends(MPIIO MPI)
-pkg_depends(QEQ MANYBODY)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
-pkg_depends(USER-MISC MANYBODY)
pkg_depends(USER-PHONON KSPACE)
-pkg_depends(CORESHELL KSPACE)
######################################################
# packages with special compiler needs or external libs
@@ -466,6 +470,11 @@ if(PKG_COMPRESS)
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
+# the windows version of LAMMPS requires a couple extra libraries
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+ list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
+endif()
+
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@@ -574,6 +583,41 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
+if(PKG_CORESHELL)
+ set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+ set(CORESHELL_SOURCES)
+ set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
+
+ # detects styles which have a CORESHELL version
+ RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+
+ get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+
+ list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+ include_directories(${CORESHELL_SOURCES_DIR})
+endif()
+
+# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
+if(PKG_QEQ)
+ set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+ file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+ file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+
+ if(NOT PKG_MANYBODY)
+ list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+ list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+ endif()
+ set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+ foreach(MY_HEADER ${QEQ_HEADERS})
+ AddStyleHeader(${MY_HEADER} FIX)
+ endforeach()
+
+ get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+ list(APPEND LIB_SOURCES ${QEQ_SOURCES})
+ include_directories(${QEQ_SOURCES_DIR})
+endif()
+
if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
@@ -585,8 +629,31 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+ # manually add package dependent source files from USER-OMP that do not provide styles
+
+ if(PKG_ASPHERE)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+ endif()
+
+ if(PKG_RIGID)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+ endif()
+
+ if(PKG_USER-REAXC)
+ list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+ endif()
+
list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
include_directories(${USER-OMP_SOURCES_DIR})
endif()
@@ -900,6 +967,80 @@ if(BUILD_EXE)
endif()
endif()
+###############################################################################
+# Build documentation
+###############################################################################
+option(BUILD_DOC "Build LAMMPS documentation" OFF)
+if(BUILD_DOC)
+ include(ProcessorCount)
+ ProcessorCount(NPROCS)
+ find_package(PythonInterp 3 REQUIRED)
+
+ set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+
+ file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
+ file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
+ list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+
+ add_custom_command(
+ OUTPUT docenv
+ COMMAND ${VIRTUALENV} docenv
+ )
+
+ set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+
+ add_custom_command(
+ OUTPUT requirements.txt
+ DEPENDS docenv
+ COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+ COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
+ COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+ )
+
+ set(RST_FILES "")
+ set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
+ file(MAKE_DIRECTORY ${RST_DIR})
+ foreach(TXT_FILE ${DOC_SOURCES})
+ get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
+ set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
+ list(APPEND RST_FILES ${RST_FILE})
+ add_custom_command(
+ OUTPUT ${RST_FILE}
+ DEPENDS requirements.txt docenv ${TXT_FILE}
+ COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
+ )
+ endforeach()
+
+ add_custom_command(
+ OUTPUT html
+ DEPENDS ${RST_FILES}
+ COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
+ COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+ )
+
+ add_custom_target(
+ doc ALL
+ DEPENDS html
+ SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
+ )
+
+ install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+endif()
+
+###############################################################################
+# Install potential files in data directory
+###############################################################################
+set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
+
+configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
+configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
+install(
+ FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh
+ ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh
+ DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
+)
+
###############################################################################
# Testing
#
diff --git a/cmake/README.md b/cmake/README.md
index bafd440a64..b6644ffda9 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_DOC</code></td>
+ <td>control whether to build LAMMPS documentation</td>
+ <td>
+ <dl>
+ <dt><code>off</code> (default)</dt>
+ <dt><code>on</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
<td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in
new file mode 100644
index 0000000000..def49bf75c
--- /dev/null
+++ b/cmake/etc/profile.d/lammps.csh.in
@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in
new file mode 100644
index 0000000000..acd75fa0cf
--- /dev/null
+++ b/cmake/etc/profile.d/lammps.sh.in
@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
diff --git a/doc/Makefile b/doc/Makefile
index c4bc80e7bd..81f3623499 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -157,7 +157,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
@(\
mkdir -p $(RSTDIR) ; \
. $(VENV)/bin/activate ;\
- txt2rst $< > $@ ;\
+ txt2rst -v $< > $@ ;\
deactivate ;\
)
diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt
new file mode 100644
index 0000000000..30e3343bd2
--- /dev/null
+++ b/doc/src/Commands.txt
@@ -0,0 +1,51 @@
+"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Packages.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html#comm)
+
+:line
+
+Commands :h2
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+<!-- RST
+
+.. toctree::
+
+ Commands_input
+ Commands_parse
+ Commands_structure
+ Commands_category
+
+.. toctree::
+
+ Commands_all
+ Commands_fix
+ Commands_compute
+ Commands_pair
+ Commands_bond
+ Commands_kspace
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"LAMMPS input scripts"_Commands_input.html
+"Parsing rules for input scripts"_Commands_parse.html
+"Input script structure"_Commands_structure.html
+"Commands by category"_Commands_category.html :all(b)
+
+"All commands"_Commands_all.html
+"Fix commands"_Commands_fix.html
+"Compute commands"_Commands_compute.html
+"Pair commands"_Commands_pair.html
+"Bond, angle, dihedral, improper commands"_Commands_bond.html
+"KSpace solvers"_Commands_kspace.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
new file mode 100644
index 0000000000..13db1272b9
--- /dev/null
+++ b/doc/src/Commands_all.txt
@@ -0,0 +1,128 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+All commands :h3
+
+An alphabetic list of all LAMMPS commmands.
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"clear"_clear.html,
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"create_box"_create_box.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"dimension"_dimension.html,
+"displace_atoms"_displace_atoms.html,
+"dump"_dump.html,
+"dump image"_dump_image.html,
+"dump_modify"_dump_modify.html,
+"dump movie"_dump_image.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
+"echo"_echo.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"group"_group.html,
+"group2ndx"_group2ndx.html,
+"if"_if.html,
+"info"_info.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"include"_include.html,
+"jump"_jump.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"label"_label.html,
+"lattice"_lattice.html,
+"log"_log.html,
+"mass"_mass.html,
+"minimize"_minimize.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"molecule"_molecule.html,
+"ndx2group"_group2ndx.html,
+"neb"_neb.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"newton"_newton.html,
+"next"_next.html,
+"package"_package.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"partition"_partition.html,
+"prd"_prd.html,
+"print"_print.html,
+"processors"_processors.html,
+"python"_python.html,
+"quit"_quit.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"region"_region.html,
+"replicate"_replicate.html,
+"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
+"reset_timestep"_reset_timestep.html,
+"restart"_restart.html,
+"run"_run.html,
+"run_style"_run_style.html,
+"set"_set.html,
+"shell"_shell.html,
+"special_bonds"_special_bonds.html,
+"suffix"_suffix.html,
+"tad"_tad.html,
+"temper"_temper.html,
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html,
+"uncompute"_uncompute.html,
+"undump"_undump.html,
+"unfix"_unfix.html,
+"units"_units.html,
+"variable"_variable.html,
+"velocity"_velocity.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
new file mode 100644
index 0000000000..314260cb14
--- /dev/null
+++ b/doc/src/Commands_bond.txt
@@ -0,0 +1,124 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Bond, angle, dihedral, and improper commands :h3
+
+:line
+
+Bond_style potentials :h3,link(bond)
+
+All LAMMPS "bond_style"_bond_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_bond_none.html,
+"zero"_bond_zero.html,
+"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_bond_class2.html,
+"fene (iko)"_bond_fene.html,
+"fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
+"harmonic (ko)"_bond_harmonic.html,
+"harmonic/shift (o)"_bond_harmonic_shift.html,
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"morse (o)"_bond_morse.html,
+"nonlinear (o)"_bond_nonlinear.html,
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html,
+"quartic (o)"_bond_quartic.html,
+"table (o)"_bond_table.html :tb(c=4,ea=c)
+
+:line
+
+Angle_style potentials :h3,link(angle)
+
+All LAMMPS "angle_style"_angle_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_angle_none.html,
+"zero"_angle_zero.html,
+"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+
+"charmm (ko)"_angle_charmm.html,
+"class2 (ko)"_angle_class2.html,
+"cosine (o)"_angle_cosine.html,
+"cosine/delta (o)"_angle_cosine_delta.html,
+"cosine/periodic (o)"_angle_cosine_periodic.html,
+"cosine/shift (o)"_angle_cosine_shift.html,
+"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
+"cosine/squared (o)"_angle_cosine_squared.html,
+"dipole (o)"_angle_dipole.html,
+"fourier (o)"_angle_fourier.html,
+"fourier/simple (o)"_angle_fourier_simple.html,
+"harmonic (iko)"_angle_harmonic.html,
+"quartic (o)"_angle_quartic.html,
+"sdk"_angle_sdk.html,
+"table (o)"_angle_table.html :tb(c=4,ea=c)
+
+:line
+
+Dihedral_style potentials :h3,link(dihedral)
+
+All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_dihedral_none.html,
+"zero"_dihedral_zero.html,
+"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
+"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
+"fourier (io)"_dihedral_fourier.html,
+"harmonic (io)"_dihedral_harmonic.html,
+"helix (o)"_dihedral_helix.html,
+"multi/harmonic (o)"_dihedral_multi_harmonic.html,
+"nharmonic (o)"_dihedral_nharmonic.html,
+"opls (iko)"_dihedral_opls.htm;,
+"quadratic (o)"_dihedral_quadratic.html,
+"spherical (o)"_dihedral_spherical.html,
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
+
+:line
+
+Improper_style potentials :h3,link(improper)
+
+All LAMMPS "improper_style"_improper_style.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_improper_none.html,
+"zero"_improper_zero.html,
+"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_improper_class2.html,
+"cossq (o)"_improper_cossq.html,
+"cvff (io)"_improper_cvff.html,
+"distance"_improper_distance.html,
+"fourier (o)"_improper_fourier.html,
+"harmonic (iko)"_improper_harmonic.html,
+"ring (o)"_improper_ring.html,
+"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt
new file mode 100644
index 0000000000..5d047c6727
--- /dev/null
+++ b/doc/src/Commands_category.txt
@@ -0,0 +1,141 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Commands by category :h3
+
+This page lists most of the LAMMPS commands, grouped by category. The
+"Commands all"_Commands_all.html doc page lists all commands
+alphabetically. It also includes long lists of style options for
+entries that appear in the following categories as a single command
+(fix, compute, pair, etc).
+
+Initialization:
+
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html :ul
+
+Setup simulation box:
+
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html :ul
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html :ul
+
+Force fields:
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"special_bonds"_special_bonds.html :ul
+
+Settings:
+
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html :ul
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html :ul
+
+Output:
+
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :ul
+
+Actions:
+
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html :ul
+
+Input script control:
+
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html :ul
+
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
new file mode 100644
index 0000000000..028e274c9b
--- /dev/null
+++ b/doc/src/Commands_compute.txt
@@ -0,0 +1,153 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Compute commands :h3
+
+An alphabetic list of all LAMMPS "compute"_compute.html commands.
+Some styles have accelerated versions. This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+"ackland/atom"_compute_ackland_atom.html,
+"aggregate/atom"_compute_cluster_atom.html,
+"angle"_compute_angle.html,
+"angle/local"_compute_angle_local.html,
+"angmom/chunk"_compute_angmom_chunk.html,
+"basal/atom"_compute_basal_atom.html,
+"body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
+"bond/local"_compute_bond_local.html,
+"centro/atom"_compute_centro_atom.html,
+"chunk/atom"_compute_chunk_atom.html,
+"cluster/atom"_compute_cluster_atom.html,
+"cna/atom"_compute_cna_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
+"com"_compute_com.html,
+"com/chunk"_compute_com_chunk.html,
+"contact/atom"_compute_contact_atom.html,
+"coord/atom"_compute_coord_atom.html,
+"damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
+"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
+"dipole/chunk"_compute_dipole_chunk.html,
+"displace/atom"_compute_displace_atom.html,
+"dpd"_compute_dpd.html,
+"dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
+"erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
+"erotate/sphere"_compute_erotate_sphere.html,
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
+"event/displace"_compute_event_displace.html,
+"fep"_compute_fep.html,
+"force/tally"_compute_tally.html,
+"fragment/atom"_compute_cluster_atom.html,
+"global/atom"_compute_global_atom.html,
+"group/group"_compute_group_group.html,
+"gyration"_compute_gyration.html,
+"gyration/chunk"_compute_gyration_chunk.html,
+"heat/flux"_compute_heat_flux.html,
+"heat/flux/tally"_compute_tally.html,
+"hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
+"improper/local"_compute_improper_local.html,
+"inertia/chunk"_compute_inertia_chunk.html,
+"ke"_compute_ke.html,
+"ke/atom"_compute_ke_atom.html,
+"ke/atom/eff"_compute_ke_atom_eff.html,
+"ke/eff"_compute_ke_eff.html,
+"ke/rigid"_compute_ke_rigid.html,
+"meso/e/atom"_compute_meso_e_atom.html,
+"meso/rho/atom"_compute_meso_rho_atom.html,
+"meso/t/atom"_compute_meso_t_atom.html,
+"msd"_compute_msd.html,
+"msd/chunk"_compute_msd_chunk.html,
+"msd/nongauss"_compute_msd_nongauss.html,
+"omega/chunk"_compute_omega_chunk.html,
+"orientorder/atom"_compute_orientorder_atom.html,
+"pair"_compute_pair.html,
+"pair/local"_compute_pair_local.html,
+"pe"_compute_pe.html,
+"pe/atom"_compute_pe_atom.html,
+"pe/mol/tally"_compute_tally.html,
+"pe/tally"_compute_tally.html,
+"plasticity/atom"_compute_plasticity_atom.html,
+"pressure"_compute_pressure.html,
+"pressure/uef"_compute_pressure_uef.html,
+"property/atom"_compute_property_atom.html,
+"property/chunk"_compute_property_chunk.html,
+"property/local"_compute_property_local.html,
+"rdf"_compute_rdf.html,
+"reduce"_compute_reduce.html,
+"reduce/region"_compute_reduce.html,
+"rigid/local"_compute_rigid_local.html,
+"saed"_compute_saed.html,
+"slice"_compute_slice.html,
+"smd/contact/radius"_compute_smd_contact_radius.html,
+"smd/damage"_compute_smd_damage.html,
+"smd/hourglass/error"_compute_smd_hourglass_error.html,
+"smd/internal/energy"_compute_smd_internal_energy.html,
+"smd/plastic/strain"_compute_smd_plastic_strain.html,
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
+"smd/rho"_compute_smd_rho.html,
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
+"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
+"smd/vol"_compute_smd_vol.html,
+"sna/atom"_compute_sna_atom.html,
+"snad/atom"_compute_sna_atom.html,
+"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
+"stress/atom"_compute_stress_atom.html,
+"stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
+"temp (k)"_compute_temp.html,
+"temp/asphere"_compute_temp_asphere.html,
+"temp/body"_compute_temp_body.html,
+"temp/chunk"_compute_temp_chunk.html,
+"temp/com"_compute_temp_com.html,
+"temp/deform"_compute_temp_deform.html,
+"temp/deform/eff"_compute_temp_deform_eff.html,
+"temp/drude"_compute_temp_drude.html,
+"temp/eff"_compute_temp_eff.html,
+"temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
+"temp/ramp"_compute_temp_ramp.html,
+"temp/region"_compute_temp_region.html,
+"temp/region/eff"_compute_temp_region_eff.html,
+"temp/rotate"_compute_temp_rotate.html,
+"temp/sphere"_compute_temp_sphere.html,
+"temp/uef"_compute_temp_uef.html,
+"ti"_compute_ti.html,
+"torque/chunk"_compute_torque_chunk.html,
+"vacf"_compute_vacf.html,
+"vcm/chunk"_compute_vcm_chunk.html,
+"voronoi/atom"_compute_voronoi_atom.html,
+"xrd"_compute_xrd.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
new file mode 100644
index 0000000000..e002c11770
--- /dev/null
+++ b/doc/src/Commands_fix.txt
@@ -0,0 +1,229 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Fix commands :h3
+
+An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles
+have accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"adapt"_fix_adapt.html,
+"adapt/fep"_fix_adapt_fep.html,
+"addforce"_fix_addforce.html,
+"addtorque"_fix_addtorque.html,
+"append/atoms"_fix_append_atoms.html,
+"atc"_fix_atc.html,
+"atom/swap"_fix_atom_swap.html,
+"ave/atom"_fix_ave_atom.html,
+"ave/chunk"_fix_ave_chunk.html,
+"ave/correlate"_fix_ave_correlate.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
+"ave/histo"_fix_ave_histo.html,
+"ave/histo/weight"_fix_ave_histo.html,
+"ave/time"_fix_ave_time.html,
+"aveforce"_fix_aveforce.html,
+"balance"_fix_balance.html,
+"bond/break"_fix_bond_break.html,
+"bond/create"_fix_bond_create.html,
+"bond/react"_fix_bond_react.html,
+"bond/swap"_fix_bond_swap.html,
+"box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
+"colvars"_fix_colvars.html,
+"controller"_fix_controller.html,
+"deform (k)"_fix_deform.html,
+"deposit"_fix_deposit.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
+"drag"_fix_drag.html,
+"drude"_fix_drude.html,
+"drude/transform/direct"_fix_drude_transform.html,
+"drude/transform/reverse"_fix_drude_transform.html,
+"dt/reset"_fix_dt_reset.html,
+"edpd/source"_fix_dpd_source.html,
+"efield"_fix_efield.html,
+"ehex"_fix_ehex.html,
+"enforce2d (k)"_fix_enforce2d.html,
+"eos/cv"_fix_eos_cv.html,
+"eos/table"_fix_eos_table.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
+"evaporate"_fix_evaporate.html,
+"external"_fix_external.html,
+"filter/corotate"_fix_filter_corotate.html,
+"flow/gauss"_fix_flow_gauss.html,
+"freeze"_fix_freeze.html,
+"gcmc"_fix_gcmc.html,
+"gld"_fix_gld.html,
+"gle"_fix_gle.html,
+"gravity (o)"_fix_gravity.html,
+"grem"_fix_grem.html,
+"halt"_fix_halt.html,
+"heat"_fix_heat.html,
+"imd"_fix_imd.html,
+"indent"_fix_indent.html,
+"ipi"_fix_ipi.html,
+"langevin (k)"_fix_langevin.html,
+"langevin/drude"_fix_langevin_drude.html,
+"langevin/eff"_fix_langevin_eff.html,
+"langevin/spin"_fix_langevin_spin.html,
+"latte"_fix_latte.html,
+"lb/fluid"_fix_lb_fluid.html,
+"lb/momentum"_fix_lb_momentum.html,
+"lb/pc"_fix_lb_pc.html,
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
+"lb/viscous"_fix_lb_viscous.html,
+"lineforce"_fix_lineforce.html,
+"manifoldforce"_fix_manifoldforce.html,
+"meso"_fix_meso.html,
+"meso/stationary"_fix_meso_stationary.html,
+"momentum (k)"_fix_momentum.html,
+"move"_fix_move.html,
+"mscg"_fix_mscg.html,
+"msst"_fix_msst.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
+"neb"_fix_neb.html,
+"nph (ko)"_fix_nh.html,
+"nph/asphere (o)"_fix_nph_asphere.html,
+"nph/body"_fix_nph_body.html,
+"nph/eff"_fix_nh_eff.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
+"nphug (o)"_fix_nphug.html,
+"npt (kio)"_fix_nh.html,
+"npt/asphere (o)"_fix_npt_asphere.html,
+"npt/body"_fix_npt_body.html,
+"npt/eff"_fix_nh_eff.html,
+"npt/sphere (o)"_fix_npt_sphere.html,
+"npt/uef"_fix_nh_uef.html,
+"nve (kio)"_fix_nve.html,
+"nve/asphere (i)"_fix_nve_asphere.html,
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/body"_fix_nve_body.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"nve/eff"_fix_nve_eff.html,
+"nve/limit"_fix_nve_limit.html,
+"nve/line"_fix_nve_line.html,
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nve/noforce"_fix_nve_noforce.html,
+"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
+"nve/tri"_fix_nve_tri.html,
+"nvk"_fix_nvk.html,
+"nvt (iko)"_fix_nh.html,
+"nvt/asphere (o)"_fix_nvt_asphere.html,
+"nvt/body"_fix_nvt_body.html,
+"nvt/eff"_fix_nh_eff.html,
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
+"nvt/sllod (io)"_fix_nvt_sllod.html,
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"nvt/sphere (o)"_fix_nvt_sphere.html,
+"nvt/uef"_fix_nh_uef.html,
+"oneway"_fix_oneway.html,
+"orient/bcc"_fix_orient.html,
+"orient/fcc"_fix_orient.html,
+"phonon"_fix_phonon.html,
+"pimd"_fix_pimd.html,
+"planeforce"_fix_planeforce.html,
+"poems"_fix_poems.html,
+"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
+"press/berendsen"_fix_press_berendsen.html,
+"print"_fix_print.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
+"qbmsst"_fix_qbmsst.html,
+"qeq/comb (o)"_fix_qeq_comb.html,
+"qeq/dynamic"_fix_qeq.html,
+"qeq/fire"_fix_qeq.html,
+"qeq/point"_fix_qeq.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/shielded"_fix_qeq.html,
+"qeq/slater"_fix_qeq.html,
+"qmmm"_fix_qmmm.html,
+"qtb"_fix_qtb.html,
+"rattle"_fix_shake.html,
+"reax/bonds"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
+"recenter"_fix_recenter.html,
+"restrain"_fix_restrain.html,
+"rhok"_fix_rhok.html,
+"rigid (o)"_fix_rigid.html,
+"rigid/nph (o)"_fix_rigid.html,
+"rigid/npt (o)"_fix_rigid.html,
+"rigid/nve (o)"_fix_rigid.html,
+"rigid/nvt (o)"_fix_rigid.html,
+"rigid/small (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
+"rx (k)"_fix_rx.html,
+"saed/vtk"_fix_saed_vtk.html,
+"setforce (k)"_fix_setforce.html,
+"shake"_fix_shake.html,
+"shardlow (k)"_fix_shardlow.html,
+"smd"_fix_smd.html,
+"smd/adjust/dt"_fix_smd_adjust_dt.html,
+"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/setvel"_fix_smd_setvel.html,
+"smd/wall/surface"_fix_smd_wall_surface.html,
+"spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
+"spring/rg"_fix_spring_rg.html,
+"spring/self"_fix_spring_self.html,
+"srd"_fix_srd.html,
+"store/force"_fix_store_force.html,
+"store/state"_fix_store_state.html,
+"tdpd/source"_fix_dpd_source.html,
+"temp/berendsen"_fix_temp_berendsen.html,
+"temp/csld"_fix_temp_csvr.html,
+"temp/csvr"_fix_temp_csvr.html,
+"temp/rescale"_fix_temp_rescale.html,
+"temp/rescale/eff"_fix_temp_rescale_eff.html,
+"tfmc"_fix_tfmc.html,
+"thermal/conductivity"_fix_thermal_conductivity.html,
+"ti/spring"_fix_ti_spring.html,
+"tmd"_fix_tmd.html,
+"ttm"_fix_ttm.html,
+"ttm/mod"_fix_ttm.html,
+"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
+"viscosity"_fix_viscosity.html,
+"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
+"wall/colloid"_fix_wall.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
+"wall/harmonic"_fix_wall.html,
+"wall/lj1043"_fix_wall.html,
+"wall/lj126"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
+"wall/piston"_fix_wall_piston.html,
+"wall/reflect (k)"_fix_wall_reflect.html,
+"wall/region"_fix_wall_region.html,
+"wall/region/ees"_fix_wall_ees.html,
+"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt
new file mode 100644
index 0000000000..8b3dda741b
--- /dev/null
+++ b/doc/src/Commands_input.txt
@@ -0,0 +1,60 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS input scripts :h3
+
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time. When the input script ends, LAMMPS exits. Each
+command causes LAMMPS to take some action. It may set an internal
+variable, read in a file, or run a simulation. Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+
+In many cases, the ordering of commands in an input script is not
+important. However the following rules apply:
+
+(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings. Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+
+timestep 0.5
+run 100
+run 100 :pre
+
+does something different than this sequence:
+
+run 100
+timestep 0.5
+run 100 :pre
+
+In the first case, the specified timestep (0.5 fs) is used for two
+simulations of 100 timesteps each. In the 2nd case, the default
+timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep is used for the 2nd one.
+
+(2) Some commands are only valid when they follow other commands. For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+
+(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect. For example, the
+"read_data"_read_data.html command initializes the system by setting
+up the simulation box and assigning atoms to processors. If default
+values are not desired, the "processors"_processors.html and
+"boundary"_boundary.html commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+
+Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed. The "Errors"_Errors.html doc page gives
+more information on what errors mean. The documentation for each
+command lists restrictions on how the command can be used.
+
diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt
new file mode 100644
index 0000000000..a126344505
--- /dev/null
+++ b/doc/src/Commands_kspace.txt
@@ -0,0 +1,36 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+KSpace solvers :h3
+
+All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"ewald (o)"_kspace_style.html,
+"ewald/disp"_kspace_style.html,
+"msm (o)"_kspace_style.html,
+"msm/cg (o)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
+"pppm/cg (o)"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
+"pppm/disp/tip4p"_kspace_style.html,
+"pppm/stagger"_kspace_style.html,
+"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
new file mode 100644
index 0000000000..eaf2720613
--- /dev/null
+++ b/doc/src/Commands_pair.txt
@@ -0,0 +1,231 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Pair_style potentials :h3
+
+All LAMMPS "pair_style"_pair_style.html commands. Some styles have
+accelerated versions. This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_pair_none.html,
+"zero"_pair_zero.html,
+"hybrid"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+
+"adp (o)"_pair_adp.html,
+"agni (o)"_pair_agni.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
+"awpmd/cut"_pair_awpmd.html,
+"beck (go)"_pair_beck.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded_polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
+"bop"_pair_bop.html,
+"born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
+"born/coul/long (go)"_pair_born.html,
+"born/coul/long/cs"_pair_born.html,
+"born/coul/msm (o)"_pair_born.html,
+"born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
+"brownian (o)"_pair_brownian.html,
+"brownian/poly (o)"_pair_brownian.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
+"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/msm (o)"_pair_buck.html,
+"buck/long/coul/long (o)"_pair_buck_long.html,
+"buck/mdf"_pair_mdf.html,
+"colloid (go)"_pair_colloid.html,
+"comb (o)"_pair_comb.html,
+"comb3"_pair_comb.html,
+"coul/cut (gko)"_pair_coul.html,
+"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/debye (gko)"_pair_coul.html,
+"coul/diel (o)"_pair_coul_diel.html,
+"coul/dsf (gko)"_pair_coul.html,
+"coul/long (gko)"_pair_coul.html,
+"coul/long/cs"_pair_coul.html,
+"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/msm"_pair_coul.html,
+"coul/shield"_pair_coul_shield.html,
+"coul/streitz"_pair_coul.html,
+"coul/wolf (ko)"_pair_coul.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
+"dpd/fdt"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
+"dpd/tstat (go)"_pair_dpd.html,
+"dsmc"_pair_dsmc.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/cd (o)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
+"edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
+"eff/cut"_pair_eff.html,
+"eim (o)"_pair_eim.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
+"gauss (go)"_pair_gauss.html,
+"gauss/cut"_pair_gauss.html,
+"gayberne (gio)"_pair_gayberne.html,
+"gran/hertz/history (o)"_pair_gran.html,
+"gran/hooke (o)"_pair_gran.html,
+"gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
+"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
+"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kim"_pair_kim.html,
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"lcbop"_pair_lcbop.html,
+"lennard/mdf"_pair_mdf.html,
+"line/lj"_pair_line_lj.html,
+"list"_pair_list.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
+"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
+"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
+"lj/class2 (gko)"_pair_class2.html,
+"lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/cubic (go)"_pair_lj_cubic.html,
+"lj/cut (gikot)"_pair_lj.html,
+"lj/cut/coul/cut (gko)"_pair_lj.html,
+"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/debye (gko)"_pair_lj.html,
+"lj/cut/coul/dsf (gko)"_pair_lj.html,
+"lj/cut/coul/long (gikot)"_pair_lj.html,
+"lj/cut/coul/long/cs"_pair_lj.html,
+"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
+"lj/cut/dipole/cut (go)"_pair_dipole.html,
+"lj/cut/dipole/long"_pair_dipole.html,
+"lj/cut/dipole/sf (go)"_pair_dipole.html,
+"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/thole/long (o)"_pair_thole.html,
+"lj/cut/tip4p/cut (o)"_pair_lj.html,
+"lj/cut/tip4p/long (ot)"_pair_lj.html,
+"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/expand (gko)"_pair_lj_expand.html,
+"lj/gromacs (gko)"_pair_gromacs.html,
+"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/dipole/long"_pair_dipole.html,
+"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/mdf"_pair_mdf.html,
+"lj/sdk (gko)"_pair_sdk.html,
+"lj/sdk/coul/long (go)"_pair_sdk.html,
+"lj/sdk/coul/msm (o)"_pair_sdk.html,
+"lj/smooth (o)"_pair_lj_smooth.html,
+"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj96/cut (go)"_pair_lj96.html,
+"lubricate (o)"_pair_lubricate.html,
+"lubricate/poly (o)"_pair_lubricate.html,
+"lubricateU"_pair_lubricateU.html,
+"lubricateU/poly"_pair_lubricateU.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
+"meam"_pair_meam.html,
+"meam/c"_pair_meam.html,
+"meam/spline (o)"_pair_meam_spline.html,
+"meam/sw/spline"_pair_meam_sw_spline.html,
+"mgpt"_pair_mgpt.html,
+"mie/cut (o)"_pair_mie.html,
+"momb"_pair_momb.html,
+"morse (gkot)"_pair_morse.html,
+"morse/smooth/linear"_pair_morse.html,
+"morse/soft"_pair_morse.html,
+"multi/lucy"_pair_multi_lucy.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
+"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nm/cut (o)"_pair_nm.html,
+"nm/cut/coul/cut (o)"_pair_nm.html,
+"nm/cut/coul/long (o)"_pair_nm.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
+"peri/eps"_pair_peri.html,
+"peri/lps (o)"_pair_peri.html,
+"peri/pmb (o)"_pair_peri.html,
+"peri/ves"_pair_peri.html,
+"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
+"quip"_pair_quip.html,
+"reax"_pair_reax.html,
+"reax/c (ko)"_pair_reaxc.html,
+"rebo (oi)"_pair_airebo.html,
+"resquared (go)"_pair_resquared.html,
+"smd/hertz"_pair_smd_hertz.html,
+"smd/tlsph"_pair_smd_tlsph.html,
+"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
+"snap (k)"_pair_snap.html,
+"soft (go)"_pair_soft.html,
+"sph/heatconduction"_pair_sph_heatconduction.html,
+"sph/idealgas"_pair_sph_idealgas.html,
+"sph/lj"_pair_sph_lj.html,
+"sph/rhosum"_pair_sph_rhosum.html,
+"sph/taitwater"_pair_sph_taitwater.html,
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
+"srp"_pair_srp.html,
+"sw (giko)"_pair_sw.html,
+"table (gko)"_pair_table.html,
+"table/rx (k)"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
+"tersoff (giko)"_pair_tersoff.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
+"tersoff/table (o)"_pair_tersoff.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
+"thole"_pair_thole.html,
+"tip4p/cut (o)"_pair_coul.html,
+"tip4p/long (o)"_pair_coul.html,
+"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tri/lj"_pair_tri_lj.html,
+"ufm (got)"_pair_ufm.html,
+"vashishta (ko)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
+"yukawa (gok)"_pair_yukawa.html,
+"yukawa/colloid (go)"_pair_yukawa_colloid.html,
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt
new file mode 100644
index 0000000000..cbe2261986
--- /dev/null
+++ b/doc/src/Commands_parse.txt
@@ -0,0 +1,136 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Parsing rules for input scripts :h3
+
+Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive. Command names are lower-case, as
+are specified command arguments. Upper case letters may be used in
+file names or user-chosen ID strings.
+
+Here are 6 rulse for how each line in the input script is parsed by
+LAMMPS:
+
+(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line. The next line is
+concatenated to the previous line by removing the "&" character and
+line break. This allows long commands to be continued across two or
+more lines. See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+
+(2) All characters from the first "#" character onward are treated as
+comment and discarded. See an exception in (6). Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line. Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+
+(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string. See an exception in
+(6).
+
+If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets. If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+"x".
+
+How the variable is converted to a text string depends on what style
+of variable it is; see the "variable"_variable.html doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them. The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command. The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+
+As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an "equal-style variable"_variable.html. This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names. For example, these 3 input script lines:
+
+variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete :pre
+
+can be replaced by
+
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+so that you do not have to define (or discard) a temporary variable X.
+
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value. The format string is used to output the result
+of the variable expression evaluation. If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+
+variable a equal 2
+variable b2 equal 4
+print "B2 = $\{b$a\}" :pre
+
+Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+"equal-style variable"_variable.html.
+
+See the "variable"_variable.html command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+
+(4) The line is broken into "words" separated by whitespace (tabs,
+spaces). Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+
+(5) The first word is the command name. All successive words in the
+line are arguments.
+
+(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes. A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above. When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line. If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed. For example:
+
+print "Volume = $v"
+print 'Volume = $v'
+if "$\{steps\} > 1000" then quit
+variable a string "red green blue &
+ purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+""" :pre
+
+In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+
+See the "dump modify format"_dump_modify.html, "print"_print.html,
+"if"_if.html, and "python"_python.html commands for examples.
+
+A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+
+NOTE: If the argument is itself a command that requires a quoted
+argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then single, double, or
+triple quotes can be nested in the usual manner. See the doc pages
+for those commands for examples. Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+
diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt
new file mode 100644
index 0000000000..b5d2c7b07b
--- /dev/null
+++ b/doc/src/Commands_structure.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Input script structure :h3
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the "Examples"_Examples.html doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+Initialization
+Atom definition
+Settings
+Run a simulation :ol
+
+The last 2 parts can be repeated as many times as desired. I.e. run a
+simulation, change some settings, run some more, etc. Each of the 4
+parts is now described in more detail. Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are "units"_units.html,
+"dimension"_dimension.html, "newton"_newton.html,
+"processors"_processors.html, "boundary"_boundary.html,
+"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+"pair_style"_pair_style.html, "bond_style"_bond_style.html,
+"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS. Read them in from a data
+or restart file via the "read_data"_read_data.html or
+"read_restart"_read_restart.html commands. These files can contain
+molecular topology information. Or create atoms on a lattice (with no
+molecular topology), using these commands: "lattice"_lattice.html,
+"region"_region.html, "create_box"_create_box.html,
+"create_atoms"_create_atoms.html. The entire set of atoms can be
+duplicated to make a larger simulation using the
+"replicate"_replicate.html command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): "pair_coeff"_pair_coeff.html,
+"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"improper_coeff"_improper_coeff.html,
+"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
+"special_bonds"_special_bonds.html.
+
+Various simulation parameters are set by these commands:
+"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
+"group"_group.html, "timestep"_timestep.html,
+"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
+"min_style"_min_style.html, "min_modify"_min_modify.html.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options. The "fix"_fix.html command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the "compute"_compute.html,
+"compute_modify"_compute_modify.html, and "variable"_variable.html
+commands.
+
+Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
+and "restart"_restart.html commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the "run"_run.html
+command. Energy minimization (molecular statics) is performed using
+the "minimize"_minimize.html command. A parallel tempering
+(replica-exchange) simulation can be run using the
+"temper"_temper.html command.
+
diff --git a/doc/src/Eqs/pair_spin_dmi_forces.jpg b/doc/src/Eqs/pair_spin_dmi_forces.jpg
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diff --git a/doc/src/Eqs/pair_spin_dmi_forces.tex b/doc/src/Eqs/pair_spin_dmi_forces.tex
new file mode 100644
index 0000000000..1c0c246db4
--- /dev/null
+++ b/doc/src/Eqs/pair_spin_dmi_forces.tex
@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+ \begin{equation}
+ \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right)
+ ~~{\rm and}~~
+ \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right)
+ , \nonumber
+ \end{equation}
+\end{varwidth}
+\end{document}
diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.jpg b/doc/src/Eqs/pair_spin_dmi_interaction.jpg
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diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.tex b/doc/src/Eqs/pair_spin_dmi_interaction.tex
index 5a5a776f03..79f63a333a 100644
--- a/doc/src/Eqs/pair_spin_dmi_interaction.tex
+++ b/doc/src/Eqs/pair_spin_dmi_interaction.tex
@@ -5,7 +5,7 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \bm{H}_{dm} = -\sum_{{ i,j}=1,i\neq j}^{N}
+ \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N}
\left( \vec{e}_{ij} \times \vec{D} \right)
\cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right),
\nonumber
diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg
index 2b0469bf4db84885fd8b81679cdd9571ba9e3574..b312a9ccdaaf44b7647f2c444c7d79a740cea88c 100644
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diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex
index 088696d5ef..ac5ef682f3 100644
--- a/doc/src/Eqs/pair_spin_exchange_forces.tex
+++ b/doc/src/Eqs/pair_spin_exchange_forces.tex
@@ -5,10 +5,12 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \vec{F}^{i} = \sum_{j}^{Neighbor} \frac{\partial {J} \left(r_{ij} \right)}{
- \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{r}_{ij}
- ~~{\rm and}~~ \vec{\omega}^{i} = \frac{1}{\hbar} \sum_{j}^{Neighbor} {J}
- \left(r_{ij} \right)\,\vec{s}_{j} \nonumber
+ \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
+ \left(r_{ij} \right)\,\vec{s}_{j}
+ ~~{\rm and}~~
+ \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
+ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
+ \nonumber
\end{equation}
\end{varwidth}
\end{document}
diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg
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zCKk{~)zak?py?A+FnVeBLW>{tCQ<tBMDR2meS2iVEtoxZWn2s&jqrg+&c~`Lb%5ac
T9!{y1RMlwg`+_6alZpQU?`}{A
diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex
index 6e598f75ac..f20b3e5740 100644
--- a/doc/src/Eqs/pair_spin_exchange_interaction.tex
+++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex
@@ -5,7 +5,7 @@
\begin{document}
\begin{varwidth}{50in}
\begin{equation}
- \bm{H}_{exchange} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+ \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
\end{equation}
\end{varwidth}
\end{document}
diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt
index 7bc520c19d..1b6206c780 100644
--- a/doc/src/Errors.txt
+++ b/doc/src/Errors.txt
@@ -1,10 +1,10 @@
"Previous Section"_Python.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_history.html :c
+Section"_Manual.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt
index c0a94c7a44..4a8e62e775 100644
--- a/doc/src/Errors_bugs.txt
+++ b/doc/src/Errors_bugs.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 86a25f7e7d..43d1a85a7b 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 1563e02901..03fc25b561 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,9 +21,9 @@ means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that error messages from "user-contributed
-packages"_Section_package.html#table_user are not listed here. If
-such an error occurs and is not self-explanatory, you'll need to look
-in the source code or contact the author of the package.
+packages"_Packages_user.html are not listed here. If such an error
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
Doc page with "WARNING messages"_Errors_warnings.html
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 0324f563b6..dd3402ba86 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,9 +21,9 @@ means that line #187 in the file src/domain.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that warning messages from "user-contributed
-packages"_Section_start.html#table_user are not listed here. If such
-a warning occurs and is not self-explanatory, you'll need to look in
-the source code or contact the author of the package.
+packages"_Packages_user.html are not listed here. If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
Doc page with "ERROR messages"_Errors_messages.html
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 08afca8b20..5bd8da2409 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_perf.html :c
+"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Tools.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,5 +143,5 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
-instructions. See the "Section 4"_Section_packages.html doc
+instructions. See the "Packages_details"_Packages_details.html doc
page for more info on specific USER packages.
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
new file mode 100644
index 0000000000..d9a60d1ef4
--- /dev/null
+++ b/doc/src/Howto.txt
@@ -0,0 +1,128 @@
+"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Examples.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html#comm)
+
+:line
+
+How to discussions :h2
+
+These doc pages describe how to perform various tasks with LAMMPS,
+both for users and developers. The
+"glossary"_http://lammps.sandia.gov website page also lists MD
+terminology with links to corresponding LAMMPS manual pages.
+
+The example input scripts included in the examples dir of the LAMMPS
+distribution and highlighted on the "Examples"_Examples.html doc page
+also show how to setup and run various kinds of simulations.
+
+<!-- RST
+
+.. toctree::
+
+ Howto_github
+ Howto_pylammps
+ Howto_bash
+
+.. toctree::
+
+ Howto_restart
+ Howto_viz
+ Howto_multiple
+ Howto_replica
+ Howto_library
+ Howto_couple
+
+.. toctree::
+
+ Howto_output
+ Howto_chunk
+
+.. toctree::
+
+ Howto_2d
+ Howto_triclinic
+ Howto_walls
+ Howto_nemd
+ Howto_granular
+ Howto_spherical
+ Howto_dispersion
+
+.. toctree::
+
+ Howto_temperature
+ Howto_thermostat
+ Howto_barostat
+ Howto_elastic
+ Howto_kappa
+ Howto_viscosity
+ Howto_diffusion
+
+.. toctree::
+
+ Howto_bioFF
+ Howto_tip3p
+ Howto_tip4p
+ Howto_spc
+
+.. toctree::
+
+ Howto_body
+ Howto_polarizable
+ Howto_coreshell
+ Howto_drude
+ Howto_drude2
+ Howto_manifold
+ Howto_spins
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"Run multiple simulations from one input script"_Howto_multiple.html
+"Multi-replica simulations"_Howto_replica.html
+"Library interface to LAMMPS"_Howto_library.html
+"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Granular models"_Howto_granular.html
+"Finite-size spherical and aspherical particles"_Howto_spherical.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+"Calculate temperature"_Howto_temperature.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+"Body style particles"_Howto_body.html
+"Polarizable models"_Howto_polarizable.html
+"Adiabatic core/shell model"_Howto_coreshell.html
+"Drude induced dipoles"_Howto_drude.html
+"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
+"Manifolds (surfaces)"_Howto_manifold.html
+"Magnetic spins"_Howto_spins.html
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt
new file mode 100644
index 0000000000..e1758c05d5
--- /dev/null
+++ b/doc/src/Howto_2d.txt
@@ -0,0 +1,48 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+2d simulations :h3
+
+Use the "dimension"_dimension.html command to specify a 2d simulation.
+
+Make the simulation box periodic in z via the "boundary"_boundary.html
+command. This is the default.
+
+If using the "create box"_create_box.html command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+
+"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
+
+If using the "read data"_read_data.html command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create_box command settings just described. For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+
+Use the "fix enforce2d"_fix_enforce2d.html command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep. The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+
+Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+
+NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
+opposed to point particles. See the "atom_style
+sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
+commands for details. By default, for 2d simulations, such particles
+will still be modeled as 3d spheres, not 2d discs (circles), meaning
+their moment of inertia will be that of a sphere. If you wish to
+model them as 2d discs, see the "set density/disc"_set.html command
+and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
+"fix nvt/sphere"_fix_nvt_sphere.html, "fix
+nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
+commands.
diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt
new file mode 100644
index 0000000000..7c3db89152
--- /dev/null
+++ b/doc/src/Howto_barostat.txt
@@ -0,0 +1,75 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Barostats :h3
+
+Barostatting means controlling the pressure in an MD simulation.
+"Thermostatting"_Howto_thermostat.html means controlling the
+temperature of the particles. Since the pressure includes a kinetic
+component due to particle velocities, both these operations require
+calculation of the temperature. Typically a target temperature (T)
+and/or pressure (P) is specified by the user, and the thermostat or
+barostat attempts to equilibrate the system to the requested T and/or
+P.
+
+Barostatting in LAMMPS is performed by "fixes"_fix.html. Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+"fix npt"_fix_nh.html
+"fix npt/sphere"_fix_npt_sphere.html
+"fix npt/asphere"_fix_npt_asphere.html
+"fix nph"_fix_nh.html
+"fix press/berendsen"_fix_press_berendsen.html :ul
+
+The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
+and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
+it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html
+and "fix nph"_fix_nh.html only use translational motion of the
+particles in computing T and P and performing thermo/barostatting.
+"Fix npt/sphere"_fix_npt_sphere.html and "fix
+npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the "compute
+pressure"_compute_pressure.html compute to calculate a current
+pressure. By default, this compute is created with a simple "compute
+temp"_compute_temp.html (see the last argument of the "compute
+pressure"_compute_pressure.html command), which is used to calculated
+the kinetic component of the pressure. The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic component which contributes to the current
+pressure. See the doc pages for the individual fixes and for the
+"fix_modify"_fix_modify.html command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+
+NOTE: As with the thermostats, the Nose/Hoover methods ("fix
+npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
+"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
+be used with one of the constant NVE fixes or with one of the NVT
+fixes.
+
+Thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes pressure
+values. As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default pressure is
+setup by the thermo command itself. It is NOT the presure associated
+with any barostatting fix you have defined or with any compute you
+have defined that calculates a presure. The doc pages for the
+barostatting fixes explain the ID of the pressure compute they create.
+Thus if you want to view these pressurse, you need to specify them
+explicitly via the "thermo_style custom"_thermo_style.html command.
+Or you can use the "thermo_modify"_thermo_modify.html command to
+re-define what pressure compute is used for default thermodynamic
+output.
diff --git a/doc/src/tutorial_bash_on_windows.txt b/doc/src/Howto_bash.txt
old mode 100644
new mode 100755
similarity index 99%
rename from doc/src/tutorial_bash_on_windows.txt
rename to doc/src/Howto_bash.txt
index 66712bdffa..f1438418e7
--- a/doc/src/tutorial_bash_on_windows.txt
+++ b/doc/src/Howto_bash.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3
[written by Richard Berger]
:line
+
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager
diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
new file mode 100644
index 0000000000..afb8a84f2e
--- /dev/null
+++ b/doc/src/Howto_bioFF.txt
@@ -0,0 +1,101 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+CHARMM, AMBER, and DREIDING force fields :h3
+
+A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system. Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly
+used in the CHARMM, AMBER, and DREIDING force fields. Setting
+coefficients is done in the input data file via the
+"read_data"_read_data.html command or in the input script with
+commands like "pair_coeff"_pair_coeff.html or
+"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
+additional tools that can use CHARMM or AMBER to assign force field
+coefficients and convert their output into LAMMPS input.
+
+See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
+field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
+field.
+
+:link(charmm,http://www.scripps.edu/brooks)
+:link(amber,http://amber.scripps.edu)
+
+These style choices compute force field formulas that are consistent
+with common options in CHARMM or AMBER. See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"angle_style"_angle_charmm.html charmm
+"dihedral_style"_dihedral_charmm.html charmmfsh
+"dihedral_style"_dihedral_charmm.html charmm
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
+"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
+
+"special_bonds"_special_bonds.html charmm
+"special_bonds"_special_bonds.html amber :ul
+
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
+released in March 2017. We recommend they be used instead of the
+older {charmm} styles. See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+doc pages.
+
+DREIDING is a generic force field developed by the "Goddard
+group"_http://www.wag.caltech.edu at Caltech and is useful for
+predicting structures and dynamics of organic, biological and
+main-group inorganic molecules. The philosophy in DREIDING is to use
+general force constants and geometry parameters based on simple
+hybridization considerations, rather than individual force constants
+and geometric parameters that depend on the particular combinations of
+atoms involved in the bond, angle, or torsion terms. DREIDING has an
+"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
+interactions involving a hydrogen atom on very electronegative atoms
+(N, O, F).
+
+See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
+
+These style choices compute force field formulas that are consistent
+with the DREIDING force field. See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"bond_style"_bond_morse.html morse :ul
+
+"angle_style"_angle_harmonic.html harmonic
+"angle_style"_angle_cosine.html cosine
+"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
+
+"dihedral_style"_dihedral_charmm.html charmm
+"improper_style"_improper_umbrella.html umbrella :ul
+
+"pair_style"_pair_buck.html buck
+"pair_style"_pair_buck.html buck/coul/cut
+"pair_style"_pair_buck.html buck/coul/long
+"pair_style"_pair_lj.html lj/cut
+"pair_style"_pair_lj.html lj/cut/coul/cut
+"pair_style"_pair_lj.html lj/cut/coul/long :ul
+
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
+
+"special_bonds"_special_bonds.html dreiding :ul
+
+:line
+
+:link(howto-MacKerell)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+:link(howto-Mayo)
+[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).
diff --git a/doc/src/body.txt b/doc/src/Howto_body.txt
similarity index 96%
rename from doc/src/body.txt
rename to doc/src/Howto_body.txt
index 4a39ac25d8..3535349b46 100644
--- a/doc/src/body.txt
+++ b/doc/src/Howto_body.txt
@@ -1,24 +1,24 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-Body particles :h2
+Body particles :h3
[Overview:]
-This doc page is not about a LAMMPS input script command, but about
-body particles, which are generalized finite-size particles.
+In LAMMPS, body particles are generalized finite-size particles.
Individual body particles can represent complex entities, such as
surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
-simpler entities that body particles. See "Section
-6.14"_Section_howto.html#howto_14 for a general overview of all
+simpler entities that body particles. See the "Howto
+spherical"_Howto_spherical.html doc page for a general overview of all
these particle types.
Body particles are used via the "atom_style body"_atom_style.html
@@ -151,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z
values in the {Atoms} section of the data file, as is the total mass
of the body particle.
-The "pair_style body"_pair_body.html command can be used with this
-body style to compute body/body and body/non-body interactions.
+The "pair_style body/nparticle"_pair_body_nparticle.html command can be used
+with this body style to compute body/body and body/non-body interactions.
For output purposes via the "compute
body/local"_compute_body_local.html and "dump local"_dump.html
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
new file mode 100644
index 0000000000..8e52acf4b8
--- /dev/null
+++ b/doc/src/Howto_chunk.txt
@@ -0,0 +1,166 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Use chunks to calculate system properties :h3
+
+In LAMMS, "chunks" are collections of atoms, as defined by the
+"compute chunk/atom"_compute_chunk_atom.html command, which assigns
+each atom to a chunk ID (or to no chunk at all). The number of chunks
+and the assignment of chunk IDs to atoms can be static or change over
+time. Examples of "chunks" are molecules or spatial bins or atoms
+with similar values (e.g. coordination number or potential energy).
+
+The per-atom chunk IDs can be used as input to two other kinds of
+commands, to calculate various properties of a system:
+
+"fix ave/chunk"_fix_ave_chunk.html
+any of the "compute */chunk"_compute.html commands :ul
+
+Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed. Then some examples are given of how to compute different
+properties with chunk commands.
+
+Compute chunk/atom command: :h4
+
+This compute can assign atoms to chunks of various styles. Only atoms
+in the specified group and optional specified region are assigned to a
+chunk. Here are some possible chunk definitions:
+
+atoms in same molecule | chunk ID = molecule ID |
+atoms of same atom type | chunk ID = atom type |
+all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
+atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
+atoms in same spatial bin | chunk ID = bin ID |
+atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
+atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
+atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
+
+Note that chunk IDs are integer values, so for atom properties or
+computes that produce a floating point value, they will be truncated
+to an integer. You could also use the compute in a variable that
+scales the floating point value to spread it across multiple integers.
+
+Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+
+This compute also calculates the number of chunks {Nchunk}, which is
+used by other commands to tally per-chunk data. {Nchunk} can be a
+static value or change over time (e.g. the number of clusters). The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+
+Note that this compute allows the per-atom output of other
+"computes"_compute.html, "fixes"_fix.html, and
+"variables"_variable.html to be used to define chunk IDs for each
+atom. This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
+doc pages for info on how to do this. You can also define a "per-atom
+variable"_variable.html in the input script that uses a formula to
+generate a chunk ID for each atom.
+
+Fix ave/chunk command: :h4
+
+This fix takes the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
+it then sums one or more specified per-atom values over the atoms in
+each chunk. The per-atom values can be any atom property, such as
+velocity, force, charge, potential energy, kinetic energy, stress,
+etc. Additional keywords are defined for per-chunk properties like
+density and temperature. More generally any per-atom value generated
+by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
+variables"_variable.html, can be summed over atoms in each chunk.
+
+Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file. The
+fix produces a global array as output with one row of values per
+chunk.
+
+Compute */chunk commands: :h4
+
+Currently the following computes operate on chunks of atoms to produce
+per-chunk values.
+
+"compute com/chunk"_compute_com_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html
+"compute inertia/chunk"_compute_inertia_chunk.html
+"compute msd/chunk"_compute_msd_chunk.html
+"compute property/chunk"_compute_property_chunk.html
+"compute temp/chunk"_compute_temp_chunk.html
+"compute torque/chunk"_compute_vcm_chunk.html
+"compute vcm/chunk"_compute_vcm_chunk.html :ul
+
+They each take the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input. As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, temperature, torque,
+and velocity of center-of-mass for each chunk of atoms. The "compute
+property/chunk"_compute_property_chunk.html command can tally the
+count of atoms in each chunk and extract other per-chunk properties.
+
+The reason these various calculations are not part of the "fix
+ave/chunk command"_fix_ave_chunk.html, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk. For example, many of them require calculation
+of a center of mass, which requires summing mass*position over the
+atoms and then dividing by summed mass.
+
+All of these computes produce a global vector or global array as
+output, wih one or more values per chunk. They can be used
+in various ways:
+
+As input to the "fix ave/time"_fix_ave_time.html command, which can
+write the values to a file and optionally time average them. :ulb,l
+
+As input to the "fix ave/histo"_fix_ave_histo.html command to
+histogram values across chunks. E.g. a histogram of cluster sizes or
+molecule diffusion rates. :l
+
+As input to special functions of "equal-style
+variables"_variable.html, like sum() and max(). E.g. to find the
+largest cluster or fastest diffusing molecule. :l
+:ule
+
+Example calculations with chunks :h4
+
+Here are examples using chunk commands to calculate various
+properties:
+
+(1) Average velocity in each of 1000 2d spatial bins:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
+fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
+
+(2) Temperature in each spatial bin, after subtracting a flow
+velocity:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
+compute vbias all temp/profile 1 0 0 y 10
+fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
+
+(3) Center of mass of each molecule:
+
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
+
+(4) Total force on each molecule and ave/max across all molecules:
+
+compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1\[2\])
+variable xmax equal max(f_1\[2\])
+thermo 1000
+thermo_style custom step temp v_xave v_xmax :pre
+
+(5) Histogram of cluster sizes:
+
+compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt
new file mode 100644
index 0000000000..4f1cd64384
--- /dev/null
+++ b/doc/src/Howto_coreshell.txt
@@ -0,0 +1,253 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Adiabatic core/shell model :h3
+
+The adiabatic core-shell model by "Mitchell and
+Fincham"_#MitchellFincham is a simple method for adding polarizability
+to a system. In order to mimic the electron shell of an ion, a
+satellite particle is attached to it. This way the ions are split into
+a core and a shell where the latter is meant to react to the
+electrostatic environment inducing polarizability. See the "Howto
+polarizable"_Howto_polarizable.html doc page for a discussion of all
+the polarizable models available in LAMMPS.
+
+Technically, shells are attached to the cores by a spring force f =
+k*r where k is a parametrized spring constant and r is the distance
+between the core and the shell. The charges of the core and the shell
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
+similar fashion the mass of the ion is distributed on the core and the
+shell with the core having the larger mass.
+
+To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
+be used since atom charge and bonds are needed. Each kind of
+core/shell pair requires two atom types and a bond type. The core and
+shell of a core/shell pair should be bonded to each other with a
+harmonic bond that provides the spring force. For example, a data file
+for NaCl, as found in examples/coreshell, has this format:
+
+432 atoms # core and shell atoms
+216 bonds # number of core/shell springs :pre
+
+4 atom types # 2 cores and 2 shells for Na and Cl
+2 bond types :pre
+
+0.0 24.09597 xlo xhi
+0.0 24.09597 ylo yhi
+0.0 24.09597 zlo zhi :pre
+
+Masses # core/shell mass ratio = 0.1 :pre
+
+1 20.690784 # Na core
+2 31.90500 # Cl core
+3 2.298976 # Na shell
+4 3.54500 # Cl shell :pre
+
+Atoms :pre
+
+1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
+2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
+3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
+4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
+(...) :pre
+
+Bonds # Bond topology for spring forces :pre
+
+1 2 1 2 # spring for core/shell pair 1
+2 2 3 4 # spring for core/shell pair 2
+(...) :pre
+
+Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
+defined between the shells. Coulombic interactions are defined
+between all cores and shells. If desired, additional bonds can be
+specified between cores.
+
+The "special_bonds"_special_bonds.html command should be used to
+turn-off the Coulombic interaction within core/shell pairs, since that
+interaction is set by the bond spring. This is done using the
+"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
+which is the default value. It needs to be considered whether one has
+to adjust the "special_bonds"_special_bonds.html weighting according
+to the molecular topology since the interactions of the shells are
+bypassed over an extra bond.
+
+Note that this core/shell implementation does not require all ions to
+be polarized. One can mix core/shell pairs and ions without a
+satellite particle if desired.
+
+Since the core/shell model permits distances of r = 0.0 between the
+core and shell, a pair style with a "cs" suffix needs to be used to
+implement a valid long-range Coulombic correction. Several such pair
+styles are provided in the CORESHELL package. See "this doc
+page"_pair_cs.html for details. All of the core/shell enabled pair
+styles require the use of a long-range Coulombic solver, as specified
+by the "kspace_style"_kspace_style.html command. Either the PPPM or
+Ewald solvers can be used.
+
+For the NaCL example problem, these pair style and bond style settings
+are used:
+
+pair_style born/coul/long/cs 20.0 20.0
+pair_coeff * * 0.0 1.000 0.00 0.00 0.00
+pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
+pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
+pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0 :pre
+
+When running dynamics with the adiabatic core/shell model, the
+following issues should be considered. The relative motion of
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation.
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
+the core/shell pair, which is an imaginary degree of freedom, from the
+real physical system. To do that, the "compute
+temp/cs"_compute_temp_cs.html command can be used, in conjunction with
+any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
+langevin"_fix_langevin. This compute uses the center-of-mass velocity
+of the core/shell pairs to calculate a temperature, and insures that
+velocity is what is rescaled for thermostatting purposes. This
+compute also works for a system with both core/shell pairs and
+non-polarized ions (ions without an attached satellite particle). The
+"compute temp/cs"_compute_temp_cs.html command requires input of two
+groups, one for the core atoms, another for the shell atoms.
+Non-polarized ions which might also be included in the treated system
+should not be included into either of these groups, they are taken
+into account by the {group-ID} (2nd argument) of the compute. The
+groups can be defined using the "group {type}"_group.html command.
+Note that to perform thermostatting using this definition of
+temperature, the "fix modify temp"_fix_modify.html command should be
+used to assign the compute to the thermostat fix. Likewise the
+"thermo_modify temp"_thermo_modify.html command can be used to make
+this temperature be output for the overall system.
+
+For the NaCl example, this can be done as follows:
+
+group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
+fix thermostatequ all nve # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
+
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
+
+If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable. However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recommendable to use the "fix
+momentum"_fix_momentum.html command in combination with "compute
+temp/cs"_compute_temp_cs.html when equilibrating the system to
+prevent any drift.
+
+When initializing the velocities of a system with core/shell pairs, it
+is also desirable to not introduce energy into the relative motion of
+the core/shell particles, but only assign a center-of-mass velocity to
+the pairs. This can be done by using the {bias} keyword of the
+"velocity create"_velocity.html command and assigning the "compute
+temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
+"velocity"_velocity.html command, e.g.
+
+velocity all create 1427 134 bias yes temp CSequ
+velocity all scale 1427 temp CSequ :pre
+
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
+
+The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment.
+The mentioned energy transfer will typically lead to a small drift
+in total energy over time. This internal energy can be monitored
+using the "compute chunk/atom"_compute_chunk_atom.html and "compute
+temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
+energies of each core/shell pair can then be summed using the sum()
+special function of the "variable"_variable.html command. Or they can
+be time/averaged and output using the "fix ave/time"_fix_ave_time.html
+command. To use these commands, each core/shell pair must be defined
+as a "chunk". If each core/shell pair is defined as its own molecule,
+the molecule ID can be used to define the chunks. If cores are bonded
+to each other to form larger molecules, the chunks can be identified
+by the "fix property/atom"_fix_property_atom.html via assigning a
+core/shell ID to each atom using a special field in the data file read
+by the "read_data"_read_data.html command. This field can then be
+accessed by the "compute property/atom"_compute_property_atom.html
+command, to use as input to the "compute
+chunk/atom"_compute_chunk_atom.html command to define the core/shell
+pairs as chunks.
+
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:
+
+fix csinfo all property/atom i_CSID # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
+compute prop all property/atom i_CSID
+(...) :pre
+
+The additional section in the date file would be formatted like this:
+
+CS-Info # header of additional section :pre
+
+1 1 # column 1 = atom ID, column 2 = core/shell ID
+2 1
+3 2
+4 2
+5 3
+6 3
+7 4
+8 4
+(...) :pre
+
+:line
+
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
new file mode 100644
index 0000000000..38595a9d16
--- /dev/null
+++ b/doc/src/Howto_couple.txt
@@ -0,0 +1,105 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Coupling LAMMPS to other codes :h3
+
+LAMMPS is designed to allow it to be coupled to other codes. For
+example, a quantum mechanics code might compute forces on a subset of
+atoms and pass those forces to LAMMPS. Or a continuum finite element
+(FE) simulation might use atom positions as boundary conditions on FE
+nodal points, compute a FE solution, and return interpolated forces on
+MD atoms.
+
+LAMMPS can be coupled to other codes in at least 3 ways. Each has
+advantages and disadvantages, which you'll have to think about in the
+context of your application.
+
+(1) Define a new "fix"_fix.html command that calls the other code. In
+this scenario, LAMMPS is the driver code. During its timestepping,
+the fix is invoked, and can make library calls to the other code,
+which has been linked to LAMMPS as a library. This is the way the
+"POEMS"_poems package that performs constrained rigid-body motion on
+groups of atoms is hooked to LAMMPS. See the "fix
+poems"_fix_poems.html command for more details. See the
+"Modify"_Modify.html doc pages for info on how to add a new fix to
+LAMMPS.
+
+:link(poems,http://www.rpi.edu/~anderk5/lab)
+
+(2) Define a new LAMMPS command that calls the other code. This is
+conceptually similar to method (1), but in this case LAMMPS and the
+other code are on a more equal footing. Note that now the other code
+is not called during the timestepping of a LAMMPS run, but between
+runs. The LAMMPS input script can be used to alternate LAMMPS runs
+with calls to the other code, invoked via the new command. The
+"run"_run.html command facilitates this with its {every} option, which
+makes it easy to run a few steps, invoke the command, run a few steps,
+invoke the command, etc.
+
+In this scenario, the other code can be called as a library, as in
+(1), or it could be a stand-alone code, invoked by a system() call
+made by the command (assuming your parallel machine allows one or more
+processors to start up another program). In the latter case the
+stand-alone code could communicate with LAMMPS thru files that the
+command writes and reads.
+
+See the "Modify command"_Modify_command.html doc page for info on how
+to add a new command to LAMMPS.
+
+(3) Use LAMMPS as a library called by another code. In this case the
+other code is the driver and calls LAMMPS as needed. Or a wrapper
+code could link and call both LAMMPS and another code as libraries.
+Again, the "run"_run.html command has options that allow it to be
+invoked with minimal overhead (no setup or clean-up) if you wish to do
+multiple short runs, driven by another program.
+
+Examples of driver codes that call LAMMPS as a library are included in
+the examples/COUPLE directory of the LAMMPS distribution; see
+examples/COUPLE/README for more details:
+
+simple: simple driver programs in C++ and C which invoke LAMMPS as a
+library :ulb,l
+
+lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
+MD with quantum forces calculated by a density functional code :l
+
+lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
+a kinetic Monte Carlo model for grain growth using MD to calculate
+strain induced across grain boundaries :l
+:ule
+
+:link(quest,http://dft.sandia.gov/Quest)
+:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
+
+"This section"_Section_start.html#start_5 of the documentation
+describes how to build LAMMPS as a library. Once this is done, you
+can interface with LAMMPS either via C++, C, Fortran, or Python (or
+any other language that supports a vanilla C-like interface). For
+example, from C++ you could create one (or more) "instances" of
+LAMMPS, pass it an input script to process, or execute individual
+commands, all by invoking the correct class methods in LAMMPS. From C
+or Fortran you can make function calls to do the same things. See the
+"Python"_Python.html doc pages for a description of the Python wrapper
+provided with LAMMPS that operates through the LAMMPS library
+interface.
+
+The files src/library.cpp and library.h contain the C-style interface
+to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
+description of the interface and how to extend it for your needs.
+
+Note that the lammps_open() function that creates an instance of
+LAMMPS takes an MPI communicator as an argument. This means that
+instance of LAMMPS will run on the set of processors in the
+communicator. Thus the calling code can run LAMMPS on all or a subset
+of processors. For example, a wrapper script might decide to
+alternate between LAMMPS and another code, allowing them both to run
+on all the processors. Or it might allocate half the processors to
+LAMMPS and half to the other code and run both codes simultaneously
+before syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt
new file mode 100644
index 0000000000..401c1e359c
--- /dev/null
+++ b/doc/src/Howto_diffusion.txt
@@ -0,0 +1,31 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate a diffusion coefficient :h3
+
+The diffusion coefficient D of a material can be measured in at least
+2 ways using various options in LAMMPS. See the examples/DIFFUSE
+directory for scripts that implement the 2 methods discussed here for
+a simple Lennard-Jones fluid model.
+
+The first method is to measure the mean-squared displacement (MSD) of
+the system, via the "compute msd"_compute_msd.html command. The slope
+of the MSD versus time is proportional to the diffusion coefficient.
+The instantaneous MSD values can be accumulated in a vector via the
+"fix vector"_fix_vector.html command, and a line fit to the vector to
+compute its slope via the "variable slope"_variable.html function, and
+thus extract D.
+
+The second method is to measure the velocity auto-correlation function
+(VACF) of the system, via the "compute vacf"_compute_vacf.html
+command. The time-integral of the VACF is proportional to the
+diffusion coefficient. The instantaneous VACF values can be
+accumulated in a vector via the "fix vector"_fix_vector.html command,
+and time integrated via the "variable trap"_variable.html function,
+and thus extract D.
diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt
new file mode 100644
index 0000000000..4ea286258e
--- /dev/null
+++ b/doc/src/Howto_dispersion.txt
@@ -0,0 +1,108 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Long-raage dispersion settings :h3
+
+The PPPM method computes interactions by splitting the pair potential
+into two parts, one of which is computed in a normal pairwise fashion,
+the so-called real-space part, and one of which is computed using the
+Fourier transform, the so called reciprocal-space or kspace part. For
+both parts, the potential is not computed exactly but is approximated.
+Thus, there is an error in both parts of the computation, the
+real-space and the kspace error. The just mentioned facts are true
+both for the PPPM for Coulomb as well as dispersion interactions. The
+deciding difference - and also the reason why the parameters for
+pppm/disp have to be selected with more care - is the impact of the
+errors on the results: The kspace error of the PPPM for Coulomb and
+dispersion interaction and the real-space error of the PPPM for
+Coulomb interaction have the character of noise. In contrast, the
+real-space error of the PPPM for dispersion has a clear physical
+interpretation: the underprediction of cohesion. As a consequence, the
+real-space error has a much stronger effect than the kspace error on
+simulation results for pppm/disp. Parameters must thus be chosen in a
+way that this error is much smaller than the kspace error.
+
+When using pppm/disp and not making any specifications on the PPPM
+parameters via the kspace modify command, parameters will be tuned
+such that the real-space error and the kspace error are equal. This
+will result in simulations that are either inaccurate or slow, both of
+which is not desirable. For selecting parameters for the pppm/disp
+that provide fast and accurate simulations, there are two approaches,
+which both have their up- and downsides.
+
+The first approach is to set desired real-space an kspace accuracies
+via the {kspace_modify force/disp/real} and {kspace_modify
+force/disp/kspace} commands. Note that the accuracies have to be
+specified in force units and are thus dependent on the chosen unit
+settings. For real units, 0.0001 and 0.002 seem to provide reasonable
+accurate and efficient computations for the real-space and kspace
+accuracies. 0.002 and 0.05 work well for most systems using lj
+units. PPPM parameters will be generated based on the desired
+accuracies. The upside of this approach is that it usually provides a
+good set of parameters and will work for both the {kspace_modify diff
+ad} and {kspace_modify diff ik} options. The downside of the method
+is that setting the PPPM parameters will take some time during the
+initialization of the simulation.
+
+The second approach is to set the parameters for the pppm/disp
+explicitly using the {kspace_modify mesh/disp}, {kspace_modify
+order/disp}, and {kspace_modify gewald/disp} commands. This approach
+requires a more experienced user who understands well the impact of
+the choice of parameters on the simulation accuracy and
+performance. This approach provides a fast initialization of the
+simulation. However, it is sensitive to errors: A combination of
+parameters that will perform well for one system might result in
+far-from-optimal conditions for other simulations. For example,
+parameters that provide accurate and fast computations for
+all-atomistic force fields can provide insufficient accuracy or
+united-atomistic force fields (which is related to that the latter
+typically have larger dispersion coefficients).
+
+To avoid inaccurate or inefficient simulations, the pppm/disp stops
+simulations with an error message if no action is taken to control the
+PPPM parameters. If the automatic parameter generation is desired and
+real-space and kspace accuracies are desired to be equal, this error
+message can be suppressed using the {kspace_modify disp/auto yes}
+command.
+
+A reasonable approach that combines the upsides of both methods is to
+make the first run using the {kspace_modify force/disp/real} and
+{kspace_modify force/disp/kspace} commands, write down the PPPM
+parameters from the outut, and specify these parameters using the
+second approach in subsequent runs (which have the same composition,
+force field, and approximately the same volume).
+
+Concerning the performance of the pppm/disp there are two more things
+to consider. The first is that when using the pppm/disp, the cutoff
+parameter does no longer affect the accuracy of the simulation
+(subject to that gewald/disp is adjusted when changing the cutoff).
+The performance can thus be increased by examining different values
+for the cutoff parameter. A lower bound for the cutoff is only set by
+the truncation error of the repulsive term of pair potentials.
+
+The second is that the mixing rule of the pair style has an impact on
+the computation time when using the pppm/disp. Fastest computations
+are achieved when using the geometric mixing rule. Using the
+arithmetic mixing rule substantially increases the computational cost.
+The computational overhead can be reduced using the {kspace_modify
+mix/disp geom} and {kspace_modify splittol} commands. The first
+command simply enforces geometric mixing of the dispersion
+coefficients in kspace computations. This introduces some error in
+the computations but will also significantly speed-up the
+simulations. The second keyword sets the accuracy with which the
+dispersion coefficients are approximated using a matrix factorization
+approach. This may result in better accuracy then using the first
+command, but will usually also not provide an equally good increase of
+efficiency.
+
+Finally, pppm/disp can also be used when no mixing rules apply.
+This can be achieved using the {kspace_modify mix/disp none} command.
+Note that the code does not check automatically whether any mixing
+rule is fulfilled. If mixing rules do not apply, the user will have
+to specify this command explicitly.
diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt
new file mode 100644
index 0000000000..ebdf5f8658
--- /dev/null
+++ b/doc/src/Howto_drude.txt
@@ -0,0 +1,77 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Drude induced dipoles :h3
+
+The thermalized Drude model represents induced dipoles by a pair of
+charges (the core atom and the Drude particle) connected by a harmonic
+spring. See the "Howto polarizable"_Howto_polarizable.html doc page
+for a discussion of all the polarizable models available in LAMMPS.
+
+The Drude model has a number of features aimed at its use in
+molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
+
+Thermostating of the additional degrees of freedom associated with the
+induced dipoles at very low temperature, in terms of the reduced
+coordinates of the Drude particles with respect to their cores. This
+makes the trajectory close to that of relaxed induced dipoles. :ulb,l
+
+Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
+pair represents a single (polarizable) atom, so the special screening
+factors in a covalent structure should be the same for the core and
+the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
+special neighbor relations from their respective cores. :l
+
+Stabilization of the interactions between induced dipoles. Drude
+dipoles on covalently bonded atoms interact too strongly due to the
+short distances, so an atom may capture the Drude particle of a
+neighbor, or the induced dipoles within the same molecule may align
+too much. To avoid this, damping at short range can be done by Thole
+functions (for which there are physical grounds). This Thole damping
+is applied to the point charges composing the induced dipole (the
+charge of the Drude particle and the opposite charge on the core, not
+to the total charge of the core atom). :l,ule
+
+A detailed tutorial covering the usage of Drude induced dipoles in
+LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page.
+
+As with the core-shell model, the cores and Drude particles should
+appear in the data file as standard atoms. The same holds for the
+springs between them, which are described by standard harmonic bonds.
+The nature of the atoms (core, Drude particle or non-polarizable) is
+specified via the "fix drude"_fix_drude.html command. The special
+list of neighbors is automatically refactored to account for the
+equivalence of core and Drude particles as regards special 1-2 to 1-4
+screening. It may be necessary to use the {extra/special/per/atom}
+keyword of the "read_data"_read_data.html command. If using "fix
+shake"_fix_shake.html, make sure no Drude particle is in this fix
+group.
+
+There are two ways to thermostat the Drude particles at a low
+temperature: use either "fix langevin/drude"_fix_langevin_drude.html
+for a Langevin thermostat, or "fix
+drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
+thermostat. The former requires use of the command "comm_modify vel
+yes"_comm_modify.html. The latter requires two separate integration
+fixes like {nvt} or {npt}. The correct temperatures of the reduced
+degrees of freedom can be calculated using the "compute
+temp/drude"_compute_temp_drude.html. This requires also to use the
+command {comm_modify vel yes}.
+
+Short-range damping of the induced dipole interactions can be achieved
+using Thole functions through the "pair style
+thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
+with a Coulomb pair style. It may be useful to use {coul/long/cs} or
+similar from the CORESHELL package if the core and Drude particle come
+too close, which can cause numerical issues.
+
+:line
+
+:link(howto-Lamoureux)
+[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
diff --git a/doc/src/tutorial_drude.txt b/doc/src/Howto_drude2.txt
similarity index 99%
rename from doc/src/tutorial_drude.txt
rename to doc/src/Howto_drude2.txt
index f6e7eed40b..a342d4a87d 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/Howto_drude2.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt
new file mode 100644
index 0000000000..68b30970ca
--- /dev/null
+++ b/doc/src/Howto_elastic.txt
@@ -0,0 +1,47 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate elastic constants :h3
+
+Elastic constants characterize the stiffness of a material. The formal
+definition is provided by the linear relation that holds between the
+stress and strain tensors in the limit of infinitesimal deformation.
+In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
+the repeated indices imply summation. s_ij are the elements of the
+symmetric stress tensor. e_kl are the elements of the symmetric strain
+tensor. C_ijkl are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has 3^4=81 elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
+is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
+derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
+most 7*6/2 = 21 distinct elements.
+
+At zero temperature, it is easy to estimate these derivatives by
+deforming the simulation box in one of the six directions using the
+"change_box"_change_box.html command and measuring the change in the
+stress tensor. A general-purpose script that does this is given in the
+examples/elastic directory described on the "Examples"_Examples.html
+doc page.
+
+Calculating elastic constants at finite temperature is more
+challenging, because it is necessary to run a simulation that perfoms
+time averages of differential properties. One way to do this is to
+measure the change in average stress tensor in an NVT simulations when
+the cell volume undergoes a finite deformation. In order to balance
+the systematic and statistical errors in this method, the magnitude of
+the deformation must be chosen judiciously, and care must be taken to
+fully equilibrate the deformed cell before sampling the stress
+tensor. Another approach is to sample the triclinic cell fluctuations
+that occur in an NPT simulation. This method can also be slow to
+converge and requires careful post-processing "(Shinoda)"_#Shinoda1
+
+:line
+
+:link(Shinoda1)
+[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
diff --git a/doc/src/tutorial_github.txt b/doc/src/Howto_github.txt
similarity index 98%
rename from doc/src/tutorial_github.txt
rename to doc/src/Howto_github.txt
index fc261bdb95..720b3317f0 100644
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/Howto_github.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,8 +25,8 @@ or improvements to LAMMPS, as it significantly reduces the amount of
work required by the LAMMPS developers. Consequently, creating a pull
request will increase your chances to have your contribution included
and will reduce the time until the integration is complete. For more
-information on the requirements to have your code included in LAMMPS,
-see the "Modify contribute"_Modify_contribute.html doc page.
+information on the requirements to have your code included into LAMMPS
+please see the "Modify contribute"_Modify_contribute.html doc page.
:line
@@ -124,7 +124,7 @@ unrelated feature, you should switch branches!
After everything is done, add the files to the branch and commit them:
- $ git add doc/src/tutorial_github.txt
+ $ git add doc/src/Howto_github.txt
$ git add doc/src/JPG/tutorial*.png :pre
IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a
@@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on
Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel's change back into our branch, and merge them:
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request*.png
$ git commit -m "Updated text and images on reverse pull requests"
$ git pull :pre
@@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request6.png
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps :pre
diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt
new file mode 100644
index 0000000000..8027369501
--- /dev/null
+++ b/doc/src/Howto_granular.txt
@@ -0,0 +1,57 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Granular models :h3
+
+Granular system are composed of spherical particles with a diameter,
+as opposed to point particles. This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+
+To run a simulation of a granular model, you will want to use
+the following commands:
+
+"atom_style sphere"_atom_style.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix gravity"_fix_gravity.html :ul
+
+This compute
+
+"compute erotate/sphere"_compute_erotate_sphere.html :ul
+
+calculates rotational kinetic energy which can be "output with
+thermodynamic info"_Howto_output.html.
+
+Use one of these 3 pair potentials, which compute forces and torques
+between interacting pairs of particles:
+
+"pair_style"_pair_style.html gran/history
+"pair_style"_pair_style.html gran/no_history
+"pair_style"_pair_style.html gran/hertzian :ul
+
+These commands implement fix options specific to granular systems:
+
+"fix freeze"_fix_freeze.html
+"fix pour"_fix_pour.html
+"fix viscous"_fix_viscous.html
+"fix wall/gran"_fix_wall_gran.html :ul
+
+The fix style {freeze} zeroes both the force and torque of frozen
+atoms, and should be used for granular system instead of the fix style
+{setforce}.
+
+For computational efficiency, you can eliminate needless pairwise
+computations between frozen atoms by using this command:
+
+"neigh_modify"_neigh_modify.html exclude :ul
+
+NOTE: By default, for 2d systems, granular particles are still modeled
+as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+will be the same as in 3d. If you wish to model granular particles in
+2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d
+doc page, where 2d simulations are discussed.
diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt
new file mode 100644
index 0000000000..b2a57ef49b
--- /dev/null
+++ b/doc/src/Howto_kappa.txt
@@ -0,0 +1,90 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate thermal conductivity :h3
+
+The thermal conductivity kappa of a material can be measured in at
+least 4 ways using various options in LAMMPS. See the examples/KAPPA
+directory for scripts that implement the 4 methods discussed here for
+a simple Lennard-Jones fluid model. Also, see the "Howto
+viscosity"_Howto_viscosity.html doc page for an analogous discussion
+for viscosity.
+
+The thermal conductivity tensor kappa is a measure of the propensity
+of a material to transmit heat energy in a diffusive manner as given
+by Fourier's law
+
+J = -kappa grad(T)
+
+where J is the heat flux in units of energy per area per time and
+grad(T) is the spatial gradient of temperature. The thermal
+conductivity thus has units of energy per distance per time per degree
+K and is often approximated as an isotropic quantity, i.e. as a
+scalar.
+
+The first method is to setup two thermostatted regions at opposite
+ends of a simulation box, or one in the middle and one at the end of a
+periodic box. By holding the two regions at different temperatures
+with a "thermostatting fix"_Howto_thermostat.html, the energy added to
+the hot region should equal the energy subtracted from the cold region
+and be proportional to the heat flux moving between the regions. See
+the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and
+"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note
+that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
+langevin"_fix_langevin.html, and "fix
+temp/rescale"_fix_temp_rescale.html store the cumulative energy they
+add/subtract.
+
+Alternatively, as a second method, the "fix heat"_fix_heat.html or
+"fix ehex"_fix_ehex.html commands can be used in place of thermostats
+on each of two regions to add/subtract specified amounts of energy to
+both regions. In both cases, the resulting temperatures of the two
+regions can be monitored with the "compute temp/region" command and
+the temperature profile of the intermediate region can be monitored
+with the "fix ave/chunk"_fix_ave_chunk.html and "compute
+ke/atom"_compute_ke_atom.html commands.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the "fix thermal/conductivity"_fix_thermal_conductivity.html
+command which implements the rNEMD algorithm of Muller-Plathe.
+Kinetic energy is swapped between atoms in two different layers of the
+simulation box. This induces a temperature gradient between the two
+layers which can be monitored with the "fix
+ave/chunk"_fix_ave_chunk.html and "compute
+ke/atom"_compute_ke_atom.html commands. The fix tallies the
+cumulative energy transfer that it performs. See the "fix
+thermal/conductivity"_fix_thermal_conductivity.html command for
+details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the heat flux
+to kappa. The heat flux can be calculated from the fluctuations of
+per-atom potential and kinetic energies and per-atom stress tensor in
+a steady-state equilibrated simulation. This is in contrast to the
+two preceding non-equilibrium methods, where energy flows continuously
+between hot and cold regions of the simulation box.
+
+The "compute heat/flux"_compute_heat_flux.html command can calculate
+the needed heat flux and describes how to implement the Green_Kubo
+formalism using additional LAMMPS commands, such as the "fix
+ave/correlate"_fix_ave_correlate.html command to calculate the needed
+auto-correlation. See the doc page for the "compute
+heat/flux"_compute_heat_flux.html command for an example input script
+that calculates the thermal conductivity of solid Ar via the GK
+formalism.
+
+:line
+
+:link(howto-Ikeshoji)
+[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
+(1994).
+
+:link(howto-Wirnsberger)
+[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
+(2015).
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
new file mode 100644
index 0000000000..0d4852fbf2
--- /dev/null
+++ b/doc/src/Howto_library.txt
@@ -0,0 +1,208 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Library interface to LAMMPS :h3
+
+As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
+be built as a library, so that it can be called by another code, used
+in a "coupled manner"_Howto_couple.html with other codes, or driven
+through a "Python interface"_Python.html.
+
+All of these methodologies use a C-style interface to LAMMPS that is
+provided in the files src/library.cpp and src/library.h. The
+functions therein have a C-style argument list, but contain C++ code
+you could write yourself in a C++ application that was invoking LAMMPS
+directly. The C++ code in the functions illustrates how to invoke
+internal LAMMPS operations. Note that LAMMPS classes are defined
+within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
+application.
+
+The examples/COUPLE and python/examples directories have example C++
+and C and Python codes which show how a driver code can link to LAMMPS
+as a library, run LAMMPS on a subset of processors, grab data from
+LAMMPS, change it, and put it back into LAMMPS.
+
+The file src/library.cpp contains the following functions for creating
+and destroying an instance of LAMMPS and sending it commands to
+execute. See the documentation in the src/library.cpp file for
+details.
+
+NOTE: You can write code for additional functions as needed to define
+how your code talks to LAMMPS and add them to src/library.cpp and
+src/library.h, as well as to the "Python interface"_Python.html. The
+added functions can access or change any internal LAMMPS data you
+wish.
+
+void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
+void lammps_close(void *)
+int lammps_version(void *)
+void lammps_file(void *, char *)
+char *lammps_command(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
+void lammps_free(void *) :pre
+
+The lammps_open() function is used to initialize LAMMPS, passing in a
+list of strings as if they were "command-line
+arguments"_Section_start.html#start_6 when LAMMPS is run in
+stand-alone mode from the command line, and a MPI communicator for
+LAMMPS to run under. It returns a ptr to the LAMMPS object that is
+created, and which is used in subsequent library calls. The
+lammps_open() function can be called multiple times, to create
+multiple instances of LAMMPS.
+
+LAMMPS will run on the set of processors in the communicator. This
+means the calling code can run LAMMPS on all or a subset of
+processors. For example, a wrapper script might decide to alternate
+between LAMMPS and another code, allowing them both to run on all the
+processors. Or it might allocate half the processors to LAMMPS and
+half to the other code and run both codes simultaneously before
+syncing them up periodically. Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.
+
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller. Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialized if necessary.
+
+The lammps_close() function is used to shut down an instance of LAMMPS
+and free all its memory.
+
+The lammps_version() function can be used to determined the specific
+version of the underlying LAMMPS code. This is particularly useful
+when loading LAMMPS as a shared library via dlopen(). The code using
+the library interface can than use this information to adapt to
+changes to the LAMMPS command syntax between versions. The returned
+LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
+20150902) that grows with every new LAMMPS version.
+
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
+
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages. The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps_file() function passes the filename of an input script.
+The lammps_command() function passes a single command as a string.
+The lammps_commands_list() function passes multiple commands in a
+char** list. In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline. The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls. See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+The file src/library.cpp also contains these functions for extracting
+information from LAMMPS and setting value within LAMMPS. Again, see
+the documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
+
+int lammps_extract_setting(void *, char *)
+void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *,
+ double *, double *, double *, int *, int *)
+void *lammps_extract_atom(void *, char *)
+void *lammps_extract_compute(void *, char *, int, int)
+void *lammps_extract_fix(void *, char *, int, int, int, int)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
+The extract_setting() function returns info on the size
+of data types (e.g. 32-bit or 64-bit atom IDs) used
+by the LAMMPS executable (a compile-time choice).
+
+The other extract functions return a pointer to various global or
+per-atom quantities stored in LAMMPS or to values calculated by a
+compute, fix, or variable. The pointer returned by the
+extract_global() function can be used as a permanent reference to a
+value which may change. For the extract_atom() method, see the
+extract() method in the src/atom.cpp file for a list of valid per-atom
+properties. New names could easily be added if the property you want
+is not listed. For the other extract functions, the underlying
+storage may be reallocated as LAMMPS runs, so you need to re-call the
+function to assure a current pointer or returned value(s).
+
+double lammps_get_thermo(void *, char *)
+int lammps_get_natoms(void *) :pre
+
+int lammps_set_variable(void *, char *, char *)
+void lammps_reset_box(void *, double *, double *, double, double, double) :pre
+
+The lammps_get_thermo() function returns the current value of a thermo
+keyword as a double precision value.
+
+The lammps_get_natoms() function returns the total number of atoms in
+the system and can be used by the caller to allocate memory for the
+lammps_gather_atoms() and lammps_scatter_atoms() functions.
+
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.
+
+The lammps_reset_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
+void lammps_gather_atoms(void *, char *, int, int, void *)
+void lammps_gather_atoms_concat(void *, char *, int, int, void *)
+void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
+void lammps_scatter_atoms(void *, char *, int, int, void *)
+void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
+
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+ imageint *, int) :pre
+
+The gather functions collect peratom info of the requested type (atom
+coords, atom types, forces, etc) from all processors, and returns the
+same vector of values to each callling processor. The scatter
+functions do the inverse. They distribute a vector of peratom values,
+passed by all calling processors, to invididual atoms, which may be
+owned by different processos.
+
+The lammps_gather_atoms() function does this for all N atoms in the
+system, ordered by atom ID, from 1 to N. The
+lammps_gather_atoms_concat() function does it for all N atoms, but
+simply concatenates the subset of atoms owned by each processor. The
+resulting vector is not ordered by atom ID. Atom IDs can be requetsed
+by the same function if the caller needs to know the ordering. The
+lammps_gather_subset() function allows the caller to request values
+for only a subset of atoms (identified by ID).
+For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
+If the count is specified as 1, they are returned
+in a packed format with all three image flags stored in a single integer.
+If the count is specified as 3, the values are unpacked into xyz flags
+by the library before returning them.
+
+The lammps_scatter_atoms() function takes a list of values for all N
+atoms in the system, ordered by atom ID, from 1 to N, and assigns
+those values to each atom in the system. The
+lammps_scatter_atoms_subset() function takes a subset of IDs as an
+argument and only scatters those values to the owning atoms.
+
+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities and image flags. It uses the coords of each atom to assign
+it as a new atom to the processor that owns it. This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation. Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.
diff --git a/doc/src/manifolds.txt b/doc/src/Howto_manifold.txt
similarity index 97%
rename from doc/src/manifolds.txt
rename to doc/src/Howto_manifold.txt
index 1013d8fab6..09a936f7d3 100644
--- a/doc/src/manifolds.txt
+++ b/doc/src/Howto_manifold.txt
@@ -2,11 +2,11 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-Manifolds (surfaces) :h2
+Manifolds (surfaces) :h3
[Overview:]
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
new file mode 100644
index 0000000000..edcb8196cf
--- /dev/null
+++ b/doc/src/Howto_multiple.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Run multiple simulations from one input script :h3
+
+This can be done in several ways. See the documentation for
+individual commands for more details on how these examples work.
+
+If "multiple simulations" means continue a previous simulation for
+more timesteps, then you simply use the "run"_run.html command
+multiple times. For example, this script
+
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+run 10000
+run 10000
+run 10000
+run 10000 :pre
+
+would run 5 successive simulations of the same system for a total of
+50,000 timesteps.
+
+If you wish to run totally different simulations, one after the other,
+the "clear"_clear.html command can be used in between them to
+re-initialize LAMMPS. For example, this script
+
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+clear
+units lj
+atom_style atomic
+read_data data.lj.new
+run 10000 :pre
+
+would run 2 independent simulations, one after the other.
+
+For large numbers of independent simulations, you can use
+"variables"_variable.html and the "next"_next.html and
+"jump"_jump.html commands to loop over the same input script
+multiple times with different settings. For example, this
+script, named in.polymer
+
+variable d index run1 run2 run3 run4 run5 run6 run7 run8
+shell cd $d
+read_data data.polymer
+run 10000
+shell cd ..
+clear
+next d
+jump in.polymer :pre
+
+would run 8 simulations in different directories, using a data.polymer
+file in each directory. The same concept could be used to run the
+same system at 8 different temperatures, using a temperature variable
+and storing the output in different log and dump files, for example
+
+variable a loop 8
+variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
+log log.$a
+read data.polymer
+velocity all create $t 352839
+fix 1 all nvt $t $t 100.0
+dump 1 all atom 1000 dump.$a
+run 100000
+clear
+next t
+next a
+jump in.polymer :pre
+
+All of the above examples work whether you are running on 1 or
+multiple processors, but assumed you are running LAMMPS on a single
+partition of processors. LAMMPS can be run on multiple partitions via
+the "-partition" command-line switch as described in "this
+section"_Section_start.html#start_6 of the manual.
+
+In the last 2 examples, if LAMMPS were run on 3 partitions, the same
+scripts could be used if the "index" and "loop" variables were
+replaced with {universe}-style variables, as described in the
+"variable"_variable.html command. Also, the "next t" and "next a"
+commands would need to be replaced with a single "next a t" command.
+With these modifications, the 8 simulations of each script would run
+on the 3 partitions one after the other until all were finished.
+Initially, 3 simulations would be started simultaneously, one on each
+partition. When one finished, that partition would then start
+the 4th simulation, and so forth, until all 8 were completed.
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
new file mode 100644
index 0000000000..f787801c36
--- /dev/null
+++ b/doc/src/Howto_nemd.txt
@@ -0,0 +1,48 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+NEMD simulations :h3
+
+Non-equilibrium molecular dynamics or NEMD simulations are typically
+used to measure a fluid's rheological properties such as viscosity.
+In LAMMPS, such simulations can be performed by first setting up a
+non-orthogonal simulation box (see the preceding Howto section).
+
+A shear strain can be applied to the simulation box at a desired
+strain rate by using the "fix deform"_fix_deform.html command. The
+"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
+the sheared fluid and integrate the SLLOD equations of motion for the
+system. Fix nvt/sllod uses "compute
+temp/deform"_compute_temp_deform.html to compute a thermal temperature
+by subtracting out the streaming velocity of the shearing atoms. The
+velocity profile or other properties of the fluid can be monitored via
+the "fix ave/chunk"_fix_ave_chunk.html command.
+
+As discussed in the previous section on non-orthogonal simulation
+boxes, the amount of tilt or skew that can be applied is limited by
+LAMMPS for computational efficiency to be 1/2 of the parallel box
+length. However, "fix deform"_fix_deform.html can continuously strain
+a box by an arbitrary amount. As discussed in the "fix
+deform"_fix_deform.html command, when the tilt value reaches a limit,
+the box is flipped to the opposite limit which is an equivalent tiling
+of periodic space. The strain rate can then continue to change as
+before. In a long NEMD simulation these box re-shaping events may
+occur many times.
+
+In a NEMD simulation, the "remap" option of "fix
+deform"_fix_deform.html should be set to "remap v", since that is what
+"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
+profile consistent with the applied shear strain rate.
+
+An alternative method for calculating viscosities is provided via the
+"fix viscosity"_fix_viscosity.html command.
+
+NEMD simulations can also be used to measure transport properties of a fluid
+through a pore or channel. Simulations of steady-state flow can be performed
+using the "fix flow/gauss"_fix_flow_gauss.html command.
diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt
new file mode 100644
index 0000000000..a204a3cc96
--- /dev/null
+++ b/doc/src/Howto_output.txt
@@ -0,0 +1,307 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3
+
+There are four basic kinds of LAMMPS output:
+
+"Thermodynamic output"_thermo_style.html, which is a list
+of quantities printed every few timesteps to the screen and logfile. :ulb,l
+
+"Dump files"_dump.html, which contain snapshots of atoms and various
+per-atom values and are written at a specified frequency. :l
+
+Certain fixes can output user-specified quantities to files: "fix
+ave/time"_fix_ave_time.html for time averaging, "fix
+ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix
+print"_fix_print.html for single-line output of
+"variables"_variable.html. Fix print can also output to the
+screen. :l
+
+"Restart files"_restart.html. :l
+:ule
+
+A simulation prints one set of thermodynamic output and (optionally)
+restart files. It can generate any number of dump files and fix
+output files, depending on what "dump"_dump.html and "fix"_fix.html
+commands you specify.
+
+As discussed below, LAMMPS gives you a variety of ways to determine
+what quantities are computed and printed when the thermodynamics,
+dump, or fix commands listed above perform output. Throughout this
+discussion, note that users can also "add their own computes and fixes
+to LAMMPS"_Modify.html which can then generate values that can then be
+output with these commands.
+
+The following sub-sections discuss different LAMMPS command related
+to output and the kind of data they operate on and produce:
+
+"Global/per-atom/local data"_#global
+"Scalar/vector/array data"_#scalar
+"Thermodynamic output"_#thermo
+"Dump file output"_#dump
+"Fixes that write output files"_#fixoutput
+"Computes that process output quantities"_#computeoutput
+"Fixes that process output quantities"_#fixprocoutput
+"Computes that generate values to output"_#compute
+"Fixes that generate values to output"_#fix
+"Variables that generate values to output"_#variable
+"Summary table of output options and data flow between commands"_#table :ul
+
+Global/per-atom/local data :h4,link(global)
+
+Various output-related commands work with three different styles of
+data: global, per-atom, or local. A global datum is one or more
+system-wide values, e.g. the temperature of the system. A per-atom
+datum is one or more values per atom, e.g. the kinetic energy of each
+atom. Local datums are calculated by each processor based on the
+atoms it owns, but there may be zero or more per atom, e.g. a list of
+bond distances.
+
+Scalar/vector/array data :h4,link(scalar)
+
+Global, per-atom, and local datums can each come in three kinds: a
+single scalar value, a vector of values, or a 2d array of values. The
+doc page for a "compute" or "fix" or "variable" that generates data
+will specify both the style and kind of data it produces, e.g. a
+per-atom vector.
+
+When a quantity is accessed, as in many of the output commands
+discussed below, it can be referenced via the following bracket
+notation, where ID in this case is the ID of a compute. The leading
+"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
+
+c_ID | entire scalar, vector, or array
+c_ID\[I\] | one element of vector, one column of array
+c_ID\[I\]\[J\] | one element of array :tb(s=|)
+
+In other words, using one bracket reduces the dimension of the data
+once (vector -> scalar, array -> vector). Using two brackets reduces
+the dimension twice (array -> scalar). Thus a command that uses
+scalar values as input can typically also process elements of a vector
+or array.
+
+Thermodynamic output :h4,link(thermo)
+
+The frequency and format of thermodynamic output is set by the
+"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
+"thermo_modify"_thermo_modify.html commands. The
+"thermo_style"_thermo_style.html command also specifies what values
+are calculated and written out. Pre-defined keywords can be specified
+(e.g. press, etotal, etc). Three additional kinds of keywords can
+also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
+or "fix"_fix.html or "variable"_variable.html provides the value to be
+output. In each case, the compute, fix, or variable must generate
+global values for input to the "thermo_style custom"_dump.html
+command.
+
+Note that thermodynamic output values can be "extensive" or
+"intensive". The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature). The
+setting for "thermo_modify norm"_thermo_modify.html determines whether
+extensive quantities are normalized or not. Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details. "Equal-style variables"_variable.html produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+
+Dump file output :h4,link(dump)
+
+Dump file output is specified by the "dump"_dump.html and
+"dump_modify"_dump_modify.html commands. There are several
+pre-defined formats (dump atom, dump xtc, etc).
+
+There is also a "dump custom"_dump.html format where the user
+specifies what values are output with each atom. Pre-defined atom
+attributes can be specified (id, x, fx, etc). Three additional kinds
+of keywords can also be specified (c_ID, f_ID, v_name), where a
+"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
+provides the values to be output. In each case, the compute, fix, or
+variable must generate per-atom values for input to the "dump
+custom"_dump.html command.
+
+There is also a "dump local"_dump.html format where the user specifies
+what local values to output. A pre-defined index keyword can be
+specified to enumerate the local values. Two additional kinds of
+keywords can also be specified (c_ID, f_ID), where a
+"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
+provides the values to be output. In each case, the compute or fix
+must generate local values for input to the "dump local"_dump.html
+command.
+
+Fixes that write output files :h4,link(fixoutput)
+
+Several fixes take various quantities as input and can write output
+files: "fix ave/time"_fix_ave_time.html, "fix
+ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
+"fix ave/correlate"_fix_ave_correlate.html, and "fix
+print"_fix_print.html.
+
+The "fix ave/time"_fix_ave_time.html command enables direct output to
+a file and/or time-averaging of global scalars or vectors. The user
+specifies one or more quantities as input. These can be global
+"compute"_compute.html values, global "fix"_fix.html values, or
+"variables"_variable.html of any style except the atom style which
+produces per-atom values. Since a variable can refer to keywords used
+by the "thermo_style custom"_thermo_style.html command (like temp or
+press) and individual per-atom values, a wide variety of quantities
+can be time averaged and/or output in this way. If the inputs are one
+or more scalar values, then the fix generate a global scalar or vector
+of output. If the inputs are one or more vector values, then the fix
+generates a global vector or array of output. The time-averaged
+output of this fix can also be used as input to other output commands.
+
+The "fix ave/chunk"_fix_ave_chunk.html command enables direct output
+to a file of chunk-averaged per-atom quantities like those output in
+dump files. Chunks can represent spatial bins or other collections of
+atoms, e.g. individual molecules. The per-atom quantities can be atom
+density (mass or number) or atom attributes such as position,
+velocity, force. They can also be per-atom quantities calculated by a
+"compute"_compute.html, by a "fix"_fix.html, or by an atom-style
+"variable"_variable.html. The chunk-averaged output of this fix can
+also be used as input to other output commands.
+
+The "fix ave/histo"_fix_ave_histo.html command enables direct output
+to a file of histogrammed quantities, which can be global or per-atom
+or local quantities. The histogram output of this fix can also be
+used as input to other output commands.
+
+The "fix ave/correlate"_fix_ave_correlate.html command enables direct
+output to a file of time-correlated quantities, which can be global
+values. The correlation matrix output of this fix can also be used as
+input to other output commands.
+
+The "fix print"_fix_print.html command can generate a line of output
+written to the screen and log file or to a separate file, periodically
+during a running simulation. The line can contain one or more
+"variable"_variable.html values for any style variable except the
+vector or atom styles). As explained above, variables themselves can
+contain references to global values generated by "thermodynamic
+keywords"_thermo_style.html, "computes"_compute.html,
+"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
+values for a specific atom. Thus the "fix print"_fix_print.html
+command is a means to output a wide variety of quantities separate
+from normal thermodynamic or dump file output.
+
+Computes that process output quantities :h4,link(computeoutput)
+
+The "compute reduce"_compute_reduce.html and "compute
+reduce/region"_compute_reduce.html commands take one or more per-atom
+or local vector quantities as inputs and "reduce" them (sum, min, max,
+ave) to scalar quantities. These are produced as output values which
+can be used as input to other output commands.
+
+The "compute slice"_compute_slice.html command take one or more global
+vector or array quantities as inputs and extracts a subset of their
+values to create a new vector or array. These are produced as output
+values which can be used as input to other output commands.
+
+The "compute property/atom"_compute_property_atom.html command takes a
+list of one or more pre-defined atom attributes (id, x, fx, etc) and
+stores the values in a per-atom vector or array. These are produced
+as output values which can be used as input to other output commands.
+The list of atom attributes is the same as for the "dump
+custom"_dump.html command.
+
+The "compute property/local"_compute_property_local.html command takes
+a list of one or more pre-defined local attributes (bond info, angle
+info, etc) and stores the values in a local vector or array. These
+are produced as output values which can be used as input to other
+output commands.
+
+Fixes that process output quantities :h4,link(fixprocoutput)
+
+The "fix vector"_fix_vector.html command can create global vectors as
+output from global scalars as input, accumulating them one element at
+a time.
+
+The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
+of per-atom vectors. The per-atom quantities can be atom attributes
+such as position, velocity, force. They can also be per-atom
+quantities calculated by a "compute"_compute.html, by a
+"fix"_fix.html, or by an atom-style "variable"_variable.html. The
+time-averaged per-atom output of this fix can be used as input to
+other output commands.
+
+The "fix store/state"_fix_store_state.html command can archive one or
+more per-atom attributes at a particular time, so that the old values
+can be used in a future calculation or output. The list of atom
+attributes is the same as for the "dump custom"_dump.html command,
+including per-atom quantities calculated by a "compute"_compute.html,
+by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
+The output of this fix can be used as input to other output commands.
+
+Computes that generate values to output :h4,link(compute)
+
+Every "compute"_compute.html in LAMMPS produces either global or
+per-atom or local values. The values can be scalars or vectors or
+arrays of data. These values can be output using the other commands
+described in this section. The doc page for each compute command
+describes what it produces. Computes that produce per-atom or local
+values have the word "atom" or "local" in their style name. Computes
+without the word "atom" or "local" produce global values.
+
+Fixes that generate values to output :h4,link(fix)
+
+Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
+local values which can be accessed by other commands. The values can
+be scalars or vectors or arrays of data. These values can be output
+using the other commands described in this section. The doc page for
+each fix command tells whether it produces any output quantities and
+describes them.
+
+Variables that generate values to output :h4,link(variable)
+
+"Variables"_variable.html defined in an input script can store one or
+more strings. But equal-style, vector-style, and atom-style or
+atomfile-style variables generate a global scalar value, global vector
+or values, or a per-atom vector, respectively, when accessed. The
+formulas used to define these variables can contain references to the
+thermodynamic keywords and to global and per-atom data generated by
+computes, fixes, and other variables. The values generated by
+variables can be used as input to and thus output by the other
+commands described in this section.
+
+Summary table of output options and data flow between commands :h4,link(table)
+
+This table summarizes the various commands that can be used for
+generating output from LAMMPS. Each command produces output data of
+some kind and/or writes data to a file. Most of the commands can take
+data from other commands as input. Thus you can link many of these
+commands together in pipeline form, where data produced by one command
+is used as input to another command and eventually written to the
+screen or to a file. Note that to hook two commands together the
+output and input data types must match, e.g. global/per-atom/local
+data and scalar/vector/array data.
+
+Also note that, as described above, when a command takes a scalar as
+input, that could be an element of a vector or array. Likewise a
+vector input could be a column of an array.
+
+Command: Input: Output:
+"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
+"dump custom"_dump.html: per-atom vectors: dump file:
+"dump local"_dump.html: local vectors: dump file:
+"fix print"_fix_print.html: global scalar from variable: screen, file:
+"print"_print.html: global scalar from variable: screen:
+"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
+"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
+"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector:
+"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
+"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
+"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
+"compute property/local"_compute_property_local.html: local vectors: local vector/array:
+"fix vector"_fix_vector.html: global scalars: global vector:
+"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
+"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
+"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file:
+"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
+"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
+"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:)
diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt
new file mode 100644
index 0000000000..b2653b117e
--- /dev/null
+++ b/doc/src/Howto_polarizable.txt
@@ -0,0 +1,81 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Polarizable models :h3
+
+In polarizable force fields the charge distributions in molecules and
+materials respond to their electrostatic environments. Polarizable
+systems can be simulated in LAMMPS using three methods:
+
+the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
+package, :ulb,l
+the adiabatic core-shell method, implemented in the
+"CORESHELL"_Howto_coreshell.html package, :l
+the thermalized Drude dipole method, implemented in the
+"USER-DRUDE"_Howto_drude.html package. :l,ule
+
+The fluctuating charge method calculates instantaneous charges on
+interacting atoms based on the electronegativity equalization
+principle. It is implemented in the "fix qeq"_fix_qeq.html which is
+available in several variants. It is a relatively efficient technique
+since no additional particles are introduced. This method allows for
+charge transfer between molecules or atom groups. However, because the
+charges are located at the interaction sites, off-plane components of
+polarization cannot be represented in planar molecules or atom groups.
+
+The two other methods share the same basic idea: polarizable atoms are
+split into one core atom and one satellite particle (called shell or
+Drude particle) attached to it by a harmonic spring. Both atoms bear
+a charge and they represent collectively an induced electric dipole.
+These techniques are computationally more expensive than the QEq
+method because of additional particles and bonds. These two
+charge-on-spring methods differ in certain features, with the
+core-shell model being normally used for ionic/crystalline materials,
+whereas the so-called Drude model is normally used for molecular
+systems and fluid states.
+
+The core-shell model is applicable to crystalline materials where the
+high symmetry around each site leads to stable trajectories of the
+core-shell pairs. However, bonded atoms in molecules can be so close
+that a core would interact too strongly or even capture the Drude
+particle of a neighbor. The Drude dipole model is relatively more
+complex in order to remediate this and other issues. Specifically, the
+Drude model includes specific thermostating of the core-Drude pairs
+and short-range damping of the induced dipoles.
+
+The three polarization methods can be implemented through a
+self-consistent calculation of charges or induced dipoles at each
+timestep. In the fluctuating charge scheme this is done by the matrix
+inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
+or Drude-dipoles the relaxed-dipoles technique would require an slow
+iterative procedure. These self-consistent solutions yield accurate
+trajectories since the additional degrees of freedom representing
+polarization are massless. An alternative is to attribute a mass to
+the additional degrees of freedom and perform time integration using
+an extended Lagrangian technique. For the fluctuating charge scheme
+this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
+charge-on-spring models by the methods outlined in the next two
+sections. The assignment of masses to the additional degrees of
+freedom can lead to unphysical trajectories if care is not exerted in
+choosing the parameters of the polarizable models and the simulation
+conditions.
+
+In the core-shell model the vibration of the shells is kept faster
+than the ionic vibrations to mimic the fast response of the
+polarizable electrons. But in molecular systems thermalizing the
+core-Drude pairs at temperatures comparable to the rest of the
+simulation leads to several problems (kinetic energy transfer, too
+short a timestep, etc.) In order to avoid these problems the relative
+motion of the Drude particles with respect to their cores is kept
+"cold" so the vibration of the core-Drude pairs is very slow,
+approaching the self-consistent regime. In both models the
+temperature is regulated using the velocities of the center of mass of
+core+shell (or Drude) pairs, but in the Drude model the actual
+relative core-Drude particle motion is thermostated separately as
+well.
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/Howto_pylammps.txt
similarity index 95%
rename from doc/src/tutorial_pylammps.txt
rename to doc/src/Howto_pylammps.txt
index 11cddb3cbf..8be4b66e78 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/Howto_pylammps.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -15,13 +15,19 @@ END_RST -->
Overview :h4
-PyLammps is a Python wrapper class which can be created on its own or use an
-existing lammps Python object. It creates a simpler, Python-like interface to
-common LAMMPS functionality. Unlike the original flat C-types interface, it
-exposes a discoverable API. It no longer requires knowledge of the underlying
-C++ code implementation. Finally, the IPyLammps wrapper builds on top of
-PyLammps and adds some additional features for IPython integration into IPython
-notebooks, e.g. for embedded visualization output from dump/image.
+PyLammps is a Python wrapper class which can be created on its own or
+use an existing lammps Python object. It creates a simpler,
+Python-like interface to common LAMMPS functionality, in contrast to
+the lammps.py wrapper on the C-style LAMMPS library interface which is
+written using Python ctypes. The lammps.py wrapper is discussed on
+the "Python library"_Python_library.html doc page.
+
+Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
+It no longer requires knowledge of the underlying C++ code
+implementation. Finally, the IPyLammps wrapper builds on top of
+PyLammps and adds some additional features for IPython integration
+into IPython notebooks, e.g. for embedded visualization output from
+dump/image.
Comparison of lammps and PyLammps interfaces :h5
@@ -40,7 +46,6 @@ communication with LAMMPS is hidden from API user
shorter, more concise Python
better IPython integration, designed for quick prototyping :ul
-
Quick Start :h4
System-wide Installation :h5
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
new file mode 100644
index 0000000000..1b44fe5374
--- /dev/null
+++ b/doc/src/Howto_replica.txt
@@ -0,0 +1,61 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Multi-replica simulations :h3
+
+Several commands in LAMMPS run mutli-replica simulations, meaning
+that multiple instances (replicas) of your simulation are run
+simultaneously, with small amounts of data exchanged between replicas
+periodically.
+
+These are the relevant commands:
+
+"neb"_neb.html for nudged elastic band calculations
+"prd"_prd.html for parallel replica dynamics
+"tad"_tad.html for temperature accelerated dynamics
+"temper"_temper.html for parallel tempering
+"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
+
+NEB is a method for finding transition states and barrier energies.
+PRD and TAD are methods for performing accelerated dynamics to find
+and perform infrequent events. Parallel tempering or replica exchange
+runs different replicas at a series of temperature to facilitate
+rare-event sampling.
+
+These commands can only be used if LAMMPS was built with the REPLICA
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+PIMD runs different replicas whose individual particles are coupled
+together by springs to model a system or ring-polymers.
+
+This commands can only be used if LAMMPS was built with the USER-MISC
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+In all these cases, you must run with one or more processors per
+replica. The processors assigned to each replica are determined at
+run-time by using the "-partition command-line
+switch"_Section_start.html#start_6 to launch LAMMPS on multiple
+partitions, which in this context are the same as replicas. E.g.
+these commands:
+
+mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
+
+would each run 8 replicas, on either 16 or 8 processors. Note the use
+of the "-in command-line switch"_Section_start.html#start_6 to specify
+the input script which is required when running in multi-replica mode.
+
+Also note that with MPI installed on a machine (e.g. your desktop),
+you can run on more (virtual) processors than you have physical
+processors. Thus the above commands could be run on a
+single-processor (or few-processor) desktop so that you can run
+a multi-replica simulation on more replicas than you have
+physical processors.
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
new file mode 100644
index 0000000000..b211775479
--- /dev/null
+++ b/doc/src/Howto_restart.txt
@@ -0,0 +1,97 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Restart a simulation :h3
+
+There are 3 ways to continue a long LAMMPS simulation. Multiple
+"run"_run.html commands can be used in the same input script. Each
+run will continue from where the previous run left off. Or binary
+restart files can be saved to disk using the "restart"_restart.html
+command. At a later time, these binary files can be read via a
+"read_restart"_read_restart.html command in a new script. Or they can
+be converted to text data files using the "-r command-line
+switch"_Section_start.html#start_6 and read by a
+"read_data"_read_data.html command in a new script.
+
+Here we give examples of 2 scripts that read either a binary restart
+file or a converted data file and then issue a new run command to
+continue where the previous run left off. They illustrate what
+settings must be made in the new script. Details are discussed in the
+documentation for the "read_restart"_read_restart.html and
+"read_data"_read_data.html commands.
+
+Look at the {in.chain} input script provided in the {bench} directory
+of the LAMMPS distribution to see the original script that these 2
+scripts are based on. If that script had the line
+
+restart 50 tmp.restart :pre
+
+added to it, it would produce 2 binary restart files (tmp.restart.50
+and tmp.restart.100) as it ran.
+
+This script could be used to read the 1st restart file and re-run the
+last 50 timesteps:
+
+read_restart tmp.restart.50 :pre
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+
+timestep 0.012 :pre
+
+run 50 :pre
+
+Note that the following commands do not need to be repeated because
+their settings are included in the restart file: {units, atom_style,
+special_bonds, pair_style, bond_style}. However these commands do
+need to be used, since their settings are not in the restart file:
+{neighbor, fix, timestep}.
+
+If you actually use this script to perform a restarted run, you will
+notice that the thermodynamic data match at step 50 (if you also put a
+"thermo 50" command in the original script), but do not match at step
+100. This is because the "fix langevin"_fix_langevin.html command
+uses random numbers in a way that does not allow for perfect restarts.
+
+As an alternate approach, the restart file could be converted to a data
+file as follows:
+
+lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
+
+Then, this script could be used to re-run the last 50 steps:
+
+units lj
+atom_style bond
+pair_style lj/cut 1.12
+pair_modify shift yes
+bond_style fene
+special_bonds 0.0 1.0 1.0 :pre
+
+read_data tmp.restart.data :pre
+
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
+
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+
+timestep 0.012 :pre
+
+reset_timestep 50
+run 50 :pre
+
+Note that nearly all the settings specified in the original {in.chain}
+script must be repeated, except the {pair_coeff} and {bond_coeff}
+commands since the new data file lists the force field coefficients.
+Also, the "reset_timestep"_reset_timestep.html command is used to tell
+LAMMPS the current timestep. This value is stored in restart files,
+but not in data files.
diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt
new file mode 100644
index 0000000000..2cbf16547b
--- /dev/null
+++ b/doc/src/Howto_spc.txt
@@ -0,0 +1,54 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+SPC water model :h3
+
+The SPC water model specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+{harmonic} and an angle style of {harmonic} or {charmm} should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid SPC model.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.820
+H charge = 0.410
+LJ epsilon of OO = 0.1553
+LJ sigma of OO = 3.166
+LJ epsilon, sigma of OH, HH = 0.0
+r0 of OH bond = 1.0
+theta of HOH angle = 109.47 :all(b),p
+
+Note that as originally proposed, the SPC model was run with a 9
+Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
+with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
+any of the parameters above, though it becomes a different model in
+that mode of usage.
+
+The SPC/E (extended) water model is the same, except
+the partial charge assignments change:
+
+O charge = -0.8476
+H charge = 0.4238 :all(b),p
+
+See the "(Berendsen)"_#howto-Berendsen reference for more details on both
+the SPC and SPC/E models.
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(howto-Berendsen)
+[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+6269-6271 (1987).
diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt
new file mode 100644
index 0000000000..1e737df655
--- /dev/null
+++ b/doc/src/Howto_spherical.txt
@@ -0,0 +1,243 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Finite-size spherical and aspherical particles :h3
+
+Typical MD models treat atoms or particles as point masses. Sometimes
+it is desirable to have a model with finite-size particles such as
+spheroids or ellipsoids or generalized aspherical bodies. The
+difference is that such particles have a moment of inertia, rotational
+energy, and angular momentum. Rotation is induced by torque coming
+from interactions with other particles.
+
+LAMMPS has several options for running simulations with these kinds of
+particles. The following aspects are discussed in turn:
+
+atom styles
+pair potentials
+time integration
+computes, thermodynamics, and dump output
+rigid bodies composed of finite-size particles :ul
+
+Example input scripts for these kinds of models are in the body,
+colloid, dipole, ellipse, line, peri, pour, and tri directories of the
+"examples directory"_Examples.html in the LAMMPS distribution.
+
+Atom styles :h4
+
+There are several "atom styles"_atom_style.html that allow for
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
+tri, peri, and body.
+
+The sphere style defines particles that are spheriods and each
+particle can have a unique diameter and mass (or density). These
+particles store an angular velocity (omega) and can be acted upon by
+torque. The "set" command can be used to modify the diameter and mass
+of individual particles, after then are created.
+
+The dipole style does not actually define finite-size particles, but
+is often used in conjunction with spherical particles, via a command
+like
+
+atom_style hybrid sphere dipole :pre
+
+This is because when dipoles interact with each other, they induce
+torques, and a particle must be finite-size (i.e. have a moment of
+inertia) in order to respond and rotate. See the "atom_style
+dipole"_atom_style.html command for details. The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+
+The ellipsoid style defines particles that are ellipsoids and thus can
+be aspherical. Each particle has a shape, specified by 3 diameters,
+and mass (or density). These particles store an angular momentum and
+their orientation (quaternion), and can be acted upon by torque. They
+do not store an angular velocity (omega), which can be in a different
+direction than angular momentum, rather they compute it as needed.
+The "set" command can be used to modify the diameter, orientation, and
+mass of individual particles, after then are created. It also has a
+brief explanation of what quaternions are.
+
+The line style defines line segment particles with two end points and
+a mass (or density). They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
+
+The tri style defines triangular particles with three corner points
+and a mass (or density). They can be used in 3d simulations, and they
+can be joined together to form rigid bodies which represent arbitrary
+particles with a triangulated surface.
+
+The peri style is used with "Peridynamic models"_pair_peri.html and
+defines particles as having a volume, that is used internally in the
+"pair_style peri"_pair_peri.html potentials.
+
+The body style allows for definition of particles which can represent
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc. The body style
+is discussed in more detail on the "Howto body"_Howto_body.html doc
+page.
+
+Note that if one of these atom styles is used (or multiple styles via
+the "atom_style hybrid"_atom_style.html command), not all particles in
+the system are required to be finite-size or aspherical.
+
+For example, in the ellipsoid style, if the 3 shape parameters are set
+to the same value, the particle will be a sphere rather than an
+ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
+diameter is set to 0.0, it will be a point particle. In the line or
+tri style, if the lineflag or triflag is specified as 0, then it
+will be a point particle.
+
+Some of the pair styles used to compute pairwise interactions between
+finite-size particles also compute the correct interaction with point
+particles as well, e.g. the interaction between a point particle and a
+finite-size particle or between two point particles. If necessary,
+"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
+interactions are computed for the appropriate style of interactions.
+Likewise, using groups to partition particles (ellipsoids versus
+spheres versus point particles) will allow you to use the appropriate
+time integrators and temperature computations for each class of
+particles. See the doc pages for various commands for details.
+
+Also note that for "2d simulations"_dimension.html, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses. This means they have the same moment of inertia as the 3d
+object. When temperature is computed, the correct degrees of freedom
+are used for rotation in a 2d versus 3d system.
+
+Pair potentials :h4
+
+When a system with finite-size particles is defined, the particles
+will only rotate and experience torque if the force field computes
+such interactions. These are the various "pair
+styles"_pair_style.html that generate torque:
+
+"pair_style gran/history"_pair_gran.html
+"pair_style gran/hertzian"_pair_gran.html
+"pair_style gran/no_history"_pair_gran.html
+"pair_style dipole/cut"_pair_dipole.html
+"pair_style gayberne"_pair_gayberne.html
+"pair_style resquared"_pair_resquared.html
+"pair_style brownian"_pair_brownian.html
+"pair_style lubricate"_pair_lubricate.html
+"pair_style line/lj"_pair_line_lj.html
+"pair_style tri/lj"_pair_tri_lj.html
+"pair_style body/nparticle"_pair_body_nparticle.html :ul
+
+The granular pair styles are used with spherical particles. The
+dipole pair style is used with the dipole atom style, which could be
+applied to spherical or ellipsoidal particles. The GayBerne and
+REsquared potentials require ellipsoidal particles, though they will
+also work if the 3 shape parameters are the same (a sphere). The
+Brownian and lubrication potentials are used with spherical particles.
+The line, tri, and body potentials are used with line segment,
+triangular, and body particles respectively.
+
+Time integration :h4
+
+There are several fixes that perform time integration on finite-size
+spherical particles, meaning the integrators update the rotational
+orientation and angular velocity or angular momentum of the particles:
+
+"fix nve/sphere"_fix_nve_sphere.html
+"fix nvt/sphere"_fix_nvt_sphere.html
+"fix npt/sphere"_fix_npt_sphere.html :ul
+
+Likewise, there are 3 fixes that perform time integration on
+ellipsoidal particles:
+
+"fix nve/asphere"_fix_nve_asphere.html
+"fix nvt/asphere"_fix_nvt_asphere.html
+"fix npt/asphere"_fix_npt_asphere.html :ul
+
+The advantage of these fixes is that those which thermostat the
+particles include the rotational degrees of freedom in the temperature
+calculation and thermostatting. The "fix langevin"_fix_langevin
+command can also be used with its {omgea} or {angmom} options to
+thermostat the rotational degrees of freedom for spherical or
+ellipsoidal particles. Other thermostatting fixes only operate on the
+translational kinetic energy of finite-size particles.
+
+These fixes perform constant NVE time integration on line segment,
+triangular, and body particles:
+
+"fix nve/line"_fix_nve_line.html
+"fix nve/tri"_fix_nve_tri.html
+"fix nve/body"_fix_nve_body.html :ul
+
+Note that for mixtures of point and finite-size particles, these
+integration fixes can only be used with "groups"_group.html which
+contain finite-size particles.
+
+Computes, thermodynamics, and dump output :h4
+
+There are several computes that calculate the temperature or
+rotational energy of spherical or ellipsoidal particles:
+
+"compute temp/sphere"_compute_temp_sphere.html
+"compute temp/asphere"_compute_temp_asphere.html
+"compute erotate/sphere"_compute_erotate_sphere.html
+"compute erotate/asphere"_compute_erotate_asphere.html :ul
+
+These include rotational degrees of freedom in their computation. If
+you wish the thermodynamic output of temperature or pressure to use
+one of these computes (e.g. for a system entirely composed of
+finite-size particles), then the compute can be defined and the
+"thermo_modify"_thermo_modify.html command used. Note that by default
+thermodynamic quantities will be calculated with a temperature that
+only includes translational degrees of freedom. See the
+"thermo_style"_thermo_style.html command for details.
+
+These commands can be used to output various attributes of finite-size
+particles:
+
+"dump custom"_dump.html
+"compute property/atom"_compute_property_atom.html
+"dump local"_dump.html
+"compute body/local"_compute_body_local.html :ul
+
+Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
+
+Rigid bodies composed of finite-size particles :h4
+
+The "fix rigid"_fix_rigid.html command treats a collection of
+particles as a rigid body, computes its inertia tensor, sums the total
+force and torque on the rigid body each timestep due to forces on its
+constituent particles, and integrates the motion of the rigid body.
+
+If any of the constituent particles of a rigid body are finite-size
+particles (spheres or ellipsoids or line segments or triangles), then
+their contribution to the inertia tensor of the body is different than
+if they were point particles. This means the rotational dynamics of
+the rigid body will be different. Thus a model of a dimer is
+different if the dimer consists of two point masses versus two
+spheroids, even if the two particles have the same mass. Finite-size
+particles that experience torque due to their interaction with other
+particles will also impart that torque to a rigid body they are part
+of.
+
+See the "fix rigid" command for example of complex rigid-body models
+it is possible to define in LAMMPS.
+
+Note that the "fix shake"_fix_shake.html command can also be used to
+treat 2, 3, or 4 particles as a rigid body, but it always assumes the
+particles are point masses.
+
+Also note that body particles cannot be modeled with the "fix
+rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles. Individual body partices are typically treated
+as rigid bodies, and their motion integrated with a command like "fix
+nve/body"_fix_nve_body.html. Interactions between pairs of body
+particles are computed via a command like "pair_style
+body/nparticle"_pair_body_nparticle.html.
diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt
new file mode 100644
index 0000000000..1b9adb49a5
--- /dev/null
+++ b/doc/src/Howto_spins.txt
@@ -0,0 +1,59 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Magnetic spins :h3
+
+The magnetic spin simualtions are enabled by the SPIN package, whose
+implementation is detailed in "Tranchida"_#Tranchida7.
+
+The model representents the simulation of atomic magnetic spins coupled
+to lattice vibrations. The dynamics of those magnetic spins can be used
+to simulate a broad range a phenomena related to magneto-elasticity, or
+or to study the influence of defects on the magnetic properties of
+materials.
+
+The magnetic spins are interacting with each others and with the
+lattice via pair interactions. Typically, the magnetic exchange
+interaction can be defined using the
+"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
+applies a magnetic torque to a given spin, considering the orientation
+of its neighboring spins and their relative distances.
+It also applies a force on the atoms as a function of the spin
+orientations and their associated inter-atomic distances.
+
+The command "fix precession/spin"_fix_precession_spin.html allows to
+apply a constant magnetic torque on all the spins in the system. This
+torque can be an external magnetic field (Zeeman interaction), or an
+uniaxial magnetic anisotropy.
+
+A Langevin thermostat can be applied to those magnetic spins using
+"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
+can be coupled to another Langevin thermostat applied to the atoms
+using "fix langevin"_fix_langevin.html in order to simulate
+thermostated spin-lattice system.
+
+The magnetic Gilbert damping can also be applied using "fix
+langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
+the thermal energy of the Langevin thermostat, or to perform a
+relaxation of the magnetic configuration toward an equilibrium state.
+
+All the computed magnetic properties can be outputed by two main
+commands. The first one is "compute spin"_compute_spin.html, that
+enables to evaluate magnetic averaged quantities, such as the total
+magnetization of the system along x, y, or z, the spin temperature, or
+the magnetic energy. The second command is "compute
+property/atom"_compute_property_atom.html. It enables to output all the
+per atom magnetic quantities. Typically, the orientation of a given
+magnetic spin, or the magnetic force acting on this spin.
+
+:line
+
+:link(Tranchida7)
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+arXiv preprint arXiv:1801.10233, (2018).
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
new file mode 100644
index 0000000000..7a318250cf
--- /dev/null
+++ b/doc/src/Howto_temperature.txt
@@ -0,0 +1,40 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calcalate temperature :h3
+
+Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant). Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motion of particles) and its thermal velocity. The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+
+LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
+
+"compute temp"_compute_temp.html
+"compute temp/sphere"_compute_temp_sphere.html
+"compute temp/asphere"_compute_temp_asphere.html
+"compute temp/com"_compute_temp_com.html
+"compute temp/deform"_compute_temp_deform.html
+"compute temp/partial"_compute_temp_partial.html
+"compute temp/profile"_compute_temp_profile.html
+"compute temp/ramp"_compute_temp_ramp.html
+"compute temp/region"_compute_temp_region.html :ul
+
+All but the first 3 calculate velocity biases directly (e.g. advection
+velocities) that are removed when computing the thermal temperature.
+"Compute temp/sphere"_compute_temp_sphere.html and "compute
+temp/asphere"_compute_temp_asphere.html compute kinetic energy for
+finite-size particles that includes rotational degrees of freedom.
+They both allow for velocity biases indirectly, via an optional extra
+argument which is another temperature compute that subtracts a velocity bias.
+This allows the translational velocity of spherical or aspherical
+particles to be adjusted in prescribed ways.
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
new file mode 100644
index 0000000000..0e2feb1869
--- /dev/null
+++ b/doc/src/Howto_thermostat.txt
@@ -0,0 +1,89 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Thermostats :h3
+
+Thermostatting means controlling the temperature of particles in an MD
+simulation. "Barostatting"_Howto_barostat.html means controlling the
+pressure. Since the pressure includes a kinetic component due to
+particle velocities, both these operations require calculation of the
+temperature. Typically a target temperature (T) and/or pressure (P)
+is specified by the user, and the thermostat or barostat attempts to
+equilibrate the system to the requested T and/or P.
+
+Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
+case by a pair style. Several thermostatting fixes are available:
+Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
+(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
+can be invoked via the {dpd/tstat} pair style:
+
+"fix nvt"_fix_nh.html
+"fix nvt/sphere"_fix_nvt_sphere.html
+"fix nvt/asphere"_fix_nvt_asphere.html
+"fix nvt/sllod"_fix_nvt_sllod.html
+"fix temp/berendsen"_fix_temp_berendsen.html
+"fix temp/csvr"_fix_temp_csvr.html
+"fix langevin"_fix_langevin.html
+"fix temp/rescale"_fix_temp_rescale.html
+"pair_style dpd/tstat"_pair_dpd.html :ul
+
+"Fix nvt"_fix_nh.html only thermostats the translational velocity of
+particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion. See the "Howto
+nemd"_Howto_nemd.html doc page for further details. "Fix
+nvt/sphere"_fix_nvt_sphere.html and "fix
+nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+
+DPD thermostatting alters pairwise interactions in a manner analogous
+to the per-particle thermostatting of "fix
+langevin"_fix_langevin.html.
+
+Any of the thermostatting fixes can use "temperature
+computes"_Howto_thermostat.html that remove bias which has two
+effects. First, the current calculated temperature, which is compared
+to the requested target temperature, is calculated with the velocity
+bias removed. Second, the thermostat adjusts only the thermal
+temperature component of the particle's velocities, which are the
+velocities with the bias removed. The removed bias is then added back
+to the adjusted velocities. See the doc pages for the individual
+fixes and for the "fix_modify"_fix_modify.html command for
+instructions on how to assign a temperature compute to a
+thermostatting fix. For example, you can apply a thermostat to only
+the x and z components of velocity by using it in conjunction with
+"compute temp/partial"_compute_temp_partial.html. Of you could
+thermostat only the thermal temperature of a streaming flow of
+particles without affecting the streaming velocity, by using "compute
+temp/profile"_compute_temp_profile.html.
+
+NOTE: Only the nvt fixes perform time integration, meaning they update
+the velocities and positions of particles due to forces and velocities
+respectively. The other thermostat fixes only adjust velocities; they
+do NOT perform time integration updates. Thus they should be used in
+conjunction with a constant NVE integration fix such as these:
+
+"fix nve"_fix_nve.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix nve/asphere"_fix_nve_asphere.html :ul
+
+Thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes temperature
+values. As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default temperature is
+setup by the thermo command itself. It is NOT the temperature
+associated with any thermostatting fix you have defined or with any
+compute you have defined that calculates a temperature. The doc pages
+for the thermostatting fixes explain the ID of the temperature compute
+they create. Thus if you want to view these temperatures, you need to
+specify them explicitly via the "thermo_style
+custom"_thermo_style.html command. Or you can use the
+"thermo_modify"_thermo_modify.html command to re-define what
+temperature compute is used for default thermodynamic output.
diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt
new file mode 100644
index 0000000000..942b42aea1
--- /dev/null
+++ b/doc/src/Howto_tip3p.txt
@@ -0,0 +1,69 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+TIP3P water model :h3
+
+The TIP3P water model as implemented in CHARMM
+"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
+charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
+the two O-H bonds and the H-O-H angle rigid. A bond style of
+{harmonic} and an angle style of {harmonic} or {charmm} should also be
+used.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
+cutoff. The K values can be used if a flexible TIP3P model (without
+fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
+set to 0.0, it corresponds to the original 1983 TIP3P model
+"(Jorgensen)"_#Jorgensen1.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.834
+H charge = 0.417
+LJ epsilon of OO = 0.1521
+LJ sigma of OO = 3.1507
+LJ epsilon of HH = 0.0460
+LJ sigma of HH = 0.4000
+LJ epsilon of OH = 0.0836
+LJ sigma of OH = 1.7753
+K of OH bond = 450
+r0 of OH bond = 0.9572
+K of HOH angle = 55
+theta of HOH angle = 104.52 :all(b),p
+
+These are the parameters to use for TIP3P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
+details:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -0.830
+H charge = 0.415
+LJ epsilon of OO = 0.102
+LJ sigma of OO = 3.188
+LJ epsilon, sigma of OH, HH = 0.0
+K of OH bond = 450
+r0 of OH bond = 0.9572
+K of HOH angle = 55
+theta of HOH angle = 104.52 :all(b),p
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(Jorgensen1)
+[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
+
+:link(Price1)
+[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
+
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
new file mode 100644
index 0000000000..f9e548e268
--- /dev/null
+++ b/doc/src/Howto_tip4p.txt
@@ -0,0 +1,112 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+TIP4P water model :h3
+
+The four-point TIP4P rigid water model extends the traditional
+three-point TIP3P model by adding an additional site, usually
+massless, where the charge associated with the oxygen atom is placed.
+This site M is located at a fixed distance away from the oxygen along
+the bisector of the HOH bond angle. A bond style of {harmonic} and an
+angle style of {harmonic} or {charmm} should also be used.
+
+A TIP4P model is run with LAMMPS using either this command
+for a cutoff model:
+
+"pair_style lj/cut/tip4p/cut"_pair_lj.html
+
+or these two commands for a long-range model:
+
+"pair_style lj/cut/tip4p/long"_pair_lj.html
+"kspace_style pppm/tip4p"_kspace_style.html :ul
+
+For both models, the bond lengths and bond angles should be held fixed
+using the "fix shake"_fix_shake.html command.
+
+These are the additional parameters (in real units) to set for O and H
+atoms and the water molecule to run a rigid TIP4P model with a cutoff
+"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
+the "pair_style"_pair_style.html command, not as part of the pair
+coefficients.
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.040
+H charge = 0.520
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.15
+LJ epsilon of O-O = 0.1550
+LJ sigma of O-O = 3.1536
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+http://dx.doi.org/10.1063/1.1931662) these values can be used:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.1794
+H charge = 0.5897
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1577
+LJ epsilon of O-O = 0.21084
+LJ sigma of O-O = 3.1668
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+http://dx.doi.org/10.1063/1.2121687), these values can be used:
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.1128
+H charge = 0.5564
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1546
+LJ epsilon of O-O = 0.1852
+LJ sigma of O-O = 3.1589
+LJ epsilon, sigma of OH, HH = 0.0
+Coulombic cutoff = 8.5 :all(b),p
+
+These are the parameters to use for TIP4P with a long-range Coulombic
+solver (e.g. Ewald or PPPM in LAMMPS):
+
+O mass = 15.9994
+H mass = 1.008
+O charge = -1.0484
+H charge = 0.5242
+r0 of OH bond = 0.9572
+theta of HOH angle = 104.52
+OM distance = 0.1250
+LJ epsilon of O-O = 0.16275
+LJ sigma of O-O = 3.16435
+LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
+
+Note that the when using the TIP4P pair style, the neighbor list
+cutoff for Coulomb interactions is effectively extended by a distance
+2 * (OM distance), to account for the offset distance of the
+fictitious charges on O atoms in water molecules. Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2*(OM distance), to shrink the size of the neighbor list.
+This leads to slightly larger cost for the long-range calculation, so
+you can test the trade-off for your model. The OM distance and the LJ
+and Coulombic cutoffs are set in the "pair_style
+lj/cut/tip4p/long"_pair_lj.html command.
+
+Wikipedia also has a nice article on "water
+models"_http://en.wikipedia.org/wiki/Water_model.
+
+:line
+
+:link(Jorgensen1)
+[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt
new file mode 100644
index 0000000000..4b299e5ae1
--- /dev/null
+++ b/doc/src/Howto_triclinic.txt
@@ -0,0 +1,213 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+Triclinic (non-orthogonal) simulation boxes :h3
+
+By default, LAMMPS uses an orthogonal simulation box to encompass the
+particles. The "boundary"_boundary.html command sets the boundary
+conditions of the box (periodic, non-periodic, etc). The orthogonal
+box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
+starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
+(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
+(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
+is created, e.g. by the "create_box"_create_box.html or
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
+where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
+parameters, as well as lx,ly,lz, can be output via the "thermo_style
+custom"_thermo_style.html command.
+
+LAMMPS also allows simulations to be performed in triclinic
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
+triclinic symmetry. The parallelepiped has its "origin" at
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
+origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
+(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
+and are called "tilt factors" because they are the amount of
+displacement applied to faces of an originally orthogonal box to
+transform it into the parallelepiped. In LAMMPS the triclinic
+simulation box edge vectors [a], [b], and [c] cannot be arbitrary
+vectors. As indicated, [a] must lie on the positive x axis. [b] must
+lie in the xy plane, with strictly positive y component. [c] may have
+any orientation with strictly positive z component. The requirement
+that [a], [b], and [c] have strictly positive x, y, and z components,
+respectively, ensures that [a], [b], and [c] form a complete
+right-handed basis. These restrictions impose no loss of generality,
+since it is possible to rotate/invert any set of 3 crystal basis
+vectors so that they conform to the restrictions.
+
+For example, assume that the 3 vectors [A],[B],[C] are the edge
+vectors of a general parallelepiped, where there is no restriction on
+[A],[B],[C] other than they form a complete right-handed basis i.e.
+[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
+rotation of [A], [B], and [C] and can be computed as follows:
+
+:c,image(Eqs/transform.jpg)
+
+where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
+indicates the corresponding unit vector. {beta} and {gamma} are angles
+between the vectors described below. Note that by construction,
+[a], [b], and [c] have strictly positive x, y, and z components, respectively.
+If it should happen that
+[A], [B], and [C] form a left-handed basis, then the above equations
+are not valid for [c]. In this case, it is necessary
+to first apply an inversion. This can be achieved
+by interchanging two basis vectors or by changing the sign of one of them.
+
+For consistency, the same rotation/inversion applied to the basis vectors
+must also be applied to atom positions, velocities,
+and any other vector quantities.
+This can be conveniently achieved by first converting to
+fractional coordinates in the
+old basis and then converting to distance coordinates in the new basis.
+The transformation is given by the following equation:
+
+:c,image(Eqs/rotate.jpg)
+
+where {V} is the volume of the box, [X] is the original vector quantity and
+[x] is the vector in the LAMMPS basis.
+
+There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary. Some commands that work
+with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
+npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions. See the command doc pages
+for details.
+
+The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
+time the simulation box is created. This happens in one of 3 ways.
+If the "create_box"_create_box.html command is used with a region of
+style {prism}, then a triclinic box is setup. See the
+"region"_region.html command for details. If the
+"read_data"_read_data.html command is used to define the simulation
+box, and the header of the data file contains a line with the "xy xz
+yz" keyword, then a triclinic box is setup. See the
+"read_data"_read_data.html command for details. Finally, if the
+"read_restart"_read_restart.html command reads a restart file which
+was written from a simulation using a triclinic box, then a triclinic
+box will be setup for the restarted simulation.
+
+Note that you can define a triclinic box with all 3 tilt factors =
+0.0, so that it is initially orthogonal. This is necessary if the box
+will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
+"fix deform"_fix_deform.html commands. Alternatively, you can use the
+"change_box"_change_box.html command to convert a simulation box from
+orthogonal to triclinic and vice versa.
+
+As with orthogonal boxes, LAMMPS defines triclinic box size parameters
+lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
+The 9 parameters, as well as lx,ly,lz, can be output via the
+"thermo_style custom"_thermo_style.html command.
+
+To avoid extremely tilted boxes (which would be computationally
+inefficient), LAMMPS normally requires that no tilt factor can skew
+the box more than half the distance of the parallel box length, which
+is the 1st dimension in the tilt factor (x for xz). This is required
+both when the simulation box is created, e.g. via the
+"create_box"_create_box.html or "read_data"_read_data.html commands,
+as well as when the box shape changes dynamically during a simulation,
+e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
+commands.
+
+For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
+the xy tilt factor must be between -5 and 5. Similarly, both xz and
+yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
+not a limitation, since if the maximum tilt factor is 5 (as in this
+example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
+... are geometrically all equivalent. If the box tilt exceeds this
+limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
+command), then the box is "flipped" to an equivalent shape with a tilt
+factor within the bounds, so the run can continue. See the "fix
+deform"_fix_deform.html doc page for further details.
+
+One exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic. In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity. In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient, due to the highly skewed simulation box.
+
+The limitation on not creating a simulation box with a tilt factor
+skewing the box more than half the distance of the parallel box length
+can be overridden via the "box"_box.html command. Setting the {tilt}
+keyword to {large} allows any tilt factors to be specified.
+
+Box flips that may occur using the "fix deform"_fix_deform.html or
+"fix npt"_fix_nh.html commands can be turned off using the {flip no}
+option with either of the commands.
+
+Note that if a simulation box has a large tilt factor, LAMMPS will run
+less efficiently, due to the large volume of communication needed to
+acquire ghost atoms around a processor's irregular-shaped sub-domain.
+For extreme values of tilt, LAMMPS may also lose atoms and generate an
+error.
+
+Triclinic crystal structures are often defined using three lattice
+constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
+{gamma}. Note that in this nomenclature, the a, b, and c lattice
+constants are the scalar lengths of the edge vectors [a], [b], and [c]
+defined above. The relationship between these 6 quantities
+(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
+
+:c,image(Eqs/box.jpg)
+
+The inverse relationship can be written as follows:
+
+:c,image(Eqs/box_inverse.jpg)
+
+The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
+out or accessed by computes using the
+"thermo_style custom"_thermo_style.html keywords
+{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
+respectively.
+
+As discussed on the "dump"_dump.html command doc page, when the BOX
+BOUNDS for a snapshot is written to a dump file for a triclinic box,
+an orthogonal bounding box which encloses the triclinic simulation box
+is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
+box, formatted as follows:
+
+ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz :pre
+
+This bounding box is convenient for many visualization programs and is
+calculated from the 9 triclinic box parameters
+(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
+
+xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+ylo_bound = ylo + MIN(0.0,yz)
+yhi_bound = yhi + MAX(0.0,yz)
+zlo_bound = zlo
+zhi_bound = zhi :pre
+
+These formulas can be inverted if you need to convert the bounding box
+back into the triclinic box parameters, e.g. xlo = xlo_bound -
+MIN(0.0,xy,xz,xy+xz).
+
+One use of triclinic simulation boxes is to model solid-state crystals
+with triclinic symmetry. The "lattice"_lattice.html command can be
+used with non-orthogonal basis vectors to define a lattice that will
+tile a triclinic simulation box via the
+"create_atoms"_create_atoms.html command.
+
+A second use is to run Parinello-Rahman dynamics via the "fix
+npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
+factors to compensate for off-diagonal components of the pressure
+tensor. The analog for an "energy minimization"_minimize.html is
+the "fix box/relax"_fix_box_relax.html command.
+
+A third use is to shear a bulk solid to study the response of the
+material. The "fix deform"_fix_deform.html command can be used for
+this purpose. It allows dynamic control of the xy, xz, yz tilt
+factors as a simulation runs. This is discussed in the next section
+on non-equilibrium MD (NEMD) simulations.
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
new file mode 100644
index 0000000000..8bcab6dd24
--- /dev/null
+++ b/doc/src/Howto_viscosity.txt
@@ -0,0 +1,133 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Calculate viscosity :h3
+
+The shear viscosity eta of a fluid can be measured in at least 5 ways
+using various options in LAMMPS. See the examples/VISCOSITY directory
+for scripts that implement the 5 methods discussed here for a simple
+Lennard-Jones fluid model. Also, see the "Howto
+kappa"_Howto_kappa.html doc page for an analogous discussion for
+thermal conductivity.
+
+Eta is a measure of the propensity of a fluid to transmit momentum in
+a direction perpendicular to the direction of velocity or momentum
+flow. Alternatively it is the resistance the fluid has to being
+sheared. It is given by
+
+J = -eta grad(Vstream)
+
+where J is the momentum flux in units of momentum per area per time.
+and grad(Vstream) is the spatial gradient of the velocity of the fluid
+moving in another direction, normal to the area through which the
+momentum flows. Viscosity thus has units of pressure-time.
+
+The first method is to perform a non-equilibrium MD (NEMD) simulation
+by shearing the simulation box via the "fix deform"_fix_deform.html
+command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
+thermostat the fluid via the SLLOD equations of motion.
+Alternatively, as a second method, one or more moving walls can be
+used to shear the fluid in between them, again with some kind of
+thermostat that modifies only the thermal (non-shearing) components of
+velocity to prevent the fluid from heating up.
+
+In both cases, the velocity profile setup in the fluid by this
+procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
+command, which determines grad(Vstream) in the equation above.
+E.g. the derivative in the y-direction of the Vx component of fluid
+motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of
+the pressure or stress tensor, as calculated by the "compute
+pressure"_compute_pressure.html command, can also be monitored, which
+is the J term in the equation above. See the "Howto
+nemd"_Howto_nemd.html doc page for details on NEMD simulations.
+
+The third method is to perform a reverse non-equilibrium MD simulation
+using the "fix viscosity"_fix_viscosity.html command which implements
+the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
+swapped between atoms in two different layers of the simulation box in
+a different dimension. This induces a velocity gradient which can be
+monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
+The fix tallies the cumulative momentum transfer that it performs.
+See the "fix viscosity"_fix_viscosity.html command for details.
+
+The fourth method is based on the Green-Kubo (GK) formula which
+relates the ensemble average of the auto-correlation of the
+stress/pressure tensor to eta. This can be done in a fully
+equilibrated simulation which is in contrast to the two preceding
+non-equilibrium methods, where momentum flows continuously through the
+simulation box.
+
+Here is an example input script that calculates the viscosity of
+liquid Ar via the GK formalism:
+
+# Sample LAMMPS input script for viscosity of liquid Ar :pre
+
+units real
+variable T equal 86.4956
+variable V equal vol
+variable dt equal 4.0
+variable p equal 400 # correlation length
+variable s equal 5 # sample interval
+variable d equal $p*$s # dump interval :pre
+
+# convert from LAMMPS real units to SI :pre
+
+variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
+variable atm2Pa equal 101325.0
+variable A2m equal 1.0e-10
+variable fs2s equal 1.0e-15
+variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
+
+# setup problem :pre
+
+dimension 3
+boundary p p p
+lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
+region box block 0 4 0 4 0 4
+create_box 1 box
+create_atoms 1 box
+mass 1 39.948
+pair_style lj/cut 13.0
+pair_coeff * * 0.2381 3.405
+timestep $\{dt\}
+thermo $d :pre
+
+# equilibration and thermalization :pre
+
+velocity all create $T 102486 mom yes rot yes dist gaussian
+fix NVT all nvt temp $T $T 10 drag 0.2
+run 8000 :pre
+
+# viscosity calculation, switch to NVE if desired :pre
+
+#unfix NVT
+#fix NVE all nve :pre
+
+reset_timestep 0
+variable pxy equal pxy
+variable pxz equal pxz
+variable pyz equal pyz
+fix SS all ave/correlate $s $p $d &
+ v_pxy v_pxz v_pyz type auto file S0St.dat ave running
+variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
+variable v11 equal trap(f_SS\[3\])*$\{scale\}
+variable v22 equal trap(f_SS\[4\])*$\{scale\}
+variable v33 equal trap(f_SS\[5\])*$\{scale\}
+thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
+run 100000
+variable v equal (v_v11+v_v22+v_v33)/3.0
+variable ndens equal count(all)/vol
+print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
+
+The fifth method is related to the above Green-Kubo method,
+but uses the Einstein formulation, analogous to the Einstein
+mean-square-displacement formulation for self-diffusivity. The
+time-integrated momentum fluxes play the role of Cartesian
+coordinates, whose mean-square displacement increases linearly
+with time at sufficiently long times.
diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt
new file mode 100644
index 0000000000..00c329c50b
--- /dev/null
+++ b/doc/src/Howto_viz.txt
@@ -0,0 +1,40 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Visualize LAMMPS snapshots :h3
+
+LAMMPS itself does not do visualization, but snapshots from LAMMPS
+simulations can be visualized (and analyzed) in a variety of ways.
+
+Mention dump image and dump movie.
+
+LAMMPS snapshots are created by the "dump"_dump.html command which can
+create files in several formats. The native LAMMPS dump format is a
+text file (see "dump atom" or "dump custom") which can be visualized
+by several popular visualization tools. The "dump
+image"_dump_image.html and "dump movie"_dump_image.html styles can
+output internally rendered images and convert a sequence of them to a
+movie during the MD run. Several programs included with LAMMPS as
+auxiliary tools can convert between LAMMPS format files and other
+formats. See the "Tools"_Tools.html doc page for details.
+
+A Python-based toolkit distributed by our group can read native LAMMPS
+dump files, including custom dump files with additional columns of
+user-specified atom information, and convert them to various formats
+or pipe them into visualization software directly. See the "Pizza.py
+WWW site"_pizza for details. Specifically, Pizza.py can convert
+LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
+Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
+RasMol visualization programs. Pizza.py has tools that do interactive
+3d OpenGL visualization and one that creates SVG images of dump file
+snapshots.
+
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+:link(ensight,http://www.ensight.com)
+:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt
new file mode 100644
index 0000000000..7522118582
--- /dev/null
+++ b/doc/src/Howto_walls.txt
@@ -0,0 +1,80 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Walls :h3
+
+Walls in an MD simulation are typically used to bound particle motion,
+i.e. to serve as a boundary condition.
+
+Walls in LAMMPS can be of rough (made of particles) or idealized
+surfaces. Ideal walls can be smooth, generating forces only in the
+normal direction, or frictional, generating forces also in the
+tangential direction.
+
+Rough walls, built of particles, can be created in various ways. The
+particles themselves can be generated like any other particle, via the
+"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
+or read in via the "read_data"_read_data.html command.
+
+Their motion can be constrained by many different commands, so that
+they do not move at all, move together as a group at constant velocity
+or in response to a net force acting on them, move in a prescribed
+fashion (e.g. rotate around a point), etc. Note that if a time
+integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
+is not used with the group that contains wall particles, their
+positions and velocities will not be updated.
+
+"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
+"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
+"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
+"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
+"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
+
+The "fix move"_fix_move.html command offers the most generality, since
+the motion of individual particles can be specified with
+"variable"_variable.html formula which depends on time and/or the
+particle position.
+
+For rough walls, it may be useful to turn off pairwise interactions
+between wall particles via the "neigh_modify
+exclude"_neigh_modify.html command.
+
+Rough walls can also be created by specifying frozen particles that do
+not move and do not interact with mobile particles, and then tethering
+other particles to the fixed particles, via a "bond"_bond_style.html.
+The bonded particles do interact with other mobile particles.
+
+Idealized walls can be specified via several fix commands. "Fix
+wall/gran"_fix_wall_gran.html creates frictional walls for use with
+granular particles; all the other commands create smooth walls.
+
+"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
+"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
+"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
+"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
+"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
+"fix wall/region"_fix_wall_region.html - use region surface as wall
+"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
+
+The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
+flat walls to move with a constant velocity, or oscillate in time.
+The "fix wall/region"_fix_wall_region.html command offers the most
+generality, since the region surface is treated as a wall, and the
+geometry of the region can be a simple primitive volume (e.g. a
+sphere, or cube, or plane), or a complex volume made from the union
+and intersection of primitive volumes. "Regions"_region.html can also
+specify a volume "interior" or "exterior" to the specified primitive
+shape or {union} or {intersection}. "Regions"_region.html can also be
+"dynamic" meaning they move with constant velocity, oscillate, or
+rotate.
+
+The only frictional idealized walls currently in LAMMPS are flat or
+curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
+command. At some point we plan to allow regoin surfaces to be used as
+frictional walls, as well as triangulated surfaces.
diff --git a/doc/src/Intro.txt b/doc/src/Intro.txt
new file mode 100644
index 0000000000..e3eaa40437
--- /dev/null
+++ b/doc/src/Intro.txt
@@ -0,0 +1,37 @@
+"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Install.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html#comm)
+
+:line
+
+Introduction :h2
+
+These pages provide a brief introduction to LAMMPS.
+
+<!-- RST
+
+.. toctree::
+
+ Intro_overview
+ Intro_features
+ Intro_nonfeatures
+ Intro_opensource
+ Intro_authors
+ Intro_website
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Overview of LAMMPS"_Intro_overview.html
+"LAMMPS features"_Intro_features.html
+"LAMMPS non-features"_Intro_nonfeatures.html
+"LAMMPS open-source license"_Intro_license.html
+"LAMMPS authors"_Intro_authors.html
+"Additional website links"_Intro_website.html :all(b)
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
new file mode 100644
index 0000000000..ce418d0ce1
--- /dev/null
+++ b/doc/src/Intro_authors.txt
@@ -0,0 +1,379 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS authors :h3
+
+The primary LAMMPS developers are at Sandia National Labs and Temple
+University:
+
+"Steve Plimpton"_sjp, sjplimp at sandia.gov
+Aidan Thompson, athomps at sandia.gov
+Stan Moore, stamoor at sandia.gov
+Axel Kohlmeyer, akohlmey at gmail.com :ul
+
+:link(sjp,http://www.cs.sandia.gov/~sjplimp)
+
+Past developers include Paul Crozier and Mark Stevens, both at Sandia,
+and Ray Shan, now at Materials Design.
+
+:line
+
+The following folks are responsible for significant contributions to
+the code, or other aspects of the LAMMPS development effort. Many of
+the packages they have written are somewhat unique to LAMMPS and the
+code would not be as general-purpose as it is without their expertise
+and efforts.
+
+Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages
+Roy Pollock (LLNL), Ewald and PPPM solvers
+Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
+Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
+Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
+Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
+Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
+Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
+Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
+Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
+Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
+Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
+Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
+Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
+
+:line
+
+As discussed on the "History
+page"_http://lammps.sandia.gov/history.html of the website, LAMMPS
+originated as a cooperative project between DOE labs and industrial
+partners. Folks involved in the design and testing of the original
+version of LAMMPS were the following:
+
+John Carpenter (Mayo Clinic, formerly at Cray Research)
+Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
+Steve Lustig (Dupont)
+Jim Belak and Roy Pollock (LLNL) :ul
+
+:line
+:line
+
+Here is a timeline for when various individuals contributed to a new
+feature or command or tool added to LAMMPS:
+
+Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
+Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
+Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
+May18 : fix bond/react : Jake Gissinger (CU Boulder)
+Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
+Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U)
+Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
+Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
+Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
+Dec17 : fix python/move : Richard Berger (Temple U)
+Nov17 : pair extep : Jaap Kroes (Radboud U)
+Oct17 : USER-UEF package : David Nicholson (MIT)
+Oct17 : fix rhok : Ulf Pederson (Roskilde U)
+Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
+Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
+Sep17 : fix latte : Christian Negre (LANL)
+Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
+Aug17 : USER-MESO package : Zhen Li (Brown University)
+Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
+Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
+Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
+Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
+Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
+Jun17 : compute cnp/atom : Paulo Branicio (USC)
+May17 : fix python and pair python : Richard Berger (Temple U)
+May17 : pair edip/multi : Chao Jiang (U Wisconsin)
+May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
+Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
+Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
+Mar17 : fix filter/corotate : Lukas Fath (KIT)
+Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
+Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
+Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
+Jan17 : fix mscg : Lauren Abbott (Sandia)
+Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
+Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
+Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
+Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
+Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
+Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
+Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
+Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
+Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
+Sep16 : kspace pppm/kk : Stan Moore (Sandia)
+Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
+Aug16 : fix controller : Aidan Thompson (Sandia)
+Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
+Jul16 : dihedral spherical : Andrew Jewett
+Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
+Jun16 : fix orient/bcc : Tegar Wicaksono (UBC)
+Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
+Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
+May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
+Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
+Apr16 : bond write : Axel Kohlmeyer (Temple U)
+Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
+Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
+Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
+Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
+Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
+Dec15 : fix qeq/fire : Ray Shan (Sandia)
+Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
+Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
+Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
+Oct15 : displace_atoms variable option : Reese Jones (Sandia)
+Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
+Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
+Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
+Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
+Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
+Aug15 : timer command : Axel Kohlmeyer (Temple U)
+Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
+Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
+Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
+Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
+Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
+Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
+Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
+Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
+Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
+Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
+Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
+Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
+Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
+Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
+Feb15 : fix tfmc : Kristof Bal (U of Antwerp)
+Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
+Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
+Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
+Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
+Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF)
+Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
+Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
+Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
+Aug14 : USER-INTEL package : Mike Brown (Intel)
+May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
+May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
+Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
+Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
+Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
+Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
+Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
+Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
+Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
+Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
+Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
+Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
+Sep13 : xmgrace tool : Vikas Varshney
+Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
+Aug13 : pair nm and variants : Julien Devemy (ICCF)
+Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
+Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
+Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
+Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
+Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
+Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia)
+Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
+Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
+Jun13 : fix tune/kspace : Paul Crozier (Sandia)
+Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
+May13 : compute msd/nongauss : Rob Hoy
+May13 : pair list : Axel Kohlmeyer (Temple U)
+May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
+Apr13 : dump_modify nfile and fileper : Christopher Knight
+Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
+Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
+Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
+Feb13 : fix species : Ray Shan (Sandia)
+Jan13 : compute voronoi/atom : Daniel Schwen
+Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
+Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
+Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
+Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
+Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
+Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
+Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
+Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
+Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
+Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
+Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
+Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
+Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
+Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
+Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
+May12 : read_dump : Tim Sirk (ARL)
+May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
+May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
+Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
+Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
+Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
+Feb12 : pair_style beck : Jon Zimmerman (Sandia)
+Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
+Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
+Jan12 : dihedral_style table : Andrew Jewett (UCSB)
+Jan12 : angle_style dipole : Mario Orsi
+Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
+Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
+Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
+Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
+Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
+Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
+Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
+Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
+Sep11 : pair_style edip : Luca Ferraro (CASPUR)
+Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
+Aug11 : fix restrain : Craig Tenney (Sandia)
+Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
+Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
+Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
+Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
+Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
+Aug11 : pair_style dipole/sf : Mario Orsi
+Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
+Aug11 : FFT support via FFTW3, MKL, ACML, KISSFFT libraries : \
+ Axel Kohlmeyer (Temple U)
+Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
+ Chandra Veer Singh (Cornell)
+Jun11 : Windows build option via Microsoft Visual Studio : \
+ Ilya Valuev (JIHT, Moscow, Russia)
+Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
+Jun11 : dump image : Nathan Fabian (Sandia)
+May11 : pppm GPU single and double : Mike Brown (ORNL)
+May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
+2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
+- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
+- : fix adapt and compute ti for thermodynamic integration for \
+ free energies : Sai Jayaraman (Sandia)
+- : pair_style born and gauss : Sai Jayaraman (Sandia)
+- : stochastic rotation dynamics (SRD) via fix srd : \
+ Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
+- : ipp Perl script tool : Reese Jones (Sandia)
+- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
+- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
+- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
+- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
+- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \
+ Paul Saxe (Materials Design) and Reese Jones (Sandia)
+- : pair_style peri/lps : Mike Parks (Sandia)
+- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
+- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
+- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
+- : public SVN & Git repositories for LAMMPS : \
+ Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
+- : compute heat/flux : German Samolyuk (ORNL) and \
+ Mario Pinto (Computational Research Lab, Pune, India)
+- : pair_style yukawa/colloid : Randy Schunk (Sandia)
+- : fix wall/colloid : Jeremy Lechman (Sandia)
+2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
+- : concentration-dependent EAM potential : \
+ Alexander Stukowski (Technical University of Darmstadt)
+- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
+- : min_style hftn : Todd Plantenga (Sandia)
+- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
+- : dump cfg : Liang Wan (Chinese Academy of Sciences)
+- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
+- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
+- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
+- : fix langevin tally : Carolyn Phillips (U Michigan)
+- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
+ Philip Howell (Siemens), Vikas Varsney (AFRL)
+- : region cone : Pim Schravendijk
+- : pair_style born/coul/long : Ahmed Ismail (Sandia)
+- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
+- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
+- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
+- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
+2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
+- : peridynamics : Mike Parks (Sandia)
+- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
+- : GROMACS pair potentials : Mark Stevens (Sandia)
+- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
+- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
+- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
+- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
+- : pair_style lubricate : Randy Schunk (Sandia)
+- : compute ackland/atom : Gerolf Ziegenhain
+- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
+ Pieter in 't Veld (Sandia)
+- : AI-REBO bond-order potential : Ase Henry (MIT)
+- : making LAMMPS a true "object" that can be instantiated \
+ multiple times, e.g. as a library : Ben FrantzDale (RPI)
+- : pymol_asphere viz tool : Mike Brown (Sandia)
+2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
+- : tensile and shear deformations : Pieter in 't Veld (Sandia)
+- : GayBerne potential : Mike Brown (Sandia)
+- : ellipsoidal particles : Mike Brown (Sandia)
+- : colloid potentials : Pieter in 't Veld (Sandia)
+- : fix heat : Paul Crozier and Ed Webb (Sandia)
+- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
+- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
+- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
+- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
+- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
+- : MEAM potential : Greg Wagner (Sandia)
+- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
+ James Fischer (High Performance Technologies), \
+ David Richie and Vincent Natoli (Stone Ridge Technologies)
+2006 : fix wall/lj126 : Mark Stevens (Sandia)
+- : Stillinger-Weber and Tersoff potentials : \
+ Aidan Thompson and Xiaowang Zhou (Sandia)
+- : region prism : Pieter in 't Veld (Sandia)
+- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : OPLS dihedral potential: Mark Stevens (Sandia)
+- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
+- : faster pair hybrid potential: James Fischer \
+ (High Performance Technologies, Inc), Vincent Natoli and \
+ David Richie (Stone Ridge Technology)
+- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
+- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
+- : grain boundary orientation fix : Koenraad Janssens and \
+ David Olmsted (Sandia)
+- : pair_style lj/smooth potential : Craig Maloney (UCSB)
+- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
+ (Johns Hopkins U) and Paul Crozier (Sandia)
+- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
+- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
+- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
+ Mark Stevens (Sandia)
+- : Finnis/Sinclair EAM: Tim Lau (MIT)
+- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
+ Frank van Swol (Sandia)
+- : TIP4P potential (4-site water): Ahmed Ismail and \
+ Amalie Frischknecht (Sandia)
+2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
+- : compressed dump files: Erik Luijten (U Illinois)
+- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
+- : electric field fix: Christina Payne (Vanderbilt U)
+- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
+ Vikas Varshney (U Akron)
+- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
+- : Morse bond potential: Jeff Greathouse (Sandia)
+- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
+- : force tables for long-range Coulombics: Paul Crozier (Sandia)
+2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
+ Christian Burisch (Bochum University, Germany)
+- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
+- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
+ Andrey Kalinichev (Sandia)
+- : parallel tempering: Mark Sears (Sandia)
+earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
+- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
+- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
+- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
+- : HTFN energy minimizer: Todd Plantenga (Sandia)
+- : class 2 force fields: Eric Simon (Cray)
+- : NVT/NPT integrators: Mark Stevens (Sandia)
+- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
+- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
new file mode 100644
index 0000000000..2bb7e25683
--- /dev/null
+++ b/doc/src/Intro_features.txt
@@ -0,0 +1,202 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS features :h3
+
+LAMMPS is a classical molecular dynamics (MD) code with these general
+classes of functionality:
+
+"General features"_#general
+"Particle and model types"_#particle
+"Interatomic potentials (force fields)"_#ff
+"Atom creation"_#create
+"Ensembles, constraints, and boundary conditions"_#ensemble
+"Integrators"_#integrate
+"Diagnostics"_#diag
+"Output"_#output
+"Multi-replica models"_#replica
+"Pre- and post-processing"_#prepost
+"Specialized features (beyond MD itself)"_#special :ul
+
+:line
+
+General features :h4,link(general)
+
+ runs on a single processor or in parallel
+ distributed-memory message-passing parallelism (MPI)
+ spatial-decomposition of simulation domain for parallelism
+ open-source distribution
+ highly portable C++
+ optional libraries used: MPI and single-processor FFT
+ GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
+ easy to extend with new features and functionality
+ runs from an input script
+ syntax for defining and using variables and formulas
+ syntax for looping over runs and breaking out of loops
+ run one or multiple simulations simultaneously (in parallel) from one script
+ build as library, invoke LAMMPS thru library interface or provided Python wrapper
+ couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
+
+Particle and model types :h4,link(particle)
+("atom style"_atom_style.html command)
+
+ atoms
+ coarse-grained particles (e.g. bead-spring polymers)
+ united-atom polymers or organic molecules
+ all-atom polymers, organic molecules, proteins, DNA
+ metals
+ granular materials
+ coarse-grained mesoscale models
+ finite-size spherical and ellipsoidal particles
+ finite-size line segment (2d) and triangle (3d) particles
+ point dipole particles
+ rigid collections of particles
+ hybrid combinations of these :ul
+
+Interatomic potentials (force fields) :h4,link(ff)
+("pair style"_pair_style.html, "bond style"_bond_style.html,
+"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
+"improper style"_improper_style.html, "kspace style"_kspace_style.html
+commands)
+
+ pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
+ Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
+ charged pairwise potentials: Coulombic, point-dipole
+ manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
+ embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
+ REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
+ long-range interactions for charge, point-dipoles, and LJ dispersion: \
+ Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
+ polarization models: "QEq"_fix_qeq.html, \
+ "core/shell model"_Howto_coreshell.html, \
+ "Drude dipole model"_Howto_drude.html
+ charge equilibration (QEq via dynamic, point, shielded, Slater methods)
+ coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
+ mesoscopic potentials: granular, Peridynamics, SPH
+ electron force field (eFF, AWPMD)
+ bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
+ quartic (breakable)
+ angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
+ class 2 (COMPASS)
+ dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
+ class 2 (COMPASS), OPLS
+ improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
+ polymer potentials: all-atom, united-atom, bead-spring, breakable
+ water potentials: TIP3P, TIP4P, SPC
+ implicit solvent potentials: hydrodynamic lubrication, Debye
+ force-field compatibility with common CHARMM, AMBER, DREIDING, \
+ OPLS, GROMACS, COMPASS options
+ access to "KIM archive"_http://openkim.org of potentials via \
+ "pair kim"_pair_kim.html
+ hybrid potentials: multiple pair, bond, angle, dihedral, improper \
+ potentials can be used in one simulation
+ overlaid potentials: superposition of multiple pair potentials :ul
+
+Atom creation :h4,link(create)
+("read_data"_read_data.html, "lattice"_lattice.html,
+"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
+"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
+
+ read in atom coords from files
+ create atoms on one or more lattices (e.g. grain boundaries)
+ delete geometric or logical groups of atoms (e.g. voids)
+ replicate existing atoms multiple times
+ displace atoms :ul
+
+Ensembles, constraints, and boundary conditions :h4,link(ensemble)
+("fix"_fix.html command)
+
+ 2d or 3d systems
+ orthogonal or non-orthogonal (triclinic symmetry) simulation domains
+ constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
+ thermostatting options for groups and geometric regions of atoms
+ pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
+ simulation box deformation (tensile and shear)
+ harmonic (umbrella) constraint forces
+ rigid body constraints
+ SHAKE bond and angle constraints
+ Monte Carlo bond breaking, formation, swapping
+ atom/molecule insertion and deletion
+ walls of various kinds
+ non-equilibrium molecular dynamics (NEMD)
+ variety of additional boundary conditions and constraints :ul
+
+Integrators :h4,link(integrate)
+("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
+
+ velocity-Verlet integrator
+ Brownian dynamics
+ rigid body integration
+ energy minimization via conjugate gradient or steepest descent relaxation
+ rRESPA hierarchical timestepping
+ rerun command for post-processing of dump files :ul
+
+Diagnostics :h4,link(diag)
+
+ see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
+
+Output :h4,link(output)
+("dump"_dump.html, "restart"_restart.html commands)
+
+ log file of thermodynamic info
+ text dump files of atom coords, velocities, other per-atom quantities
+ binary restart files
+ parallel I/O of dump and restart files
+ per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
+ user-defined system-wide (log file) or per-atom (dump file) calculations
+ spatial and time averaging of per-atom quantities
+ time averaging of system-wide quantities
+ atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
+
+Multi-replica models :h4,link(replica)
+
+"nudged elastic band"_neb.html
+"parallel replica dynamics"_prd.html
+"temperature accelerated dynamics"_tad.html
+"parallel tempering"_temper.html :ul
+
+Pre- and post-processing :h4,link(prepost)
+
+A handful of pre- and post-processing tools are packaged with LAMMPS,
+some of which can convert input and output files to/from formats used
+by other codes; see the "Toos"_Tools.html doc page. :ulb,l
+
+Our group has also written and released a separate toolkit called
+"Pizza.py"_pizza which provides tools for doing setup, analysis,
+plotting, and visualization for LAMMPS simulations. Pizza.py is
+written in "Python"_python and is available for download from "the
+Pizza.py WWW site"_pizza. :l,ule
+
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+:link(python,http://www.python.org)
+
+Specialized features :h4,link(special)
+
+LAMMPS can be built with optional packages which implement a variety
+of additional capabilities. See the "Packages"_Packages.html doc
+page for details.
+
+These are LAMMPS capabilities which you may not think of as typical
+classical MD options:
+
+"static"_balance.html and "dynamic load-balancing"_fix_balance.html
+"generalized aspherical particles"_Howto_body.html
+"stochastic rotation dynamics (SRD)"_fix_srd.html
+"real-time visualization and interactive MD"_fix_imd.html
+calculate "virtual diffraction patterns"_compute_xrd.html
+"atom-to-continuum coupling"_fix_atc.html with finite elements
+coupled rigid body integration via the "POEMS"_fix_poems.html library
+"QM/MM coupling"_fix_qmmm.html
+Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html
+"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
+"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
+"Peridynamics mesoscale modeling"_pair_peri.html
+"Lattice Boltzmann fluid"_fix_lb_fluid.html
+"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
+"two-temperature electron model"_fix_ttm.html :ul
diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt
new file mode 100644
index 0000000000..41f001fc8b
--- /dev/null
+++ b/doc/src/Intro_nonfeatures.txt
@@ -0,0 +1,83 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS non-features :h3
+
+LAMMPS is designed to be a fast, parallel engine for molecular
+dynamics (MD) simulations. It provides only a modest amount of
+functionality for setting up simulations and analyzing their output.
+
+Specifically, LAMMPS does not:
+
+run thru a GUI
+build molecular systems
+assign force-field coefficients automagically
+perform sophisticated analyses of your MD simulation
+visualize your MD simulation interactively
+plot your output data :ul
+
+Here are suggestions on how to perform these tasks:
+
+GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+the library interface is provided. Thus, GUI interfaces can be
+written in Python (or C or C++ if desired) that run LAMMPS and
+visualize or plot its output. Examples of this are provided in the
+python directory and described on the "Python"_Python.html doc
+page. :ulb,l
+
+Builder: Several pre-processing tools are packaged with LAMMPS. Some
+of them convert input files in formats produced by other MD codes such
+as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them
+are simple programs that will build simple molecular systems, such as
+linear bead-spring polymer chains. The moltemplate program is a true
+molecular builder that will generate complex molecular models. See
+the "Tools"_Tools.html doc page for details on tools packaged with
+LAMMPS. The "Pre/post processing
+page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
+describes a variety of 3rd party tools for this task. :l
+
+Force-field assignment: The conversion tools described in the previous
+bullet for CHARMM, AMBER, and Insight will also assign force field
+coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
+or Accelerys force field files. :l
+
+Simulation analyses: If you want to perform analyses on-the-fly as
+your simulation runs, see the "compute"_compute.html and
+"fix"_fix.html doc pages, which list commands that can be used in a
+LAMMPS input script. Also see the "Modify"_Modify.html doc page for
+info on how to add your own analysis code or algorithms to LAMMPS.
+For post-processing, LAMMPS output such as "dump file
+snapshots"_dump.html can be converted into formats used by other MD or
+post-processing codes. Some post-processing tools packaged with
+LAMMPS will do these conversions. Scripts provided with the {python}
+tool in the tools directory can extract and massage data in dump files
+to make it easier to import into other programs. See the
+"Tools"_Tools.html doc page for details on these various options. :l
+
+Visualization: LAMMPS can produce JPG or PNG snapshot images
+on-the-fly via its "dump image"_dump_image.html command. For
+high-quality, interactive visualization there are many excellent and
+free tools available. See the "Other Codes
+page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
+visualization packages that can use LAMMPS output data. :l
+
+Plotting: See the next bullet about Pizza.py as well as the
+"Python"_Python.html doc page for examples of plotting LAMMPS output.
+Scripts provided with the {python} tool in the tools directory will
+extract and massage data in log and dump files to make it easier to
+analyze and plot. See the "Tools"_Tools.html doc page for more
+discussion of the various tools. :l
+
+Pizza.py: Our group has also written a separate toolkit called
+"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
+setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
+simulations. It thus provides some functionality for several of the
+above bullets. Pizza.py is written in "Python"_http://www.python.org
+and is available for download from "this
+page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule
diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt
new file mode 100644
index 0000000000..e0d57f7ce1
--- /dev/null
+++ b/doc/src/Intro_opensource.txt
@@ -0,0 +1,44 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS open-source license :h3
+
+LAMMPS is a freely-available open-source code, distributed under the
+terms of the "GNU Public License"_gnu, which means you can use or
+modify the code however you wish.
+
+LAMMPS comes with no warranty of any kind. As each source file states
+in its header, it is a copyrighted code that is distributed free-of-
+charge, under the terms of the "GNU Public License"_gnu (GPL). This
+is often referred to as open-source distribution - see
+"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal
+text of the GPL is in the LICENSE file included in the LAMMPS
+distribution.
+
+:link(gnu,http://www.gnu.org/copyleft/gpl.html)
+:link(gnuorg,http://www.gnu.org)
+:link(opensource,http://www.opensource.org)
+
+Here is a summary of what the GPL means for LAMMPS users:
+
+(1) Anyone is free to use, modify, or extend LAMMPS in any way they
+choose, including for commercial purposes.
+
+(2) If you distribute a modified version of LAMMPS, it must remain
+open-source, meaning you distribute it under the terms of the GPL.
+You should clearly annotate such a code as a derivative version of
+LAMMPS.
+
+(3) If you release any code that includes LAMMPS source code, then it
+must also be open-sourced, meaning you distribute it under the terms
+of the GPL.
+
+(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
+source file headers (including the copyright and GPL notices) should
+remain part of the code.
diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt
new file mode 100644
index 0000000000..49c14bc5f0
--- /dev/null
+++ b/doc/src/Intro_overview.txt
@@ -0,0 +1,58 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Overview of LAMMPS :h3
+
+LAMMPS is a classical molecular dynamics (MD) code that models
+ensembles of particles in a liquid, solid, or gaseous state. It can
+model atomic, polymeric, biological, solid-state (metals, ceramics,
+oxides), granular, coarse-grained, or macroscopic systems using a
+variety of interatomic potentials (force fields) and boundary
+conditions. It can model 2d or 3d systems with only a few particles
+up to millions or billions.
+
+LAMMPS can be built and run on a laptop or destop machine, but is
+designed for parallel computers. It will run on any parallel machine
+that supports the "MPI"_mpi message-passing library. This includes
+shared-memory boxes and distributed-memory clusters and
+supercomputers.
+
+:link(mpi,http://www-unix.mcs.anl.gov/mpi)
+
+LAMMPS is written in C++. Earlier versions were written in F77 and
+F90. See the "History page"_http://lammps.sandia.gov/history.html of
+the website for details. All versions can be downloaded from the
+"LAMMPS website"_lws.
+
+LAMMPS is designed to be easy to modify or extend with new
+capabilities, such as new force fields, atom types, boundary
+conditions, or diagnostics. See the "Modify"_Modify.html doc page for
+more details.
+
+In the most general sense, LAMMPS integrates Newton's equations of
+motion for a collection of interacting particles. A single particle
+can be an atom or molecule or electron, a coarse-grained cluster of
+atoms, or a mesoscopic or macroscopic clump of material. The
+interaction models that LAMMPS includes are mostly short-range in
+nature; some long-range models are included as well.
+
+LAMMPS uses neighbor lists to keep track of nearby particles. The
+lists are optimized for systems with particles that are repulsive at
+short distances, so that the local density of particles never becomes
+too large. This is in contrast to methods used for modeling plasmas
+or gravitational bodies (e.g. galaxy formation).
+
+On parallel machines, LAMMPS uses spatial-decomposition techniques to
+partition the simulation domain into small sub-domains of equal
+computational cost, one of which is assigned to each processor.
+Processors communicate and store "ghost" atom information for atoms
+that border their sub-domain.
+
+
+
diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt
new file mode 100644
index 0000000000..a8af94157c
--- /dev/null
+++ b/doc/src/Intro_website.txt
@@ -0,0 +1,42 @@
+"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Additional website links :h3
+
+The "LAMMPS website"_lws has a variety of additional info about
+LAMMPS, beyond what is in this manual. Some of the other pages in
+this Intr are included in this list.
+
+"Brief intro and recently added significant features"_lws
+"List of features"_http://lammps.sandia.gov/features.html
+"List of non-features"_http://lammps.sandia.gov/non_features.html
+"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul
+
+"Download info"_http://lammps.sandia.gov/download.html
+"GitHub site"_https://github.com/lammps/lammps
+"SourceForge site"_https://sourceforge.net/projects/lammps
+"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul
+
+"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html
+"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html
+"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html
+"Mail list"_http://lammps.sandia.gov/mail.html
+"Workshops"_http://lammps.sandia.gov/workshops.html
+"Tutorials"_http://lammps.sandia.gov/tutorials.html
+"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul
+
+"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html
+"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html
+"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul
+
+"Benchmark performance"_http://lammps.sandia.gov/bench.html
+"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html
+"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html
+"History of LAMMPS development"_http://lammps.sandia.gov/history.html
+"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 4481c911a0..a5e8b63640 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
-<
+<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Jul 2018 version">
+<META NAME="docnumber" CONTENT="2 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -14,90 +14,53 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html#comm)
:line
-LAMMPS Documentation :c,h1
-16 Jul 2018 version :c,h2
-
-Version info: :h3
-
-The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on "this page of
-the WWW site"_bug. Every 2-4 months one of the incremental releases
-is subjected to more thorough testing and labeled as a {stable} version.
-
-Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-
-If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current [development] version of LAMMPS. :ulb,l
+<H1></H1>
-If you browse the HTML doc pages included in your tarball, they
-describe the version you have. :l
-
-The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
-about once per month. This is because it is large, and we don't want
-it to be part of every patch. :l
+LAMMPS Documentation :c,h1
+2 Aug 2018 version :c,h2
-There is also a "Developer.pdf"_Developer.pdf file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS. :l
-:ule
+"What is a LAMMPS version?"_Manual_version.html
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
-LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers. It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE. It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
+LAMMPS is a classical molecular dynamics simulation code with a focus
+on materials modeling. It was designed to run efficiently on parallel
+computers. It was developed originally at Sandia National
+Laboratories, a US Department of Energy facility. The majority of
+funding for LAMMPS has come from the US Department of Energy (DOE).
+LAMMPS is an open-source code, distributed freely under the terms of
+the GNU Public License (GPL).
-The current core group of LAMMPS developers is at Sandia National
-Labs and Temple University:
+The "LAMMPS website"_lws has a variety of information about the code.
+It includes links to an on-line version of this manual, a "mail
+list"_http://lammps.sandia.gov/mail.html where users can post
+questions, and a "GitHub site"https://github.com/lammps/lammps where
+all LAMMPS development is coordinated.
-"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
-Aidan Thompson, athomps at sandia.gov :l
-Stan Moore, stamoor at sandia.gov :l
-"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
-:ule
+:line
-Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
-all at Sandia. The [LAMMPS home page] at
-"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information
-about the code and its uses. Interaction with external LAMMPS developers,
-bug reports and feature requests are mainly coordinated through the
-"LAMMPS project on GitHub."_https://github.com/lammps/lammps
-The lammps.org domain, currently hosting "public continuous integration
-testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://packages.lammps.org is located
-at Temple University and managed by Richard Berger,
-richard.berger at temple.edu.
+"PDF file"_Manual.pdf of the entire manual, generated by
+"htmldoc"_http://freecode.com/projects/htmldoc
-:link(bug,http://lammps.sandia.gov/bug.html)
-:link(sjp,http://www.sandia.gov/~sjplimp)
-:link(ako,http://goo.gl/1wk0)
+The content for this manual is part of the LAMMPS distribution.
+You can build a local copy of the Manual as HTML pages or a PDF file,
+by following the steps on the "this page"_Build_manual.html.
+
+There is also a "Developer.pdf"_Developer.pdf document which gives
+a brief description of the basic code structure of LAMMPS.
:line
-The LAMMPS documentation is organized into the following sections. If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
+This manual is organized into the following sections.
Once you are familiar with LAMMPS, you may want to bookmark "this
-page"_Section_commands.html#comm at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
+page"_Commands.html since it gives quick access to a doc page for
+every LAMMPS command.
<!-- RST
@@ -108,26 +71,23 @@ it gives quick access to documentation for all LAMMPS commands.
:name: userdoc
:includehidden:
- Section_intro
+ Intro
Section_start
- Section_commands
- Section_packages
- Section_accelerate
- Section_howto
+ Commands
+ Packages
+ Speed
+ Howto
Examples
- Section_perf
Tools
Modify
Python
Errors
- Section_history
.. toctree::
:caption: Index
:name: index
:hidden:
- tutorials
commands
fixes
computes
@@ -146,12 +106,7 @@ Indices and tables
END_RST -->
<!-- HTML_ONLY -->
-"Introduction"_Section_intro.html :olb,l
- 1.1 "What is LAMMPS"_intro_1 :ulb,b
- 1.2 "LAMMPS features"_intro_2 :b
- 1.3 "LAMMPS non-features"_intro_3 :b
- 1.4 "Open source distribution"_intro_4 :b
- 1.5 "Acknowledgments and citations"_intro_5 :ule,b
+"Introduction"_Intro.html :olb,l
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
@@ -161,70 +116,17 @@ END_RST -->
2.6 "Command-line options"_start_6 :b
2.7 "Screen output"_start_7 :b
2.8 "Tips for users of previous versions"_start_8 :ule,b
-"Commands"_Section_commands.html :l
- 3.1 "LAMMPS input script"_cmd_1 :ulb,b
- 3.2 "Parsing rules"_cmd_2 :b
- 3.3 "Input script structure"_cmd_3 :b
- 3.4 "Commands listed by category"_cmd_4 :b
- 3.5 "Commands listed alphabetically"_cmd_5 :ule,b
-"Packages"_Section_packages.html :l
- 4.1 "Standard packages"_pkg_1 :ulb,b
- 4.2 "User packages"_pkg_2 :ule,b
-"Accelerating LAMMPS performance"_Section_accelerate.html :l
- 5.1 "Measuring performance"_acc_1 :ulb,b
- 5.2 "Algorithms and code options to boost performace"_acc_2 :b
- 5.3 "Accelerator packages with optimized styles"_acc_3 :b
- 5.3.1 "GPU package"_accelerate_gpu.html :b
- 5.3.2 "USER-INTEL package"_accelerate_intel.html :b
- 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
- 5.3.4 "USER-OMP package"_accelerate_omp.html :b
- 5.3.5 "OPT package"_accelerate_opt.html :b
- 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
-"How-to discussions"_Section_howto.html :l
- 6.1 "Restarting a simulation"_howto_1 :ulb,b
- 6.2 "2d simulations"_howto_2 :b
- 6.3 "CHARMM and AMBER force fields"_howto_3 :b
- 6.4 "Running multiple simulations from one input script"_howto_4 :b
- 6.5 "Multi-replica simulations"_howto_5 :b
- 6.6 "Granular models"_howto_6 :b
- 6.7 "TIP3P water model"_howto_7 :b
- 6.8 "TIP4P water model"_howto_8 :b
- 6.9 "SPC water model"_howto_9 :b
- 6.10 "Coupling LAMMPS to other codes"_howto_10 :b
- 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
- 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
- 6.13 "NEMD simulations"_howto_13 :b
- 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
- 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
- 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
- 6.17 "Walls"_howto_17 :b
- 6.18 "Elastic constants"_howto_18 :b
- 6.19 "Library interface to LAMMPS"_howto_19 :b
- 6.20 "Calculating thermal conductivity"_howto_20 :b
- 6.21 "Calculating viscosity"_howto_21 :b
- 6.22 "Calculating a diffusion coefficient"_howto_22 :b
- 6.23 "Using chunks to calculate system properties"_howto_23 :b
- 6.24 "Setting parameters for pppm/disp"_howto_24 :b
- 6.25 "Polarizable models"_howto_25 :b
- 6.26 "Adiabatic core/shell model"_howto_26 :b
- 6.27 "Drude induced dipoles"_howto_27 :ule,b
+"Commands"_Commands.html :l
+"Optional packages"_Packages.html :l
+"Accelerate performance"_Speed.html :l
+"How-to discussions"_Howto.html :l
"Example scripts"_Examples.html :l
-"Performance & scalability"_Section_perf.html :l
"Auxiliary tools"_Tools.html :l
"Modify & extend LAMMPS"_Modify.html :l
"Use Python with LAMMPS"_Python.html :l
"Errors"_Errors.html :l
-"Future and history"_Section_history.html :l
- 13.1 "Coming attractions"_hist_1 :ulb,b
- 13.2 "Past versions"_hist_2 :ule,b
:ole
-:link(intro_1,Section_intro.html#intro_1)
-:link(intro_2,Section_intro.html#intro_2)
-:link(intro_3,Section_intro.html#intro_3)
-:link(intro_4,Section_intro.html#intro_4)
-:link(intro_5,Section_intro.html#intro_5)
-
:link(start_1,Section_start.html#start_1)
:link(start_2,Section_start.html#start_2)
:link(start_3,Section_start.html#start_3)
@@ -234,50 +136,6 @@ END_RST -->
:link(start_7,Section_start.html#start_7)
:link(start_8,Section_start.html#start_8)
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
-:link(pkg_1,Section_packages.html#pkg_1)
-:link(pkg_2,Section_packages.html#pkg_2)
-
-:link(acc_1,Section_accelerate.html#acc_1)
-:link(acc_2,Section_accelerate.html#acc_2)
-:link(acc_3,Section_accelerate.html#acc_3)
-:link(acc_4,Section_accelerate.html#acc_4)
-
-:link(howto_1,Section_howto.html#howto_1)
-:link(howto_2,Section_howto.html#howto_2)
-:link(howto_3,Section_howto.html#howto_3)
-:link(howto_4,Section_howto.html#howto_4)
-:link(howto_5,Section_howto.html#howto_5)
-:link(howto_6,Section_howto.html#howto_6)
-:link(howto_7,Section_howto.html#howto_7)
-:link(howto_8,Section_howto.html#howto_8)
-:link(howto_9,Section_howto.html#howto_9)
-:link(howto_10,Section_howto.html#howto_10)
-:link(howto_11,Section_howto.html#howto_11)
-:link(howto_12,Section_howto.html#howto_12)
-:link(howto_13,Section_howto.html#howto_13)
-:link(howto_14,Section_howto.html#howto_14)
-:link(howto_15,Section_howto.html#howto_15)
-:link(howto_16,Section_howto.html#howto_16)
-:link(howto_17,Section_howto.html#howto_17)
-:link(howto_18,Section_howto.html#howto_18)
-:link(howto_19,Section_howto.html#howto_19)
-:link(howto_20,Section_howto.html#howto_20)
-:link(howto_21,Section_howto.html#howto_21)
-:link(howto_22,Section_howto.html#howto_22)
-:link(howto_23,Section_howto.html#howto_23)
-:link(howto_24,Section_howto.html#howto_24)
-:link(howto_25,Section_howto.html#howto_25)
-:link(howto_26,Section_howto.html#howto_26)
-:link(howto_27,Section_howto.html#howto_27)
-
-:link(hist_1,Section_history.html#hist_1)
-:link(hist_2,Section_history.html#hist_2)
<!-- END_HTML_ONLY -->
</BODY>
diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt
new file mode 100644
index 0000000000..8583eabf86
--- /dev/null
+++ b/doc/src/Manual_version.txt
@@ -0,0 +1,33 @@
+"Higher level section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+What does a LAMMPS version mean: :h3
+
+The LAMMPS "version" is the date when it was released, such as 1 May
+2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
+feature, we release it in the next {patch} release, which are
+typically made every couple of weeks. Info on patch releases are on
+"this website page"_http://lammps.sandia.gov/bug.html. Every few
+months, the latest patch release is subjected to more thorough testing
+and labeled as a {stable} version.
+
+Each version of LAMMPS contains all the features and bug-fixes up to
+and including its version date.
+
+The version date is printed to the screen and logfile every time you
+run LAMMPS. It is also in the file src/version.h and in the LAMMPS
+directory name created when you unpack a tarball. And it is on the
+first page of the "manual"_Manual.html.
+
+If you browse the HTML doc pages on the LAMMPS WWW site, they always
+describe the most current patch release of LAMMPS. :ulb,l
+
+If you browse the HTML doc pages included in your tarball, they
+describe the version you have, which may be older. :l,ule
+
diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt
index ae0b0dc6bd..f828bd5d74 100644
--- a/doc/src/Modify.txt
+++ b/doc/src/Modify.txt
@@ -4,7 +4,7 @@ Section"_Python.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt
index afa1c319d2..60c7dccb29 100644
--- a/doc/src/Modify_atom.txt
+++ b/doc/src/Modify_atom.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt
index b1dc8130cd..0114ae10c8 100644
--- a/doc/src/Modify_body.txt
+++ b/doc/src/Modify_body.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -14,10 +14,9 @@ Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
-See "Section 6.14"_Section_howto.html#howto_14 of the manual for
-an overview of using body particles and the "body"_body.html doc page
-for details on the various body styles LAMMPS supports. New styles
-can be created to add new kinds of body particles to LAMMPS.
+See the "Howto body"_Howto_body.html doc page for an overview of using
+body particles and the various body styles LAMMPS supports. New
+styles can be created to add new kinds of body particles to LAMMPS.
Body_nparticle.cpp is an example of a body particle that is treated as
a rigid body containing N sub-particles.
diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt
index f0828a0c3b..7ceea3f910 100644
--- a/doc/src/Modify_bond.txt
+++ b/doc/src/Modify_bond.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt
index 6fc9aad1fc..4576f6c806 100644
--- a/doc/src/Modify_command.txt
+++ b/doc/src/Modify_command.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt
index b02b8a983e..2f6481dbd5 100644
--- a/doc/src/Modify_compute.txt
+++ b/doc/src/Modify_compute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index 80795b5e20..ef9fe6a717 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,14 +32,14 @@ How quickly your contribution will be integrated depends largely on
how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
-typical requirements. Once you have prepared everything, see "this
-tutorial"_tutorial_github.html for instructions on how to submit your
-changes or new files through a GitHub pull request. If you prefer to
-submit patches or full files, you should first make certain, that your
-code works correctly with the latest patch-level version of LAMMPS and
-contains all bugfixes from it. Then create a gzipped tar file of all
-changed or added files or a corresponding patch file using 'diff -u'
-or 'diff -c' and compress it with gzip. Please only use gzip
+typical requirements. Once you have prepared everything, see the
+"Howto github"_Howto_github.html doc page for instructions on how to
+submit your changes or new files through a GitHub pull request. If you
+prefer to submit patches or full files, you should first make certain,
+that your code works correctly with the latest patch-level version of
+LAMMPS and contains all bugfixes from it. Then create a gzipped tar
+file of all changed or added files or a corresponding patch file using
+'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
@@ -54,8 +54,9 @@ packages by typing "make package" in the LAMMPS src directory.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
-used as a license for the rest of LAMMPS. See "Section
-1.4"_Section_intro.html#intro_4 for details.
+used as a license for the rest of LAMMPS. See the "Open
+source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS
+website for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt
index 81af54e003..cfe96f5d3d 100644
--- a/doc/src/Modify_dump.txt
+++ b/doc/src/Modify_dump.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt
index ba985475cc..b095ebc4b5 100644
--- a/doc/src/Modify_fix.txt
+++ b/doc/src/Modify_fix.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt
index 21407bf2e9..d5f018411d 100644
--- a/doc/src/Modify_kspace.txt
+++ b/doc/src/Modify_kspace.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt
index 5dcf0f1e67..8252a576f3 100644
--- a/doc/src/Modify_min.txt
+++ b/doc/src/Modify_min.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt
index f9964d964b..cf94b40281 100644
--- a/doc/src/Modify_overview.txt
+++ b/doc/src/Modify_overview.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt
index 8c234dc621..0ebf2daa30 100644
--- a/doc/src/Modify_pair.txt
+++ b/doc/src/Modify_pair.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt
index 9fbf359292..cdf192323a 100644
--- a/doc/src/Modify_region.txt
+++ b/doc/src/Modify_region.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt
index 001a9f99e1..1772bae87a 100644
--- a/doc/src/Modify_thermo.txt
+++ b/doc/src/Modify_thermo.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt
index 3c5b29cd1a..b163272f3e 100644
--- a/doc/src/Modify_variable.txt
+++ b/doc/src/Modify_variable.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
new file mode 100644
index 0000000000..a7f45a99b7
--- /dev/null
+++ b/doc/src/Packages.txt
@@ -0,0 +1,39 @@
+"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Speed.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Optional packages :h2
+
+This section gives an overview of the optional packages that extend
+LAMMPS functionality. Packages are groups of files that enable a
+specific set of features. For example, force fields for molecular
+systems or rigid-body constraint are in packages. You can see the
+list of all packages and "make" commands to manage them by typing
+"make package" from within the src directory of the LAMMPS
+distribution. "Section 2.3"_Section_start.html#start_3 gives general
+info on how to install and un-install packages as part of the LAMMPS
+build process.
+
+<!-- RST
+
+.. toctree::
+
+ Packages_standard
+ Packages_user
+ Packages_details
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Standard packages"_Packages_standard.html
+"User packages"_Packages_user.html
+"Details on each package"_Packages_details.html :ul
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Section_packages.txt b/doc/src/Packages_details.txt
similarity index 85%
rename from doc/src/Section_packages.txt
rename to doc/src/Packages_details.txt
index 340a77310d..eb92fe4dc4 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Packages_details.txt
@@ -1,159 +1,96 @@
-"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_accelerate.html :c
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-4. Packages :h2
-
-This section gives an overview of the optional packages that extend
-LAMMPS functionality with instructions on how to build LAMMPS with
-each of them. Packages are groups of files that enable a specific set
-of features. For example, force fields for molecular systems or
-granular systems are in packages. You can see the list of all
-packages and "make" commands to manage them by typing "make package"
-from within the src directory of the LAMMPS distribution. "Section
-2.3"_Section_start.html#start_3 gives general info on how to install
-and un-install packages as part of the LAMMPS build process.
-
-There are two kinds of packages in LAMMPS, standard and user packages:
-
-"Table of standard packages"_#table_standard
-"Table of user packages"_#table_user :ul
-
-Either of these kinds of packages may work as is, may require some
-additional code compiled located in the lib folder, or may require
-an external library to be downloaded, compiled, installed, and LAMMPS
-configured to know about its location and additional compiler flags.
-You can often do the build of the internal or external libraries
-in one step by typing "make lib-name args='...'" from the src dir,
-with appropriate arguments included in args='...'. If you just type
-"make lib-name" you should see a help message about supported flags
-and some examples. For more details about this, please study the
-tables below and the sections about the individual packages.
-
-Standard packages are supported by the LAMMPS developers and are
-written in a syntax and style consistent with the rest of LAMMPS.
-This means the developers will answer questions about them, debug and
-fix them if necessary, and keep them compatible with future changes to
-LAMMPS.
-
-User packages have been contributed by users, and begin with the
-"user" prefix. If they are a single command (single file), they are
-typically in the user-misc package. User packages don't necessarily
-meet the requirements of the standard packages. This means the
-developers will try to keep things working and usually can answer
-technical questions about compiling the package. If you have problems
-using a feature provided in a user package, you may need to contact
-the contributor directly to get help. Information on how to submit
-additions you make to LAMMPS as single files or as a standard or user
-package are given in the "Modify contribute"_Modify.html doc page.
-
-Following the next two tables is a sub-section for each package. It
-lists authors (if applicable) and summarizes the package contents. It
-has specific instructions on how to install the package, including (if
-necessary) downloading or building any extra library it requires. It
-also gives links to documentation, example scripts, and
-pictures/movies (if available) that illustrate use of the package.
+:link(lc,Commands_all.html)
+
+:line
+
+Package details :h3
+
+Here is a brief description of all the standard and user packages in
+LAMMPS. It lists authors (if applicable) and summarizes the package
+contents. It has specific instructions on how to install the package,
+including, if necessary, info on how to download or build any extra
+library it requires. It also gives links to documentation, example
+scripts, and pictures/movies (if available) that illustrate use of the
+package.
NOTE: To see the complete list of commands a package adds to LAMMPS,
-just look at the files in its src directory, e.g. "ls src/GRANULAR".
-Files with names that start with fix, compute, atom, pair, bond,
-angle, etc correspond to commands with the same style names.
-
-In these two tables, the "Example" column is a sub-directory in the
-examples directory of the distribution which has an input script that
-uses the package. E.g. "peptide" refers to the examples/peptide
-directory; USER/atc refers to the examples/USER/atc directory. The
-"Library" column indicates whether an extra library is needed to build
-and use the package:
-
-dash = no library
-sys = system library: you likely have it on your machine
-int = internal library: provided with LAMMPS, but you may need to build it
-ext = external library: you will need to download and install it on your machine :ul
-
-:line
-:line
-
-[Standard packages] :link(table_standard),p
-
-Package, Description, Doc page, Example, Library
-"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
-"BODY"_#BODY, body-style particles, "body"_body.html, body, -
-"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
-"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
-"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
-"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_#MISC, miscellanous single-file commands, -, -, -
-"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
-"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
-"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
-"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
-"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
-"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
-"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_#SPIN, magnetic atomic spin dynamics, "Section 6.6.28"_Section_howto.html#howto_28, SPIN, -
-"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
-
-[USER packages] :link(table_user),p
-
-Package, Description, Doc page, Example, Library
-"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
-"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
-"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, -
-"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
-"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
-"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
-"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
-"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
-"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
-"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+you can examine the files in its src directory, e.g. "ls
+src/GRANULAR". Files with names that start with fix, compute, atom,
+pair, bond, angle, etc correspond to commands with the same style name
+as contained in the file name.
+
+"ASPHERE"_#ASPHERE,
+"BODY"_#BODY,
+"CLASS2"_#CLASS2,
+"COLLOID"_#COLLOID,
+"COMPRESS"_#COMPRESS,
+"CORESHELL"_#CORESHELL,
+"DIPOLE"_#DIPOLE,
+"GPU"_#GPU,
+"GRANULAR"_#GRANULAR,
+"KIM"_#KIM,
+"KOKKOS"_#KOKKOS,
+"KSPACE"_#KSPACE,
+"LATTE"_#LATTE,
+"MANYBODY"_#MANYBODY,
+"MC"_#MC,
+"MEAM"_#MEAM,
+"MISC"_#MISC,
+"MOLECULE"_#MOLECULE,
+"MPIIO"_#MPIIO,
+"MSCG"_#MSCG,
+"OPT"_#OPT,
+"PERI"_#PERI,
+"POEMS"_#POEMS,
+"PYTHON"_#PYTHON,
+"QEQ"_#QEQ,
+"REAX"_#REAX,
+"REPLICA"_#REPLICA,
+"RIGID"_#RIGID,
+"SHOCK"_#SHOCK,
+"SNAP"_#SNAP,
+"SPIN"_#SPIN,
+"SRD"_#SRD,
+"VORONOI"_#VORONOI :tb(c=6,ea=c)
+
+"USER-ATC"_#USER-ATC,
+"USER-AWPMD"_#USER-AWPMD,
+"USER-BOCS"_#USER-BOCS,
+"USER-CGDNA"_#USER-CGDNA,
+"USER-CGSDK"_#USER-CGSDK,
+"USER-COLVARS"_#USER-COLVARS,
+"USER-DIFFRACTION"_#USER-DIFFRACTION,
+"USER-DPD"_#USER-DPD,
+"USER-DRUDE"_#USER-DRUDE,
+"USER-EFF"_#USER-EFF,
+"USER-FEP"_#USER-FEP,
+"USER-H5MD"_#USER-H5MD,
+"USER-INTEL"_#USER-INTEL,
+"USER-LB"_#USER-LB,
+"USER-MANIFOLD"_#USER-MANIFOLD,
+"USER-MEAMC"_#USER-MEAMC,
+"USER-MESO"_#USER-MESO,
+"USER-MGPT"_#USER-MGPT,
+"USER-MISC"_#USER-MISC,
+"USER-MOFFF"_#USER-MOFFF,
+"USER-MOLFILE"_#USER-MOLFILE,
+"USER-NETCDF"_#USER-NETCDF,
+"USER-OMP"_#USER-OMP,
+"USER-PHONON"_#USER-PHONON,
+"USER-QMMM"_#USER-QMMM,
+"USER-QTB"_#USER-QTB,
+"USER-QUIP"_#USER-QUIP,
+"USER-REAXC"_#USER-REAXC,
+"USER-SMD"_#USER-SMD,
+"USER-SMTBQ"_#USER-SMTBQ,
+"USER-SPH"_#USER-SPH,
+"USER-TALLY"_#USER-TALLY,
+"USER-UEF"_#USER-UEF,
+"USER-VTK"_#USER-VTK :tb(c=6,ea=c)
:line
:line
@@ -176,7 +113,7 @@ make machine :pre
[Supporting info:]
src/ASPHERE: filenames -> commands
-"Section 6.14"_Section_howto.html#howto_14
+"Howto spherical"_Howto_spherical.html
"pair_style gayberne"_pair_gayberne.html
"pair_style resquared"_pair_resquared.html
"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
@@ -194,7 +131,8 @@ BODY package :link(BODY),h4
Body-style particles with internal structure. Computes,
time-integration fixes, pair styles, as well as the body styles
-themselves. See the "body"_body.html doc page for an overview.
+themselves. See the "Howto body"_Howto_body.html doc page for an
+overview.
[Install or un-install:]
@@ -207,10 +145,10 @@ make machine :pre
[Supporting info:]
src/BODY filenames -> commands
-"body"_body.html
+"Howto_body"_Howto_body.html
"atom_style body"_atom_style.html
"fix nve/body"_fix_nve_body.html
-"pair_style body"_pair_body.html
+"pair_style body/nparticle"_pair_body_nparticle.html
examples/body :ul
:line
@@ -322,9 +260,9 @@ Compute and pair styles that implement the adiabatic core/shell model
for polarizability. The pair styles augment Born, Buckingham, and
Lennard-Jones styles with core/shell capabilities. The "compute
temp/cs"_compute_temp_cs.html command calculates the temperature of a
-system with core/shell particles. See "Section
-6.26"_Section_howto.html#howto_26 for an overview of how to use this
-package.
+system with core/shell particles. See the "Howto
+coreshell"_Howto_coreshell.html doc page for an overview of how to use
+this package.
[Author:] Hendrik Heenen (Technical U of Munich).
@@ -339,8 +277,8 @@ make machine :pre
[Supporting info:]
src/CORESHELL: filenames -> commands
-"Section 6.26"_Section_howto.html#howto_26
-"Section 6.25"_Section_howto.html#howto_25
+"Howto coreshell"_Howto_coreshell.html
+"Howto polarizable"_Howto_polarizable.html
"compute temp/cs"_compute_temp_cs.html
"pair_style born/coul/long/cs"_pair_cs.html
"pair_style buck/coul/long/cs"_pair_cs.html
@@ -380,14 +318,14 @@ GPU package :link(GPU),h4
[Contents:]
Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for GPUs. All such styles have a "gpu" as a
-suffix in their style name. The GPU code can be compiled with either
-CUDA or OpenCL, however the OpenCL variants are no longer actively
-maintained and only the CUDA versions are regularly tested.
-"Section 5.3.1"_accelerate_gpu.html gives details of what
-hardware and GPU software is required on your system,
-and details on how to build and use this package. Its styles can be
-invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
+solver optimized for GPUs. All such styles have a "gpu" as a suffix
+in their style name. The GPU code can be compiled with either CUDA or
+OpenCL, however the OpenCL variants are no longer actively maintained
+and only the CUDA versions are regularly tested. The "Speed
+gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
+software is required on your system, and details on how to build and
+use this package. Its styles can be invoked at run time via the "-sf
+gpu" or "-suffix gpu" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
package, which has GPU-enabled styles.
@@ -453,12 +391,12 @@ GPU library.
src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.1"_accelerate_gpu.html
+"Speed packages"_Speed_packages.html
+"Speed gpu"_Speed_gpu.html.html
"Section 2.6 -sf gpu"_Section_start.html#start_6
"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
+"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -482,7 +420,7 @@ make machine :pre
[Supporting info:]
src/GRANULAR: filenames -> commands
-"Section 6.6"_Section_howto.html#howto_6,
+"Howto granular"_Howto_granular.html
"fix pour"_fix_pour.html
"fix wall/gran"_fix_wall_gran.html
"pair_style gran/hooke"_pair_gran.html
@@ -549,8 +487,8 @@ See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
-https://openkim.org/kim-api in the "What is in the KIM API source
-package?" section
+https://openkim.org/kim-api on the "What is in the KIM API source
+package?" page.
You can then install/un-install the package and build LAMMPS in the
usual manner:
@@ -579,10 +517,10 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
-style name. "Section 5.3.3"_accelerate_kokkos.html gives details of
-what hardware and software is required on your system, and how to
-build and use this package. Its styles can be invoked at run time via
-the "-sf kk" or "-suffix kk" "command-line
+style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
+details of what hardware and software is required on your system, and
+how to build and use this package. Its styles can be invoked at run
+time via the "-sf kk" or "-suffix kk" "command-line
switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs, KNLs, and GPUs.
@@ -649,13 +587,13 @@ make machine :pre
src/KOKKOS: filenames -> commands
src/KOKKOS/README
lib/kokkos/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.3"_accelerate_kokkos.html
+"Speed packages"_Speed_packages.html
+"Speed kokkos"_Speed_kokkos.html
"Section 2.6 -k on ..."_Section_start.html#start_6
"Section 2.6 -sf kk"_Section_start.html#start_6
"Section 2.6 -pk kokkos"_Section_start.html#start_6
"package kokkos"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -689,11 +627,11 @@ make machine :pre
src/KSPACE: filenames -> commands
"kspace_style"_kspace_style.html
"doc/PDF/kspace.pdf"_PDF/kspace.pdf
-"Section 6.7"_Section_howto.html#howto_7
-"Section 6.8"_Section_howto.html#howto_8
-"Section 6.9"_Section_howto.html#howto_9
+"Howto tip3p"_Howto_tip3p.html
+"Howto tip4p"_Howto_tip4p.html
+"Howto spc"_Howto_spc.html
"pair_style coul"_pair_coul.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name
+"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
examples/peptide
bench/in.rhodo :ul
@@ -777,7 +715,7 @@ make machine :pre
[Supporting info:]
src/MANYBODY: filenames -> commands
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+"Commands pair"_Commands_pair.html page
examples/comb
examples/eim
examples/nb3d
@@ -940,7 +878,7 @@ src/MOLECULE: filenames -> commands
"improper_style"_improper_style.html
"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
"pair_style lj/charmm/coul/charmm"_pair_charmm.html
-"Section 6.3"_Section_howto.html#howto_3
+"Howto bioFF"_Howto_bioFF.html
examples/cmap
examples/dreiding
examples/micelle,
@@ -1048,9 +986,9 @@ OPT package :link(OPT),h4
A handful of pair styles which are optimized for improved CPU
performance on single or multiple cores. These include EAM, LJ,
CHARMM, and Morse potentials. The styles have an "opt" suffix in
-their style name. "Section 5.3.5"_accelerate_opt.html gives details
-of how to build and use this package. Its styles can be invoked at
-run time via the "-sf opt" or "-suffix opt" "command-line
+their style name. The "Speed opt"_Speed_opt.html doc page gives
+details of how to build and use this package. Its styles can be
+invoked at run time via the "-sf opt" or "-suffix opt" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
@@ -1076,10 +1014,10 @@ CCFLAGS: add -restrict for Intel compilers :ul
[Supporting info:]
src/OPT: filenames -> commands
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.5"_accelerate_opt.html
+"Speed packages"_Speed_packages.html
+"Speed opt"_Speed_opt.html
"Section 2.6 -sf opt"_Section_start.html#start_6
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
+"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -1180,8 +1118,8 @@ A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and the "Python"_Python.html doc page for other
-ways to use LAMMPS and Python together.
+LAMMPS in this manner and all the "Python"_Python.html doc pages for
+other ways to use LAMMPS and Python together.
[Install or un-install:]
@@ -1202,7 +1140,7 @@ to Makefile.lammps) if the LAMMPS build fails.
[Supporting info:]
src/PYTHON: filenames -> commands
-"Python call"_Python_call.html
+"Python call"_Python.html
lib/python/README
examples/python :ul
@@ -1292,8 +1230,8 @@ REPLICA package :link(REPLICA),h4
[Contents:]
A collection of multi-replica methods which can be used when running
-multiple LAMMPS simulations (replicas). See "Section
-6.5"_Section_howto.html#howto_5 for an overview of how to run
+multiple LAMMPS simulations (replicas). See the "Howto
+replica"_Howto_replica.html doc page for an overview of how to run
multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
@@ -1312,7 +1250,7 @@ make machine :pre
[Supporting info:]
src/REPLICA: filenames -> commands
-"Section 6.5"_Section_howto.html#howto_5
+"Howto replica"_Howto_replica.html
"neb"_neb.html
"prd"_prd.html
"tad"_tad.html
@@ -1435,7 +1373,7 @@ make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
-"Section 6.28"_Section_howto.html#howto_28
+"Howto spin"_Howto_spin.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
@@ -1894,10 +1832,10 @@ USER-DRUDE package :link(USER-DRUDE),h4
[Contents:]
Fixes, pair styles, and a compute to simulate thermalized Drude
-oscillators as a model of polarization. See "Section
-6.27"_Section_howto.html#howto_27 for an overview of how to use the
-package. There are auxiliary tools for using this package in
-tools/drude.
+oscillators as a model of polarization. See the "Howto
+drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
+for an overview of how to use the package. There are auxiliary tools
+for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
@@ -1913,8 +1851,9 @@ make machine :pre
[Supporting info:]
src/USER-DRUDE: filenames -> commands
-"Section 6.27"_Section_howto.html#howto_27
-"Section 6.25"_Section_howto.html#howto_25
+"Howto drude"_Howto_drude.html
+"Howto drude2"_Howto_drude2.html
+"Howto polarizable"_Howto_polarizable.html
src/USER-DRUDE/README
"fix drude"_fix_drude.html
"fix drude/transform/*"_fix_drude_transform.html
@@ -2065,8 +2004,8 @@ USER-INTEL package :link(USER-INTEL),h4
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
-All of them have an "intel" in their style name. "Section
-5.3.2"_accelerate_intel.html gives details of what hardware and
+All of them have an "intel" in their style name. The "Speed
+intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
"-suffix intel" "command-line switches"_Section_start.html#start_6.
@@ -2116,7 +2055,7 @@ hardware target, to produce a separate executable.
You should also typically install the USER-OMP package, as it can be
used in tandem with the USER-INTEL package to good effect, as
-explained in "Section 5.3.2"_accelerate_intel.html.
+explained on the "Speed intel"_Speed_intel.html doc page.
make yes-user-intel yes-user-omp
make machine :pre
@@ -2128,12 +2067,12 @@ make machine :pre
src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.2"_accelerate_gpu.html
+"Speed packages"_Speed_packages.html
+"Speed intel"_Speed_intel.html
"Section 2.6 -sf intel"_Section_start.html#start_6
"Section 2.6 -pk intel"_Section_start.html#start_6
"package intel"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2254,7 +2193,7 @@ make machine :pre
src/USER-MANIFOLD: filenames -> commands
src/USER-MANIFOLD/README
-"doc/manifolds"_manifolds.html
+"Howto manifold"_Howto_manifold.html
"fix manifoldforce"_fix_manifoldforce.html
"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
@@ -2475,10 +2414,10 @@ USER-OMP package :link(USER-OMP),h4
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
kspace styles which are altered to enable threading on many-core CPUs
via OpenMP directives. All of them have an "omp" in their style name.
-"Section 5.3.4"_accelerate_omp.html gives details of what hardware and
-compilers are required on your system, and how to build and use this
-package. Its styles can be invoked at run time via the "-sf omp" or
-"-suffix omp" "command-line switches"_Section_start.html#start_6.
+The "Speed omp"_Speed_omp.html doc page gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package. Its styles can be invoked at run time via the "-sf omp"
+or "-suffix omp" "command-line switches"_Section_start.html#start_6.
Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
CPUs.
@@ -2513,12 +2452,12 @@ LINKFLAGS: add -fopenmp :ul
src/USER-OMP: filenames -> commands
src/USER-OMP/README
-"Section 5.3"_Section_accelerate.html#acc_3
-"Section 5.3.4"_accelerate_omp.html
+"Speed packages"_Speed_packages.html
+"Speed omp"_Speed_omp.html
"Section 2.6 -sf omp"_Section_start.html#start_6
"Section 2.6 -pk omp"_Section_start.html#start_6
"package omp"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
new file mode 100644
index 0000000000..7e64345602
--- /dev/null
+++ b/doc/src/Packages_standard.txt
@@ -0,0 +1,65 @@
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Standard packages :h3
+
+This is the list of standard packages in LAMMPS. The link for each
+package name gives more details.
+
+Standard packages are supported by the LAMMPS developers and are
+written in a syntax and style consistent with the rest of LAMMPS.
+This means the developers will answer questions about them, debug and
+fix them if necessary, and keep them compatible with future changes to
+LAMMPS.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory. The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+dash = no library
+sys = system library: you likely have it on your machine
+int = internal library: provided with LAMMPS, but you may need to build it
+ext = external library: you will need to download and install it on your machine :ul
+
+Package, Description, Doc page, Example, Library
+"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
+"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, -
+"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
+"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
+"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
+"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
+"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
+"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
+"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
+"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, -
+"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
+"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
+"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
+"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
+"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
+"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
+"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
+"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
+"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
+"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
+"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
new file mode 100644
index 0000000000..c8728148f9
--- /dev/null
+++ b/doc/src/Packages_user.txt
@@ -0,0 +1,74 @@
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+User packages :h3
+
+This is a list of user packages in LAMMPS. The link for each package
+name gives more details.
+
+User packages have been contributed by users, and begin with the
+"user" prefix. If a contribution is a single command (single file),
+it is typically in the user-misc package. User packages don't
+necessarily meet the requirements of the "standard
+packages"_Packages_standard.html. This means the developers will try
+to keep things working and usually can answer technical questions
+about compiling the package. If you have problems using a specific
+feature provided in a user package, you may need to contact the
+contributor directly to get help. Information on how to submit
+additions you make to LAMMPS as single files or as a standard or user
+package is explained on the "Modify contribute"_Modify_contribute.html
+doc page.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory; USER/atc
+refers to the examples/USER/atc directory. The "Library" column
+indicates whether an extra library is needed to build and use the
+package:
+
+dash = no library
+sys = system library: you likely have it on your machine
+int = internal library: provided with LAMMPS, but you may need to build it
+ext = external library: you will need to download and install it on your machine :ul
+
+Package, Description, Doc page, Example, Library
+"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
+"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
+"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
+"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
+"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
+"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
+"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
+"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
+"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
+"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
+"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
+"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
+"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
+"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
+"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
+"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
+"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
+"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
+"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
+"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
+"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
+"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
+"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
+"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
+"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
+"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
+"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
+"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Python.txt b/doc/src/Python.txt
index 169670d669..2c9c6872bb 100644
--- a/doc/src/Python.txt
+++ b/doc/src/Python.txt
@@ -4,7 +4,7 @@ Section"_Errors.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 3e30a5a7c7..621f1fe241 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt
index fbca381e8b..46e5fee2b9 100644
--- a/doc/src/Python_examples.txt
+++ b/doc/src/Python_examples.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt
index 631f6c4a7f..6591360ae2 100644
--- a/doc/src/Python_install.txt
+++ b/doc/src/Python_install.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index 4babbb746c..8d0c724a45 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,8 +21,8 @@ from lammps import lammps :pre
These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see they
correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program, and which are described in
-"Section 6.19"_Section_howto.html#howto_19 of the manual.
+from a C++ or C or Fortran program, and which are described on the
+"Howto library"_Howto_library.html doc page.
The python/examples directory has Python scripts which show how Python
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
@@ -165,11 +165,11 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
-See "Section 6.15"_Section_howto.html#howto_15 of the manual for a
-discussion of global, per-atom, and local data, and of scalar, vector,
-and array data types. See the doc pages for individual
-"computes"_compute.html and "fixes"_fix.html for a description of what
-they calculate and store.
+See the "Howto output"_Howto_output.html doc page for a discussion of
+global, per-atom, and local data, and of scalar, vector, and array
+data types. See the doc pages for individual "computes"_compute.html
+and "fixes"_fix.html for a description of what they calculate and
+store.
For extract_variable(), an "equal-style or atom-style
variable"_variable.html is evaluated and its result returned.
diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt
index 8377bbb3d0..6e0a2ce319 100644
--- a/doc/src/Python_mpi.txt
+++ b/doc/src/Python_mpi.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt
index ad5ed192ee..d7baa93e2e 100644
--- a/doc/src/Python_pylammps.txt
+++ b/doc/src/Python_pylammps.txt
@@ -3,12 +3,12 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
PyLammps interface :h3
PyLammps is a Python wrapper class which can be created on its own or
-use an existing lammps Python object. It has its own "PyLammps
-Tutorial"_tutorial_pylammps.html doc page.
+use an existing lammps Python object. It has its own "Howto
+pylammps"_Howto_pylammps.html doc page.
diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt
index 03ab2ed3d7..a94dc07f2d 100644
--- a/doc/src/Python_run.txt
+++ b/doc/src/Python_run.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1aafbe2e84..1a921e4025 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 5f361a500b..4a05d5c468 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
deleted file mode 100644
index d5cbf77a84..0000000000
--- a/doc/src/Section_accelerate.txt
+++ /dev/null
@@ -1,391 +0,0 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_howto.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-5. Accelerating LAMMPS performance :h2
-
-This section describes various methods for improving LAMMPS
-performance for different classes of problems running on different
-kinds of machines.
-
-There are two thrusts to the discussion that follows. The
-first is using code options that implement alternate algorithms
-that can speed-up a simulation. The second is to use one
-of the several accelerator packages provided with LAMMPS that
-contain code optimized for certain kinds of hardware, including
-multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
-
-5.1 "Measuring performance"_#acc_1 :ulb,l
-5.2 "Algorithms and code options to boost performace"_#acc_2 :l
-5.3 "Accelerator packages with optimized styles"_#acc_3 :l
- 5.3.1 "GPU package"_accelerate_gpu.html :l
- 5.3.2 "USER-INTEL package"_accelerate_intel.html :l
- 5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
- 5.3.4 "USER-OMP package"_accelerate_omp.html :l
- 5.3.5 "OPT package"_accelerate_opt.html :l
-5.4 "Comparison of various accelerator packages"_#acc_4 :l
-:ule
-
-The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
-web site gives performance results for the various accelerator
-packages discussed in Section 5.2, for several of the standard LAMMPS
-benchmark problems, as a function of problem size and number of
-compute nodes, on different hardware platforms.
-
-:line
-:line
-
-5.1 Measuring performance :h3,link(acc_1)
-
-Before trying to make your simulation run faster, you should
-understand how it currently performs and where the bottlenecks are.
-
-The best way to do this is run the your system (actual number of
-atoms) for a modest number of timesteps (say 100 steps) on several
-different processor counts, including a single processor if possible.
-Do this for an equilibrium version of your system, so that the
-100-step timings are representative of a much longer run. There is
-typically no need to run for 1000s of timesteps to get accurate
-timings; you can simply extrapolate from short runs.
-
-For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_7 of the manual has an overview.
-
-Running on one (or a few processors) should give a good estimate of
-the serial performance and what portions of the timestep are taking
-the most time. Running the same problem on a few different processor
-counts should give an estimate of parallel scalability. I.e. if the
-simulation runs 16x faster on 16 processors, its 100% parallel
-efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
-
-The most important data to look at in the timing info is the timing
-breakdown and relative percentages. For example, trying different
-options for speeding up the long-range solvers will have little impact
-if they only consume 10% of the run time. If the pairwise time is
-dominating, you may want to look at GPU or OMP versions of the pair
-style, as discussed below. Comparing how the percentages change as
-you increase the processor count gives you a sense of how different
-operations within the timestep are scaling. Note that if you are
-running with a Kspace solver, there is additional output on the
-breakdown of the Kspace time. For PPPM, this includes the fraction
-spent on FFTs, which can be communication intensive.
-
-Another important detail in the timing info are the histograms of
-atoms counts and neighbor counts. If these vary widely across
-processors, you have a load-imbalance issue. This often results in
-inaccurate relative timing data, because processors have to wait when
-communication occurs for other processors to catch up. Thus the
-reported times for "Communication" or "Other" may be higher than they
-really are, due to load-imbalance. If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
-LAMMPS, to obtain synchronized timings.
-
-:line
-
-5.2 General strategies :h3,link(acc_2)
-
-NOTE: this section 5.2 is still a work in progress
-
-Here is a list of general ideas for improving simulation performance.
-Most of them are only applicable to certain models and certain
-bottlenecks in the current performance, so let the timing data you
-generate be your guide. It is hard, if not impossible, to predict how
-much difference these options will make, since it is a function of
-problem size, number of processors used, and your machine. There is
-no substitute for identifying performance bottlenecks, and trying out
-various options.
-
-rRESPA
-2-FFT PPPM
-Staggered PPPM
-single vs double PPPM
-partial charge PPPM
-verlet/split run style
-processor command for proc layout and numa layout
-load-balancing: balance and fix balance :ul
-
-2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
-2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
-PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
-achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
-cost is the performance bottleneck (typically large problems running
-on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
-
-Staggered PPPM performs calculations using two different meshes, one
-shifted slightly with respect to the other. This can reduce force
-aliasing errors and increase the accuracy of the method, but also
-doubles the amount of work required. For high relative accuracy, using
-staggered PPPM allows one to half the mesh size in each dimension as
-compared to regular PPPM, which can give around a 4x speedup in the
-kspace time. However, for low relative accuracy, using staggered PPPM
-gives little benefit and can be up to 2x slower in the kspace
-time. For example, the rhodopsin benchmark was run on a single
-processor, and results for kspace time vs. relative accuracy for the
-different methods are shown in the figure below. For this system,
-staggered PPPM (using ik differentiation) becomes useful when using a
-relative accuracy of slightly greater than 1e-5 and above.
-
-:c,image(JPG/rhodo_staggered.jpg)
-
-NOTE: Using staggered PPPM may not give the same increase in accuracy
-of energy and pressure as it does in forces, so some caution must be
-used if energy and/or pressure are quantities of interest, such as
-when using a barostat.
-
-:line
-
-5.3 Packages with optimized styles :h3,link(acc_3)
-
-Accelerated versions of various "pair_style"_pair_style.html,
-"fixes"_fix.html, "computes"_compute.html, and other commands have
-been added to LAMMPS, which will typically run faster than the
-standard non-accelerated versions. Some require appropriate hardware
-to be present on your system, e.g. GPUs or Intel Xeon Phi
-coprocessors.
-
-All of these commands are in packages provided with LAMMPS. An
-overview of packages is give in "Section
-packages"_Section_packages.html.
-
-These are the accelerator packages
-currently in LAMMPS, either as standard or user packages:
-
-"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
-"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
-"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
-"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations
-"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
-
-<!-- RST
-
-.. toctree::
- :maxdepth: 1
- :hidden:
-
- accelerate_gpu
- accelerate_intel
- accelerate_kokkos
- accelerate_omp
- accelerate_opt
-
-END_RST -->
-
-Inverting this list, LAMMPS currently has acceleration support for
-three kinds of hardware, via the listed packages:
-
-Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages
-NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages
-Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:)
-
-Which package is fastest for your hardware may depend on the size
-problem you are running and what commands (accelerated and
-non-accelerated) are invoked by your input script. While these doc
-pages include performance guidelines, there is no substitute for
-trying out the different packages appropriate to your hardware.
-
-Any accelerated style has the same name as the corresponding standard
-style, except that a suffix is appended. Otherwise, the syntax for
-the command that uses the style is identical, their functionality is
-the same, and the numerical results it produces should also be the
-same, except for precision and round-off effects.
-
-For example, all of these styles are accelerated variants of the
-Lennard-Jones "pair_style lj/cut"_pair_lj.html:
-
-"pair_style lj/cut/gpu"_pair_lj.html
-"pair_style lj/cut/intel"_pair_lj.html
-"pair_style lj/cut/kk"_pair_lj.html
-"pair_style lj/cut/omp"_pair_lj.html
-"pair_style lj/cut/opt"_pair_lj.html :ul
-
-To see what accelerate styles are currently available, see
-"Section 3.5"_Section_commands.html#cmd_5 of the manual. The
-doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
-"fix nve"_fix_nve.html) also list any accelerated variants available
-for that style.
-
-To use an accelerator package in LAMMPS, and one or more of the styles
-it provides, follow these general steps. Details vary from package to
-package and are explained in the individual accelerator doc pages,
-listed above:
-
-build the accelerator library |
- only for GPU package |
-install the accelerator package |
- make yes-opt, make yes-user-intel, etc |
-add compile/link flags to Makefile.machine in src/MAKE |
- only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
-re-build LAMMPS |
- make machine |
-prepare and test a regular LAMMPS simulation |
- lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
- only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
- only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
-:tb(c=2,s=|)
-
-Note that the first 4 steps can be done as a single command with
-suitable make command invocations. This is discussed in "Section
-4"_Section_packages.html of the manual, and its use is
-illustrated in the individual accelerator sections. Typically these
-steps only need to be done once, to create an executable that uses one
-or more accelerator packages.
-
-The last 4 steps can all be done from the command-line when LAMMPS is
-launched, without changing your input script, as illustrated in the
-individual accelerator sections. Or you can add
-"package"_package.html and "suffix"_suffix.html commands to your input
-script.
-
-NOTE: With a few exceptions, you can build a single LAMMPS executable
-with all its accelerator packages installed. Note however that the
-USER-INTEL and KOKKOS packages require you to choose one of their
-hardware options when building for a specific platform. I.e. CPU or
-Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
-option for the KOKKOS package.
-
-These are the exceptions. You cannot build a single executable with:
-
-both the USER-INTEL Phi and KOKKOS Phi options
-the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
-
-See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages. As an example, here is a command that builds with all the
-GPU related packages installed (GPU, KOKKOS with Cuda), including
-settings to build the needed auxiliary GPU libraries for Kepler GPUs:
-
-Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
- -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
-
-The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages. See its README file for
-details.
-
-Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines. See the README files in
-those dirs.
-
-As mentioned above, the "Benchmark
-page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
-performance results for the various accelerator packages for several
-of the standard LAMMPS benchmark problems, as a function of problem
-size and number of compute nodes, on different hardware platforms.
-
-Here is a brief summary of what the various packages provide. Details
-are in the individual accelerator sections.
-
-Styles with a "gpu" suffix are part of the GPU package, and can be run
-on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
-factors, discussed in the accelerator sections. :ulb,l
-
-Styles with an "intel" suffix are part of the USER-INTEL
-package. These styles support vectorized single and mixed precision
-calculations, in addition to full double precision. In extreme cases,
-this can provide speedups over 3.5x on CPUs. The package also
-supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
-coprocessors. This can result in additional speedup over 2x depending
-on the hardware configuration. :l
-
-Styles with a "kk" suffix are part of the KOKKOS package, and can be
-run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
-Xeon Phi in "native" mode. The speed-up depends on a variety of
-factors, as discussed on the KOKKOS accelerator page. :l
-
-Styles with an "omp" suffix are part of the USER-OMP package and allow
-a pair-style to be run in multi-threaded mode using OpenMP. This can
-be useful on nodes with high-core counts when using less MPI processes
-than cores is advantageous, e.g. when running with PPPM so that FFTs
-are run on fewer MPI processors or when the many MPI tasks would
-overload the available bandwidth for communication. :l
-
-Styles with an "opt" suffix are part of the OPT package and typically
-speed-up the pairwise calculations of your simulation by 5-25% on a
-CPU. :l
-:ule
-
-The individual accelerator package doc pages explain:
-
-what hardware and software the accelerated package requires
-how to build LAMMPS with the accelerated package
-how to run with the accelerated package either via command-line switches or modifying the input script
-speed-ups to expect
-guidelines for best performance
-restrictions :ul
-
-:line
-
-5.4 Comparison of various accelerator packages :h3,link(acc_4)
-
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
-The next section compares and contrasts the various accelerator
-options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
-
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
-
-As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other. We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine. See the benchmarking
-section below for examples where this has been done.
-
-[Guidelines for using each package optimally:]
-
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
-
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep. The
-KOKKOS/CUDA package only does this on timesteps when a CPU calculation
-is required (e.g. to invoke a fix or compute that is non-GPU-ized).
-Hence, if you can formulate your input script to only use GPU-ized
-fixes and computes, and avoid doing I/O too often (thermo output, dump
-file snapshots, restart files), then the data transfer cost of the
-KOKKOS/CUDA package can be very low, causing it to run faster than the
-GPU package. :l
-
-The GPU package is often faster than the KOKKOS/CUDA package, if the
-number of atoms per GPU is smaller. The crossover point, in terms of
-atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
-strongly on the pair style. For example, for a simple Lennard Jones
-system the crossover (in single precision) is often about 50K-100K
-atoms per GPU. When performing double precision calculations the
-crossover point can be significantly smaller. :l
-
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU. If the GPU package is running with several MPI processes
-assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
-
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU. Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU. In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l
-:ule
-
-[Differences between the two packages:]
-
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations. :ulb,l
-
-The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
-:ule
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
deleted file mode 100644
index 19301e9d01..0000000000
--- a/doc/src/Section_commands.txt
+++ /dev/null
@@ -1,1293 +0,0 @@
-"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-3. Commands :h2
-
-This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-
-3.1 "LAMMPS input script"_#cmd_1
-3.2 "Parsing rules"_#cmd_2
-3.3 "Input script structure"_#cmd_3
-3.4 "Commands listed by category"_#cmd_4
-3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
-
-:line
-:line
-
-3.1 LAMMPS input script :link(cmd_1),h4
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time. When the input script ends, LAMMPS exits. Each
-command causes LAMMPS to take some action. It may set an internal
-variable, read in a file, or run a simulation. Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important. However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings. Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5
-run 100
-run 100 :pre
-
-does something different than this sequence:
-
-run 100
-timestep 0.5
-run 100 :pre
-
-In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each. In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands. For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect. For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors. If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed. The "Errors"_Errors.html doc page gives
-more information on what errors mean. The documentation for each
-command lists restrictions on how the command can be used.
-
-:line
-
-3.2 Parsing rules :link(cmd_2),h4
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive. Command names are lower-case, as
-are specified command arguments. Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here is how each line in the input script is parsed by LAMMPS:
-
-(1) If the last printable character on the line is a "&" character,
-the command is assumed to continue on the next line. The next line is
-concatenated to the previous line by removing the "&" character and
-line break. This allows long commands to be continued across two or
-more lines. See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded. See an exception in (6). Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line. Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string. See an exception in
-(6).
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets. If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them. The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command. The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html. This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names. For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Additionally, the "immediate" variable expression may be followed by a
-colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-The format string must be appropriate for a double-precision
-floating-point value. The format string is used to output the result
-of the variable expression evaluation. If a format string is not
-specified a high-precision "%.20g" is used as the default.
-
-This can be useful for formatting print output to a desired precion:
-
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable a equal 2
-variable b2 equal 4
-print "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by whitespace (tabs,
-spaces). Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name. All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either single or double or triple quotes. A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above. When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line. If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed. For example:
-
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
- purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
-
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
-
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
-
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
-
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner. See the doc pages
-for those commands for examples. Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-
-:line
-
-3.3 Input script structure :h3,link(cmd_3)
-
-This section describes the structure of a typical LAMMPS input script.
-The examples directory in the LAMMPS distribution contains many sample
-input scripts; the corresponding problems are discussed on the
-"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW
-Site"_lws.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired. I.e. run a
-simulation, change some settings, run some more, etc. Each of the 4
-parts is now described in more detail. Remember that almost all the
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS. Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands. These files can contain
-molecular topology information. Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html. The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options. The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command. Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command. A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
-:line
-
-3.4 Commands listed by category :link(cmd_4),h4
-
-This section lists core LAMMPS commands, grouped by category.
-The "next section"_#cmd_5 lists all commands alphabetically. The
-next section also includes (long) lists of style options for entries
-that appear in the following categories as a single command (fix,
-compute, pair, etc). Commands that are added by user packages are not
-included in the categories here, but they are in the next section.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html
-
-Settings:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html
-
-Input script control:
-
-"clear"_clear.html,
-"echo"_echo.html,
-"if"_if.html,
-"include"_include.html,
-"jump"_jump.html,
-"label"_label.html,
-"log"_log.html,
-"next"_next.html,
-"print"_print.html,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html
-
-:line
-
-3.5 Individual commands :h3,link(cmd_5),link(comm)
-
-This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands. The "previous
-section"_#cmd_4 lists the same commands, grouped by category. Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built. Not all packages are included in a
-default LAMMPS build. These dependencies are listed as Restrictions
-in the command's documentation.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
-"dump movie"_dump_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"info"_info.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"molecule"_molecule.html,
-"neb"_neb.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"python"_python.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_ids"_reset_ids.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html :tb(c=3,ea=c)
-
-:line
-
-Fix styles :h3
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description. Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Section_accelerate.html.
-This is indicated by additional letters in parenthesis: g = GPU, i =
-USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"atom/swap"_fix_atom_swap.html,
-"aveforce"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.html,
-"ave/time"_fix_ave_time.html,
-"balance"_fix_balance.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"cmap"_fix_cmap.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.html,
-"enforce2d (k)"_fix_enforce2d.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"freeze"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gravity (o)"_fix_gravity.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"latte"_fix_latte.html,
-"langevin (k)"_fix_langevin.html,
-"langevin/spin"_fix_langevin_spin.hmtl,
-"lineforce"_fix_lineforce.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (ko)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (kio)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (kio)"_fix_nve.html,
-"nve/asphere (i)"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/body"_fix_nve_body.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
-"nve/spin"_fix_nve_spin.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.html,
-"planeforce"_fix_planeforce.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"precession/spin"_fix_precession_spin.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"temp/berendsen"_fix_temp_berendsen.html,
-"temp/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"bond/react"_fix_bond_react.html,
-"colvars"_fix_colvars.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
-"edpd/source"_fix_dpd_source.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"gle"_fix_gle.html,
-"grem"_fix_grem.html,
-"imd"_fix_imd.html,
-"ipi"_fix_ipi.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso/stationary"_fix_meso_stationary.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"nph/eff"_fix_nh_eff.html,
-"npt/eff"_fix_nh_eff.html,
-"npt/uef"_fix_nh_uef.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/eff"_fix_nve_eff.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nvk"_fix_nvk.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"nvt/uef"_fix_nh_uef.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"rhok"_fix_rhok.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h3
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.html,
-"displace/atom"_compute_displace_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"heat/flux"_compute_heat_flux.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/chunk"_compute_property_chunk.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"spin"_compute_spin.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.html,
-"temp/com"_compute_temp_com.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/partial"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"ackland/atom"_compute_ackland_atom.html,
-"basal/atom"_compute_basal_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"entropy/atom"_compute_entropy_atom.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"heat/flux/tally"_compute_tally.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"meso/e/atom"_compute_meso_e_atom.html,
-"meso/rho/atom"_compute_meso_rho_atom.html,
-"meso/t/atom"_compute_meso_t_atom.html,
-"pe/tally"_compute_tally.html,
-"pe/mol/tally"_compute_tally.html,
-"pressure/uef"_compute_pressure_uef.html,
-"saed"_compute_saed.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp/drude"_compute_temp_drude.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html,
-"temp/uef"_compute_temp_uef.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h3
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials. Click on the style itself for a full description. Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
-"atm"_pair_atm.html,
-"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded/polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (go)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (gkot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"reax"_pair_reax.html,
-"rebo (oi)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (giko)"_pair_sw.html,
-"spin/dmi"_pair_spin_dmi.html,
-"spin/exchange"_pair_spin_exchange.html,
-"spin/magelec"_pair_spin_magelec.html,
-"spin/neel"_pair_spin_neel.html,
-"table (gko)"_pair_table.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"agni (o)"_pair_agni.html,
-"awpmd/cut"_pair_awpmd.html,
-"buck/mdf"_pair_mdf.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"coul/shield"_pair_coul_shield.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"eam/cd (o)"_pair_eam.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss/cut"_pair_gauss.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lennard/mdf"_pair_mdf.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meam.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"momb"_pair_momb.html,
-"morse/smooth/linear"_pair_morse.html,
-"morse/soft"_pair_morse.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"srp"_pair_srp.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h3
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials. Click on the style itself for a full description. Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-"charmm (ko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (iko)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"harmonic (io)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html,
-"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials. Click on the style itself for a full
-description. Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-"class2 (ko)"_improper_class2.html,
-"cvff (io)"_improper_cvff.html,
-"harmonic (iko)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"distance"_improper_distance.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h3
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers. Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Section_accelerate.html. This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt
deleted file mode 100644
index 6bbd1e4d99..0000000000
--- a/doc/src/Section_history.txt
+++ /dev/null
@@ -1,135 +0,0 @@
-"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Manual.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-13. Future and history :h2
-
-This section lists features we plan to add to LAMMPS, features of
-previous versions of LAMMPS, and features of other parallel molecular
-dynamics codes our group has distributed.
-
-13.1 "Coming attractions"_#hist_1
-13.2 "Past versions"_#hist_2 :all(b)
-
-:line
-:line
-
-13.1 Coming attractions :h3,link(hist_1)
-
-As of summer 2016 we are using the "LAMMPS project issue tracker
-on GitHub"_https://github.com/lammps/lammps/issues for keeping
-track of suggested, planned or pending new features. This includes
-discussions of how to best implement them, or why they would be
-useful. Especially if a planned or proposed feature is non-trivial
-to add, e.g. because it requires changes to some of the core
-classes of LAMMPS, people planning to contribute a new feature to
-LAMMS are encouraged to submit an issue about their planned
-implementation this way in order to receive feedback from the
-LAMMPS core developers. They will provide suggestions about
-the validity of the proposed approach and possible improvements,
-pitfalls or alternatives.
-
-Please see some of the closed issues for examples of how to
-suggest code enhancements, submit proposed changes, or report
-possible bugs and how they are resolved.
-
-As an alternative to using GitHub, you may e-mail the
-"core developers"_http://lammps.sandia.gov/authors.html or send
-an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html
-if you want to have your suggestion added to the list.
-
-:line
-
-13.2 Past versions :h3,link(hist_2)
-
-LAMMPS development began in the mid 1990s under a cooperative research
-& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
-and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
-to develop a large-scale parallel classical MD code; the coding effort
-was led by Steve Plimpton at Sandia.
-
-After the CRADA ended, a final F77 version, LAMMPS 99, was
-released. As development of LAMMPS continued at Sandia, its memory
-management was converted to F90; a final F90 version was released as
-LAMMPS 2001.
-
-The current LAMMPS is a rewrite in C++ and was first publicly released
-as an open source code in 2004. It includes many new features beyond
-those in LAMMPS 99 or 2001. It also includes features from older
-parallel MD codes written at Sandia, namely ParaDyn, Warp, and
-GranFlow (see below).
-
-In late 2006 we began merging new capabilities into LAMMPS that were
-developed by Aidan Thompson at Sandia for his MD code GRASP, which has
-a parallel framework similar to LAMMPS. Most notably, these have
-included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
-and the associated charge-equilibration routines needed for ReaxFF.
-
-The "History link"_http://lammps.sandia.gov/history.html on the
-LAMMPS WWW page gives a timeline of features added to the
-C++ open-source version of LAMMPS over the last several years.
-
-These older codes are available for download from the "LAMMPS WWW
-site"_lws, except for Warp & GranFlow which were primarily used
-internally. A brief listing of their features is given here.
-
-LAMMPS 2001
-
- F90 + MPI
- dynamic memory
- spatial-decomposition parallelism
- NVE, NVT, NPT, NPH, rRESPA integrators
- LJ and Coulombic pairwise force fields
- all-atom, united-atom, bead-spring polymer force fields
- CHARMM-compatible force fields
- class 2 force fields
- 3d/2d Ewald & PPPM
- various force and temperature constraints
- SHAKE
- Hessian-free truncated-Newton minimizer
- user-defined diagnostics :ul
-
-LAMMPS 99
-
- F77 + MPI
- static memory allocation
- spatial-decomposition parallelism
- most of the LAMMPS 2001 features with a few exceptions
- no 2d Ewald & PPPM
- molecular force fields are missing a few CHARMM terms
- no SHAKE :ul
-
-Warp
-
- F90 + MPI
- spatial-decomposition parallelism
- embedded atom method (EAM) metal potentials + LJ
- lattice and grain-boundary atom creation
- NVE, NVT integrators
- boundary conditions for applying shear stresses
- temperature controls for actively sheared systems
- per-atom energy and centro-symmetry computation and output :ul
-
-ParaDyn
-
- F77 + MPI
- atom- and force-decomposition parallelism
- embedded atom method (EAM) metal potentials
- lattice atom creation
- NVE, NVT, NPT integrators
- all serial DYNAMO features for controls and constraints :ul
-
-GranFlow
-
- F90 + MPI
- spatial-decomposition parallelism
- frictional granular potentials
- NVE integrator
- boundary conditions for granular flow and packing and walls
- particle insertion :ul
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
deleted file mode 100644
index 3c5fe47057..0000000000
--- a/doc/src/Section_howto.txt
+++ /dev/null
@@ -1,3011 +0,0 @@
-"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Examples.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-6. How-to discussions :h2
-
-This section describes how to perform common tasks using LAMMPS.
-
-6.1 "Restarting a simulation"_#howto_1
-6.2 "2d simulations"_#howto_2
-6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3
-6.4 "Running multiple simulations from one input script"_#howto_4
-6.5 "Multi-replica simulations"_#howto_5
-6.6 "Granular models"_#howto_6
-6.7 "TIP3P water model"_#howto_7
-6.8 "TIP4P water model"_#howto_8
-6.9 "SPC water model"_#howto_9
-6.10 "Coupling LAMMPS to other codes"_#howto_10
-6.11 "Visualizing LAMMPS snapshots"_#howto_11
-6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
-6.13 "NEMD simulations"_#howto_13
-6.14 "Finite-size spherical and aspherical particles"_#howto_14
-6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
-6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
-6.17 "Walls"_#howto_17
-6.18 "Elastic constants"_#howto_18
-6.19 "Library interface to LAMMPS"_#howto_19
-6.20 "Calculating thermal conductivity"_#howto_20
-6.21 "Calculating viscosity"_#howto_21
-6.22 "Calculating a diffusion coefficient"_#howto_22
-6.23 "Using chunks to calculate system properties"_#howto_23
-6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
-6.25 "Polarizable models"_#howto_25
-6.26 "Adiabatic core/shell model"_#howto_26
-6.27 "Drude induced dipoles"_#howto_27
-6.28 "Magnetic spins"_#howto_28 :all(b)
-
-The example input scripts included in the LAMMPS distribution and
-highlighted on the "Examples"_Examples.html doc page also show how to
-setup and run various kinds of simulations.
-
-:line
-:line
-
-6.1 Restarting a simulation :link(howto_1),h4
-
-There are 3 ways to continue a long LAMMPS simulation. Multiple
-"run"_run.html commands can be used in the same input script. Each
-run will continue from where the previous run left off. Or binary
-restart files can be saved to disk using the "restart"_restart.html
-command. At a later time, these binary files can be read via a
-"read_restart"_read_restart.html command in a new script. Or they can
-be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_6 and read by a
-"read_data"_read_data.html command in a new script.
-
-Here we give examples of 2 scripts that read either a binary restart
-file or a converted data file and then issue a new run command to
-continue where the previous run left off. They illustrate what
-settings must be made in the new script. Details are discussed in the
-documentation for the "read_restart"_read_restart.html and
-"read_data"_read_data.html commands.
-
-Look at the {in.chain} input script provided in the {bench} directory
-of the LAMMPS distribution to see the original script that these 2
-scripts are based on. If that script had the line
-
-restart 50 tmp.restart :pre
-
-added to it, it would produce 2 binary restart files (tmp.restart.50
-and tmp.restart.100) as it ran.
-
-This script could be used to read the 1st restart file and re-run the
-last 50 timesteps:
-
-read_restart tmp.restart.50 :pre
-
-neighbor 0.4 bin
-neigh_modify every 1 delay 1 :pre
-
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
-
-timestep 0.012 :pre
-
-run 50 :pre
-
-Note that the following commands do not need to be repeated because
-their settings are included in the restart file: {units, atom_style,
-special_bonds, pair_style, bond_style}. However these commands do
-need to be used, since their settings are not in the restart file:
-{neighbor, fix, timestep}.
-
-If you actually use this script to perform a restarted run, you will
-notice that the thermodynamic data match at step 50 (if you also put a
-"thermo 50" command in the original script), but do not match at step
-100. This is because the "fix langevin"_fix_langevin.html command
-uses random numbers in a way that does not allow for perfect restarts.
-
-As an alternate approach, the restart file could be converted to a data
-file as follows:
-
-lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
-
-Then, this script could be used to re-run the last 50 steps:
-
-units lj
-atom_style bond
-pair_style lj/cut 1.12
-pair_modify shift yes
-bond_style fene
-special_bonds 0.0 1.0 1.0 :pre
-
-read_data tmp.restart.data :pre
-
-neighbor 0.4 bin
-neigh_modify every 1 delay 1 :pre
-
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
-
-timestep 0.012 :pre
-
-reset_timestep 50
-run 50 :pre
-
-Note that nearly all the settings specified in the original {in.chain}
-script must be repeated, except the {pair_coeff} and {bond_coeff}
-commands since the new data file lists the force field coefficients.
-Also, the "reset_timestep"_reset_timestep.html command is used to tell
-LAMMPS the current timestep. This value is stored in restart files,
-but not in data files.
-
-:line
-
-6.2 2d simulations :link(howto_2),h4
-
-Use the "dimension"_dimension.html command to specify a 2d simulation.
-
-Make the simulation box periodic in z via the "boundary"_boundary.html
-command. This is the default.
-
-If using the "create box"_create_box.html command to define a
-simulation box, set the z dimensions narrow, but finite, so that the
-create_atoms command will tile the 3d simulation box with a single z
-plane of atoms - e.g.
-
-"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
-
-If using the "read data"_read_data.html command to read in a file of
-atom coordinates, set the "zlo zhi" values to be finite but narrow,
-similar to the create_box command settings just described. For each
-atom in the file, assign a z coordinate so it falls inside the
-z-boundaries of the box - e.g. 0.0.
-
-Use the "fix enforce2d"_fix_enforce2d.html command as the last
-defined fix to insure that the z-components of velocities and forces
-are zeroed out every timestep. The reason to make it the last fix is
-so that any forces induced by other fixes will be zeroed out.
-
-Many of the example input scripts included in the LAMMPS distribution
-are for 2d models.
-
-NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
-opposed to point particles. See the "atom_style
-sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
-commands for details. By default, for 2d simulations, such particles
-will still be modeled as 3d spheres, not 2d discs (circles), meaning
-their moment of inertia will be that of a sphere. If you wish to
-model them as 2d discs, see the "set density/disc"_set.html command
-and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
-"fix nvt/sphere"_fix_nvt_sphere.html, "fix
-nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
-commands.
-
-:line
-
-6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4
-
-A force field has 2 parts: the formulas that define it and the
-coefficients used for a particular system. Here we only discuss
-formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, and DREIDING force fields. Setting
-coefficients is done in the input data file via the
-"read_data"_read_data.html command or in the input script with
-commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for
-additional tools that can use CHARMM or AMBER to assign force field
-coefficients and convert their output into LAMMPS input.
-
-See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force
-field.
-
-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
-
-These style choices compute force field formulas that are consistent
-with common options in CHARMM or AMBER. See each command's
-documentation for the formula it computes.
-
-"bond_style"_bond_harmonic.html harmonic
-"angle_style"_angle_charmm.html charmm
-"dihedral_style"_dihedral_charmm.html charmmfsh
-"dihedral_style"_dihedral_charmm.html charmm
-"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
-"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
-"pair_style"_pair_charmm.html lj/charmm/coul/charmm
-"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
-"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
-
-"special_bonds"_special_bonds.html charmm
-"special_bonds"_special_bonds.html amber :ul
-
-NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
-released in March 2017. We recommend they be used instead of the
-older {charmm} styles. See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
-doc pages.
-
-DREIDING is a generic force field developed by the "Goddard
-group"_http://www.wag.caltech.edu at Caltech and is useful for
-predicting structures and dynamics of organic, biological and
-main-group inorganic molecules. The philosophy in DREIDING is to use
-general force constants and geometry parameters based on simple
-hybridization considerations, rather than individual force constants
-and geometric parameters that depend on the particular combinations of
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
-interactions involving a hydrogen atom on very electronegative atoms
-(N, O, F).
-
-See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
-
-These style choices compute force field formulas that are consistent
-with the DREIDING force field. See each command's
-documentation for the formula it computes.
-
-"bond_style"_bond_harmonic.html harmonic
-"bond_style"_bond_morse.html morse :ul
-
-"angle_style"_angle_harmonic.html harmonic
-"angle_style"_angle_cosine.html cosine
-"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
-
-"dihedral_style"_dihedral_charmm.html charmm
-"improper_style"_improper_umbrella.html umbrella :ul
-
-"pair_style"_pair_buck.html buck
-"pair_style"_pair_buck.html buck/coul/cut
-"pair_style"_pair_buck.html buck/coul/long
-"pair_style"_pair_lj.html lj/cut
-"pair_style"_pair_lj.html lj/cut/coul/cut
-"pair_style"_pair_lj.html lj/cut/coul/long :ul
-
-"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
-"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
-
-"special_bonds"_special_bonds.html dreiding :ul
-
-:line
-
-6.4 Running multiple simulations from one input script :link(howto_4),h4
-
-This can be done in several ways. See the documentation for
-individual commands for more details on how these examples work.
-
-If "multiple simulations" means continue a previous simulation for
-more timesteps, then you simply use the "run"_run.html command
-multiple times. For example, this script
-
-units lj
-atom_style atomic
-read_data data.lj
-run 10000
-run 10000
-run 10000
-run 10000
-run 10000 :pre
-
-would run 5 successive simulations of the same system for a total of
-50,000 timesteps.
-
-If you wish to run totally different simulations, one after the other,
-the "clear"_clear.html command can be used in between them to
-re-initialize LAMMPS. For example, this script
-
-units lj
-atom_style atomic
-read_data data.lj
-run 10000
-clear
-units lj
-atom_style atomic
-read_data data.lj.new
-run 10000 :pre
-
-would run 2 independent simulations, one after the other.
-
-For large numbers of independent simulations, you can use
-"variables"_variable.html and the "next"_next.html and
-"jump"_jump.html commands to loop over the same input script
-multiple times with different settings. For example, this
-script, named in.polymer
-
-variable d index run1 run2 run3 run4 run5 run6 run7 run8
-shell cd $d
-read_data data.polymer
-run 10000
-shell cd ..
-clear
-next d
-jump in.polymer :pre
-
-would run 8 simulations in different directories, using a data.polymer
-file in each directory. The same concept could be used to run the
-same system at 8 different temperatures, using a temperature variable
-and storing the output in different log and dump files, for example
-
-variable a loop 8
-variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
-log log.$a
-read data.polymer
-velocity all create $t 352839
-fix 1 all nvt $t $t 100.0
-dump 1 all atom 1000 dump.$a
-run 100000
-clear
-next t
-next a
-jump in.polymer :pre
-
-All of the above examples work whether you are running on 1 or
-multiple processors, but assumed you are running LAMMPS on a single
-partition of processors. LAMMPS can be run on multiple partitions via
-the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_6 of the manual.
-
-In the last 2 examples, if LAMMPS were run on 3 partitions, the same
-scripts could be used if the "index" and "loop" variables were
-replaced with {universe}-style variables, as described in the
-"variable"_variable.html command. Also, the "next t" and "next a"
-commands would need to be replaced with a single "next a t" command.
-With these modifications, the 8 simulations of each script would run
-on the 3 partitions one after the other until all were finished.
-Initially, 3 simulations would be started simultaneously, one on each
-partition. When one finished, that partition would then start
-the 4th simulation, and so forth, until all 8 were completed.
-
-:line
-
-6.5 Multi-replica simulations :link(howto_5),h4
-
-Several commands in LAMMPS run mutli-replica simulations, meaning
-that multiple instances (replicas) of your simulation are run
-simultaneously, with small amounts of data exchanged between replicas
-periodically.
-
-These are the relevant commands:
-
-"neb"_neb.html for nudged elastic band calculations
-"prd"_prd.html for parallel replica dynamics
-"tad"_tad.html for temperature accelerated dynamics
-"temper"_temper.html for parallel tempering
-"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul
-
-NEB is a method for finding transition states and barrier energies.
-PRD and TAD are methods for performing accelerated dynamics to find
-and perform infrequent events. Parallel tempering or replica exchange
-runs different replicas at a series of temperature to facilitate
-rare-event sampling.
-
-These commands can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
-
-PIMD runs different replicas whose individual particles are coupled
-together by springs to model a system or ring-polymers.
-
-This commands can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
-
-In all these cases, you must run with one or more processors per
-replica. The processors assigned to each replica are determined at
-run-time by using the "-partition command-line
-switch"_Section_start.html#start_6 to launch LAMMPS on multiple
-partitions, which in this context are the same as replicas. E.g.
-these commands:
-
-mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
-mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
-
-would each run 8 replicas, on either 16 or 8 processors. Note the use
-of the "-in command-line switch"_Section_start.html#start_6 to specify
-the input script which is required when running in multi-replica mode.
-
-Also note that with MPI installed on a machine (e.g. your desktop),
-you can run on more (virtual) processors than you have physical
-processors. Thus the above commands could be run on a
-single-processor (or few-processor) desktop so that you can run
-a multi-replica simulation on more replicas than you have
-physical processors.
-
-:line
-
-6.6 Granular models :link(howto_6),h4
-
-Granular system are composed of spherical particles with a diameter,
-as opposed to point particles. This means they have an angular
-velocity and torque can be imparted to them to cause them to rotate.
-
-To run a simulation of a granular model, you will want to use
-the following commands:
-
-"atom_style sphere"_atom_style.html
-"fix nve/sphere"_fix_nve_sphere.html
-"fix gravity"_fix_gravity.html :ul
-
-This compute
-
-"compute erotate/sphere"_compute_erotate_sphere.html :ul
-
-calculates rotational kinetic energy which can be "output with
-thermodynamic info"_Section_howto.html#howto_15.
-
-Use one of these 3 pair potentials, which compute forces and torques
-between interacting pairs of particles:
-
-"pair_style"_pair_style.html gran/history
-"pair_style"_pair_style.html gran/no_history
-"pair_style"_pair_style.html gran/hertzian :ul
-
-These commands implement fix options specific to granular systems:
-
-"fix freeze"_fix_freeze.html
-"fix pour"_fix_pour.html
-"fix viscous"_fix_viscous.html
-"fix wall/gran"_fix_wall_gran.html :ul
-
-The fix style {freeze} zeroes both the force and torque of frozen
-atoms, and should be used for granular system instead of the fix style
-{setforce}.
-
-For computational efficiency, you can eliminate needless pairwise
-computations between frozen atoms by using this command:
-
-"neigh_modify"_neigh_modify.html exclude :ul
-
-NOTE: By default, for 2d systems, granular particles are still modeled
-as 3d spheres, not 2d discs (circles), meaning their moment of inertia
-will be the same as in 3d. If you wish to model granular particles in
-2d as 2d discs, see the note on this topic in "Section
-6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
-
-:line
-
-6.7 TIP3P water model :link(howto_7),h4
-
-The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
-the two O-H bonds and the H-O-H angle rigid. A bond style of
-{harmonic} and an angle style of {harmonic} or {charmm} should also be
-used.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
-cutoff. The K values can be used if a flexible TIP3P model (without
-fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
-set to 0.0, it corresponds to the original 1983 TIP3P model
-"(Jorgensen)"_#Jorgensen1.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.834
-H charge = 0.417
-LJ epsilon of OO = 0.1521
-LJ sigma of OO = 3.1507
-LJ epsilon of HH = 0.0460
-LJ sigma of HH = 0.4000
-LJ epsilon of OH = 0.0836
-LJ sigma of OH = 1.7753
-K of OH bond = 450
-r0 of OH bond = 0.9572
-K of HOH angle = 55
-theta of HOH angle = 104.52 :all(b),p
-
-These are the parameters to use for TIP3P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
-details:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.830
-H charge = 0.415
-LJ epsilon of OO = 0.102
-LJ sigma of OO = 3.188
-LJ epsilon, sigma of OH, HH = 0.0
-K of OH bond = 450
-r0 of OH bond = 0.9572
-K of HOH angle = 55
-theta of HOH angle = 104.52 :all(b),p
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.8 TIP4P water model :link(howto_8),h4
-
-The four-point TIP4P rigid water model extends the traditional
-three-point TIP3P model by adding an additional site, usually
-massless, where the charge associated with the oxygen atom is placed.
-This site M is located at a fixed distance away from the oxygen along
-the bisector of the HOH bond angle. A bond style of {harmonic} and an
-angle style of {harmonic} or {charmm} should also be used.
-
-A TIP4P model is run with LAMMPS using either this command
-for a cutoff model:
-
-"pair_style lj/cut/tip4p/cut"_pair_lj.html
-
-or these two commands for a long-range model:
-
-"pair_style lj/cut/tip4p/long"_pair_lj.html
-"kspace_style pppm/tip4p"_kspace_style.html :ul
-
-For both models, the bond lengths and bond angles should be held fixed
-using the "fix shake"_fix_shake.html command.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
-the "pair_style"_pair_style.html command, not as part of the pair
-coefficients.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.040
-H charge = 0.520
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.15
-LJ epsilon of O-O = 0.1550
-LJ sigma of O-O = 3.1536
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
-http://dx.doi.org/10.1063/1.1931662) these values can be used:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.1794
-H charge = 0.5897
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1577
-LJ epsilon of O-O = 0.21084
-LJ sigma of O-O = 3.1668
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
-http://dx.doi.org/10.1063/1.2121687), these values can be used:
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.1128
-H charge = 0.5564
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1546
-LJ epsilon of O-O = 0.1852
-LJ sigma of O-O = 3.1589
-LJ epsilon, sigma of OH, HH = 0.0
-Coulombic cutoff = 8.5 :all(b),p
-
-These are the parameters to use for TIP4P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS):
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -1.0484
-H charge = 0.5242
-r0 of OH bond = 0.9572
-theta of HOH angle = 104.52
-OM distance = 0.1250
-LJ epsilon of O-O = 0.16275
-LJ sigma of O-O = 3.16435
-LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
-
-Note that the when using the TIP4P pair style, the neighbor list
-cutoff for Coulomb interactions is effectively extended by a distance
-2 * (OM distance), to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*(OM distance), to shrink the size of the neighbor list.
-This leads to slightly larger cost for the long-range calculation, so
-you can test the trade-off for your model. The OM distance and the LJ
-and Coulombic cutoffs are set in the "pair_style
-lj/cut/tip4p/long"_pair_lj.html command.
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.9 SPC water model :link(howto_9),h4
-
-The SPC water model specifies a 3-site rigid water molecule with
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
-the two O-H bonds and the H-O-H angle rigid. A bond style of
-{harmonic} and an angle style of {harmonic} or {charmm} should also be
-used.
-
-These are the additional parameters (in real units) to set for O and H
-atoms and the water molecule to run a rigid SPC model.
-
-O mass = 15.9994
-H mass = 1.008
-O charge = -0.820
-H charge = 0.410
-LJ epsilon of OO = 0.1553
-LJ sigma of OO = 3.166
-LJ epsilon, sigma of OH, HH = 0.0
-r0 of OH bond = 1.0
-theta of HOH angle = 109.47 :all(b),p
-
-Note that as originally proposed, the SPC model was run with a 9
-Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
-with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
-any of the parameters above, though it becomes a different model in
-that mode of usage.
-
-The SPC/E (extended) water model is the same, except
-the partial charge assignments change:
-
-O charge = -0.8476
-H charge = 0.4238 :all(b),p
-
-See the "(Berendsen)"_#howto-Berendsen reference for more details on both
-the SPC and SPC/E models.
-
-Wikipedia also has a nice article on "water
-models"_http://en.wikipedia.org/wiki/Water_model.
-
-:line
-
-6.10 Coupling LAMMPS to other codes :link(howto_10),h4
-
-LAMMPS is designed to allow it to be coupled to other codes. For
-example, a quantum mechanics code might compute forces on a subset of
-atoms and pass those forces to LAMMPS. Or a continuum finite element
-(FE) simulation might use atom positions as boundary conditions on FE
-nodal points, compute a FE solution, and return interpolated forces on
-MD atoms.
-
-LAMMPS can be coupled to other codes in at least 3 ways. Each has
-advantages and disadvantages, which you'll have to think about in the
-context of your application.
-
-(1) Define a new "fix"_fix.html command that calls the other code. In
-this scenario, LAMMPS is the driver code. During its timestepping,
-the fix is invoked, and can make library calls to the other code,
-which has been linked to LAMMPS as a library. This is the way the
-"POEMS"_poems package that performs constrained rigid-body motion on
-groups of atoms is hooked to LAMMPS. See the "fix
-poems"_fix_poems.html command for more details. See the
-"Modify"_Modify.html doc page for info on how to add a new fix to
-LAMMPS.
-
-:link(poems,http://www.rpi.edu/~anderk5/lab)
-
-(2) Define a new LAMMPS command that calls the other code. This is
-conceptually similar to method (1), but in this case LAMMPS and the
-other code are on a more equal footing. Note that now the other code
-is not called during the timestepping of a LAMMPS run, but between
-runs. The LAMMPS input script can be used to alternate LAMMPS runs
-with calls to the other code, invoked via the new command. The
-"run"_run.html command facilitates this with its {every} option, which
-makes it easy to run a few steps, invoke the command, run a few steps,
-invoke the command, etc.
-
-In this scenario, the other code can be called as a library, as in
-(1), or it could be a stand-alone code, invoked by a system() call
-made by the command (assuming your parallel machine allows one or more
-processors to start up another program). In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
-command writes and reads.
-
-See the "Modify"_Modify.html doc page for how to add a new command to
-LAMMPS.
-
-(3) Use LAMMPS as a library called by another code. In this case the
-other code is the driver and calls LAMMPS as needed. Or a wrapper
-code could link and call both LAMMPS and another code as libraries.
-Again, the "run"_run.html command has options that allow it to be
-invoked with minimal overhead (no setup or clean-up) if you wish to do
-multiple short runs, driven by another program.
-
-Examples of driver codes that call LAMMPS as a library are included in
-the examples/COUPLE directory of the LAMMPS distribution; see
-examples/COUPLE/README for more details:
-
-simple: simple driver programs in C++ and C which invoke LAMMPS as a
-library :ulb,l
-
-lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
-MD with quantum forces calculated by a density functional code :l
-
-lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
-a kinetic Monte Carlo model for grain growth using MD to calculate
-strain induced across grain boundaries :l
-:ule
-
-:link(quest,http://dft.sandia.gov/Quest)
-:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
-
-"This section"_Section_start.html#start_5 of the documentation
-describes how to build LAMMPS as a library. Once this is done, you
-can interface with LAMMPS either via C++, C, Fortran, or Python (or
-any other language that supports a vanilla C-like interface). For
-example, from C++ you could create one (or more) "instances" of
-LAMMPS, pass it an input script to process, or execute individual
-commands, all by invoking the correct class methods in LAMMPS. From C
-or Fortran you can make function calls to do the same things. See the
-"Python"_Python.html doc page for a description of the Python wrapper
-provided with LAMMPS that operates through the LAMMPS library
-interface.
-
-The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the
-manual for a description of the interface and how to extend it for
-your needs.
-
-Note that the lammps_open() function that creates an instance of
-LAMMPS takes an MPI communicator as an argument. This means that
-instance of LAMMPS will run on the set of processors in the
-communicator. Thus the calling code can run LAMMPS on all or a subset
-of processors. For example, a wrapper script might decide to
-alternate between LAMMPS and another code, allowing them both to run
-on all the processors. Or it might allocate half the processors to
-LAMMPS and half to the other code and run both codes simultaneously
-before syncing them up periodically. Or it might instantiate multiple
-instances of LAMMPS to perform different calculations.
-
-:line
-
-6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
-
-LAMMPS itself does not do visualization, but snapshots from LAMMPS
-simulations can be visualized (and analyzed) in a variety of ways.
-
-LAMMPS snapshots are created by the "dump"_dump.html command which can
-create files in several formats. The native LAMMPS dump format is a
-text file (see "dump atom" or "dump custom") which can be visualized
-by several popular visualization tools. The "dump
-image"_dump_image.html and "dump movie"_dump_image.html styles can
-output internally rendered images and convert a sequence of them to a
-movie during the MD run. Several programs included with LAMMPS as
-auxiliary tools can convert between LAMMPS format files and other
-formats. See the "Tools"_Tools.html doc page for details.
-
-A Python-based toolkit distributed by our group can read native LAMMPS
-dump files, including custom dump files with additional columns of
-user-specified atom information, and convert them to various formats
-or pipe them into visualization software directly. See the "Pizza.py
-WWW site"_pizza for details. Specifically, Pizza.py can convert
-LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats.
-Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
-RasMol visualization programs. Pizza.py has tools that do interactive
-3d OpenGL visualization and one that creates SVG images of dump file
-snapshots.
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(ensight,http://www.ensight.com)
-:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
-
-:line
-
-6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4
-
-By default, LAMMPS uses an orthogonal simulation box to encompass the
-particles. The "boundary"_boundary.html command sets the boundary
-conditions of the box (periodic, non-periodic, etc). The orthogonal
-box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
-starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
-(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
-(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box
-is created, e.g. by the "create_box"_create_box.html or
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
-where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
-parameters, as well as lx,ly,lz, can be output via the "thermo_style
-custom"_thermo_style.html command.
-
-LAMMPS also allows simulations to be performed in triclinic
-(non-orthogonal) simulation boxes shaped as a parallelepiped with
-triclinic symmetry. The parallelepiped has its "origin" at
-(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
-origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
-(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values
-and are called "tilt factors" because they are the amount of
-displacement applied to faces of an originally orthogonal box to
-transform it into the parallelepiped. In LAMMPS the triclinic
-simulation box edge vectors [a], [b], and [c] cannot be arbitrary
-vectors. As indicated, [a] must lie on the positive x axis. [b] must
-lie in the xy plane, with strictly positive y component. [c] may have
-any orientation with strictly positive z component. The requirement
-that [a], [b], and [c] have strictly positive x, y, and z components,
-respectively, ensures that [a], [b], and [c] form a complete
-right-handed basis. These restrictions impose no loss of generality,
-since it is possible to rotate/invert any set of 3 crystal basis
-vectors so that they conform to the restrictions.
-
-For example, assume that the 3 vectors [A],[B],[C] are the edge
-vectors of a general parallelepiped, where there is no restriction on
-[A],[B],[C] other than they form a complete right-handed basis i.e.
-[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear
-rotation of [A], [B], and [C] and can be computed as follows:
-
-:c,image(Eqs/transform.jpg)
-
-where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
-indicates the corresponding unit vector. {beta} and {gamma} are angles
-between the vectors described below. Note that by construction,
-[a], [b], and [c] have strictly positive x, y, and z components, respectively.
-If it should happen that
-[A], [B], and [C] form a left-handed basis, then the above equations
-are not valid for [c]. In this case, it is necessary
-to first apply an inversion. This can be achieved
-by interchanging two basis vectors or by changing the sign of one of them.
-
-For consistency, the same rotation/inversion applied to the basis vectors
-must also be applied to atom positions, velocities,
-and any other vector quantities.
-This can be conveniently achieved by first converting to
-fractional coordinates in the
-old basis and then converting to distance coordinates in the new basis.
-The transformation is given by the following equation:
-
-:c,image(Eqs/rotate.jpg)
-
-where {V} is the volume of the box, [X] is the original vector quantity and
-[x] is the vector in the LAMMPS basis.
-
-There is no requirement that a triclinic box be periodic in any
-dimension, though it typically should be in at least the 2nd dimension
-of the tilt (y in xy) if you want to enforce a shift in periodic
-boundary conditions across that boundary. Some commands that work
-with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
-npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
-boundary conditions in specific dimensions. See the command doc pages
-for details.
-
-The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
-time the simulation box is created. This happens in one of 3 ways.
-If the "create_box"_create_box.html command is used with a region of
-style {prism}, then a triclinic box is setup. See the
-"region"_region.html command for details. If the
-"read_data"_read_data.html command is used to define the simulation
-box, and the header of the data file contains a line with the "xy xz
-yz" keyword, then a triclinic box is setup. See the
-"read_data"_read_data.html command for details. Finally, if the
-"read_restart"_read_restart.html command reads a restart file which
-was written from a simulation using a triclinic box, then a triclinic
-box will be setup for the restarted simulation.
-
-Note that you can define a triclinic box with all 3 tilt factors =
-0.0, so that it is initially orthogonal. This is necessary if the box
-will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
-"fix deform"_fix_deform.html commands. Alternatively, you can use the
-"change_box"_change_box.html command to convert a simulation box from
-orthogonal to triclinic and vice versa.
-
-As with orthogonal boxes, LAMMPS defines triclinic box size parameters
-lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
-The 9 parameters, as well as lx,ly,lz, can be output via the
-"thermo_style custom"_thermo_style.html command.
-
-To avoid extremely tilted boxes (which would be computationally
-inefficient), LAMMPS normally requires that no tilt factor can skew
-the box more than half the distance of the parallel box length, which
-is the 1st dimension in the tilt factor (x for xz). This is required
-both when the simulation box is created, e.g. via the
-"create_box"_create_box.html or "read_data"_read_data.html commands,
-as well as when the box shape changes dynamically during a simulation,
-e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html
-commands.
-
-For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
-the xy tilt factor must be between -5 and 5. Similarly, both xz and
-yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
-not a limitation, since if the maximum tilt factor is 5 (as in this
-example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are geometrically all equivalent. If the box tilt exceeds this
-limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html
-command), then the box is "flipped" to an equivalent shape with a tilt
-factor within the bounds, so the run can continue. See the "fix
-deform"_fix_deform.html doc page for further details.
-
-One exception to this rule is if the 1st dimension in the tilt
-factor (x for xy) is non-periodic. In that case, the limits on the
-tilt factor are not enforced, since flipping the box in that dimension
-does not change the atom positions due to non-periodicity. In this
-mode, if you tilt the system to extreme angles, the simulation will
-simply become inefficient, due to the highly skewed simulation box.
-
-The limitation on not creating a simulation box with a tilt factor
-skewing the box more than half the distance of the parallel box length
-can be overridden via the "box"_box.html command. Setting the {tilt}
-keyword to {large} allows any tilt factors to be specified.
-
-Box flips that may occur using the "fix deform"_fix_deform.html or
-"fix npt"_fix_nh.html commands can be turned off using the {flip no}
-option with either of the commands.
-
-Note that if a simulation box has a large tilt factor, LAMMPS will run
-less efficiently, due to the large volume of communication needed to
-acquire ghost atoms around a processor's irregular-shaped sub-domain.
-For extreme values of tilt, LAMMPS may also lose atoms and generate an
-error.
-
-Triclinic crystal structures are often defined using three lattice
-constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
-{gamma}. Note that in this nomenclature, the a, b, and c lattice
-constants are the scalar lengths of the edge vectors [a], [b], and [c]
-defined above. The relationship between these 6 quantities
-(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
-(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
-
-:c,image(Eqs/box.jpg)
-
-The inverse relationship can be written as follows:
-
-:c,image(Eqs/box_inverse.jpg)
-
-The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
-out or accessed by computes using the
-"thermo_style custom"_thermo_style.html keywords
-{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
-respectively.
-
-As discussed on the "dump"_dump.html command doc page, when the BOX
-BOUNDS for a snapshot is written to a dump file for a triclinic box,
-an orthogonal bounding box which encloses the triclinic simulation box
-is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
-box, formatted as follows:
-
-ITEM: BOX BOUNDS xy xz yz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz :pre
-
-This bounding box is convenient for many visualization programs and is
-calculated from the 9 triclinic box parameters
-(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
-
-xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
-xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
-ylo_bound = ylo + MIN(0.0,yz)
-yhi_bound = yhi + MAX(0.0,yz)
-zlo_bound = zlo
-zhi_bound = zhi :pre
-
-These formulas can be inverted if you need to convert the bounding box
-back into the triclinic box parameters, e.g. xlo = xlo_bound -
-MIN(0.0,xy,xz,xy+xz).
-
-One use of triclinic simulation boxes is to model solid-state crystals
-with triclinic symmetry. The "lattice"_lattice.html command can be
-used with non-orthogonal basis vectors to define a lattice that will
-tile a triclinic simulation box via the
-"create_atoms"_create_atoms.html command.
-
-A second use is to run Parinello-Rahman dynamics via the "fix
-npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
-factors to compensate for off-diagonal components of the pressure
-tensor. The analog for an "energy minimization"_minimize.html is
-the "fix box/relax"_fix_box_relax.html command.
-
-A third use is to shear a bulk solid to study the response of the
-material. The "fix deform"_fix_deform.html command can be used for
-this purpose. It allows dynamic control of the xy, xz, yz tilt
-factors as a simulation runs. This is discussed in the next section
-on non-equilibrium MD (NEMD) simulations.
-
-:line
-
-6.13 NEMD simulations :link(howto_13),h4
-
-Non-equilibrium molecular dynamics or NEMD simulations are typically
-used to measure a fluid's rheological properties such as viscosity.
-In LAMMPS, such simulations can be performed by first setting up a
-non-orthogonal simulation box (see the preceding Howto section).
-
-A shear strain can be applied to the simulation box at a desired
-strain rate by using the "fix deform"_fix_deform.html command. The
-"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
-the sheared fluid and integrate the SLLOD equations of motion for the
-system. Fix nvt/sllod uses "compute
-temp/deform"_compute_temp_deform.html to compute a thermal temperature
-by subtracting out the streaming velocity of the shearing atoms. The
-velocity profile or other properties of the fluid can be monitored via
-the "fix ave/chunk"_fix_ave_chunk.html command.
-
-As discussed in the previous section on non-orthogonal simulation
-boxes, the amount of tilt or skew that can be applied is limited by
-LAMMPS for computational efficiency to be 1/2 of the parallel box
-length. However, "fix deform"_fix_deform.html can continuously strain
-a box by an arbitrary amount. As discussed in the "fix
-deform"_fix_deform.html command, when the tilt value reaches a limit,
-the box is flipped to the opposite limit which is an equivalent tiling
-of periodic space. The strain rate can then continue to change as
-before. In a long NEMD simulation these box re-shaping events may
-occur many times.
-
-In a NEMD simulation, the "remap" option of "fix
-deform"_fix_deform.html should be set to "remap v", since that is what
-"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
-profile consistent with the applied shear strain rate.
-
-An alternative method for calculating viscosities is provided via the
-"fix viscosity"_fix_viscosity.html command.
-
-NEMD simulations can also be used to measure transport properties of a fluid
-through a pore or channel. Simulations of steady-state flow can be performed
-using the "fix flow/gauss"_fix_flow_gauss.html command.
-
-:line
-
-6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
-
-Typical MD models treat atoms or particles as point masses. Sometimes
-it is desirable to have a model with finite-size particles such as
-spheroids or ellipsoids or generalized aspherical bodies. The
-difference is that such particles have a moment of inertia, rotational
-energy, and angular momentum. Rotation is induced by torque coming
-from interactions with other particles.
-
-LAMMPS has several options for running simulations with these kinds of
-particles. The following aspects are discussed in turn:
-
-atom styles
-pair potentials
-time integration
-computes, thermodynamics, and dump output
-rigid bodies composed of finite-size particles :ul
-
-Example input scripts for these kinds of models are in the body,
-colloid, dipole, ellipse, line, peri, pour, and tri directories of the
-"examples directory"_Examples.html in the LAMMPS distribution.
-
-Atom styles :h4
-
-There are several "atom styles"_atom_style.html that allow for
-definition of finite-size particles: sphere, dipole, ellipsoid, line,
-tri, peri, and body.
-
-The sphere style defines particles that are spheriods and each
-particle can have a unique diameter and mass (or density). These
-particles store an angular velocity (omega) and can be acted upon by
-torque. The "set" command can be used to modify the diameter and mass
-of individual particles, after then are created.
-
-The dipole style does not actually define finite-size particles, but
-is often used in conjunction with spherical particles, via a command
-like
-
-atom_style hybrid sphere dipole :pre
-
-This is because when dipoles interact with each other, they induce
-torques, and a particle must be finite-size (i.e. have a moment of
-inertia) in order to respond and rotate. See the "atom_style
-dipole"_atom_style.html command for details. The "set" command can be
-used to modify the orientation and length of the dipole moment of
-individual particles, after then are created.
-
-The ellipsoid style defines particles that are ellipsoids and thus can
-be aspherical. Each particle has a shape, specified by 3 diameters,
-and mass (or density). These particles store an angular momentum and
-their orientation (quaternion), and can be acted upon by torque. They
-do not store an angular velocity (omega), which can be in a different
-direction than angular momentum, rather they compute it as needed.
-The "set" command can be used to modify the diameter, orientation, and
-mass of individual particles, after then are created. It also has a
-brief explanation of what quaternions are.
-
-The line style defines line segment particles with two end points and
-a mass (or density). They can be used in 2d simulations, and they can
-be joined together to form rigid bodies which represent arbitrary
-polygons.
-
-The tri style defines triangular particles with three corner points
-and a mass (or density). They can be used in 3d simulations, and they
-can be joined together to form rigid bodies which represent arbitrary
-particles with a triangulated surface.
-
-The peri style is used with "Peridynamic models"_pair_peri.html and
-defines particles as having a volume, that is used internally in the
-"pair_style peri"_pair_peri.html potentials.
-
-The body style allows for definition of particles which can represent
-complex entities, such as surface meshes of discrete points,
-collections of sub-particles, deformable objects, etc. The body style
-is discussed in more detail on the "body"_body.html doc page.
-
-Note that if one of these atom styles is used (or multiple styles via
-the "atom_style hybrid"_atom_style.html command), not all particles in
-the system are required to be finite-size or aspherical.
-
-For example, in the ellipsoid style, if the 3 shape parameters are set
-to the same value, the particle will be a sphere rather than an
-ellipsoid. If the 3 shape parameters are all set to 0.0 or if the
-diameter is set to 0.0, it will be a point particle. In the line or
-tri style, if the lineflag or triflag is specified as 0, then it
-will be a point particle.
-
-Some of the pair styles used to compute pairwise interactions between
-finite-size particles also compute the correct interaction with point
-particles as well, e.g. the interaction between a point particle and a
-finite-size particle or between two point particles. If necessary,
-"pair_style hybrid"_pair_hybrid.html can be used to insure the correct
-interactions are computed for the appropriate style of interactions.
-Likewise, using groups to partition particles (ellipsoids versus
-spheres versus point particles) will allow you to use the appropriate
-time integrators and temperature computations for each class of
-particles. See the doc pages for various commands for details.
-
-Also note that for "2d simulations"_dimension.html, atom styles sphere
-and ellipsoid still use 3d particles, rather than as circular disks or
-ellipses. This means they have the same moment of inertia as the 3d
-object. When temperature is computed, the correct degrees of freedom
-are used for rotation in a 2d versus 3d system.
-
-Pair potentials :h4
-
-When a system with finite-size particles is defined, the particles
-will only rotate and experience torque if the force field computes
-such interactions. These are the various "pair
-styles"_pair_style.html that generate torque:
-
-"pair_style gran/history"_pair_gran.html
-"pair_style gran/hertzian"_pair_gran.html
-"pair_style gran/no_history"_pair_gran.html
-"pair_style dipole/cut"_pair_dipole.html
-"pair_style gayberne"_pair_gayberne.html
-"pair_style resquared"_pair_resquared.html
-"pair_style brownian"_pair_brownian.html
-"pair_style lubricate"_pair_lubricate.html
-"pair_style line/lj"_pair_line_lj.html
-"pair_style tri/lj"_pair_tri_lj.html
-"pair_style body"_pair_body.html :ul
-
-The granular pair styles are used with spherical particles. The
-dipole pair style is used with the dipole atom style, which could be
-applied to spherical or ellipsoidal particles. The GayBerne and
-REsquared potentials require ellipsoidal particles, though they will
-also work if the 3 shape parameters are the same (a sphere). The
-Brownian and lubrication potentials are used with spherical particles.
-The line, tri, and body potentials are used with line segment,
-triangular, and body particles respectively.
-
-Time integration :h4
-
-There are several fixes that perform time integration on finite-size
-spherical particles, meaning the integrators update the rotational
-orientation and angular velocity or angular momentum of the particles:
-
-"fix nve/sphere"_fix_nve_sphere.html
-"fix nvt/sphere"_fix_nvt_sphere.html
-"fix npt/sphere"_fix_npt_sphere.html :ul
-
-Likewise, there are 3 fixes that perform time integration on
-ellipsoidal particles:
-
-"fix nve/asphere"_fix_nve_asphere.html
-"fix nvt/asphere"_fix_nvt_asphere.html
-"fix npt/asphere"_fix_npt_asphere.html :ul
-
-The advantage of these fixes is that those which thermostat the
-particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting. The "fix langevin"_fix_langevin
-command can also be used with its {omgea} or {angmom} options to
-thermostat the rotational degrees of freedom for spherical or
-ellipsoidal particles. Other thermostatting fixes only operate on the
-translational kinetic energy of finite-size particles.
-
-These fixes perform constant NVE time integration on line segment,
-triangular, and body particles:
-
-"fix nve/line"_fix_nve_line.html
-"fix nve/tri"_fix_nve_tri.html
-"fix nve/body"_fix_nve_body.html :ul
-
-Note that for mixtures of point and finite-size particles, these
-integration fixes can only be used with "groups"_group.html which
-contain finite-size particles.
-
-Computes, thermodynamics, and dump output :h4
-
-There are several computes that calculate the temperature or
-rotational energy of spherical or ellipsoidal particles:
-
-"compute temp/sphere"_compute_temp_sphere.html
-"compute temp/asphere"_compute_temp_asphere.html
-"compute erotate/sphere"_compute_erotate_sphere.html
-"compute erotate/asphere"_compute_erotate_asphere.html :ul
-
-These include rotational degrees of freedom in their computation. If
-you wish the thermodynamic output of temperature or pressure to use
-one of these computes (e.g. for a system entirely composed of
-finite-size particles), then the compute can be defined and the
-"thermo_modify"_thermo_modify.html command used. Note that by default
-thermodynamic quantities will be calculated with a temperature that
-only includes translational degrees of freedom. See the
-"thermo_style"_thermo_style.html command for details.
-
-These commands can be used to output various attributes of finite-size
-particles:
-
-"dump custom"_dump.html
-"compute property/atom"_compute_property_atom.html
-"dump local"_dump.html
-"compute body/local"_compute_body_local.html :ul
-
-Attributes include the dipole moment, the angular velocity, the
-angular momentum, the quaternion, the torque, the end-point and
-corner-point coordinates (for line and tri particles), and
-sub-particle attributes of body particles.
-
-Rigid bodies composed of finite-size particles :h4
-
-The "fix rigid"_fix_rigid.html command treats a collection of
-particles as a rigid body, computes its inertia tensor, sums the total
-force and torque on the rigid body each timestep due to forces on its
-constituent particles, and integrates the motion of the rigid body.
-
-If any of the constituent particles of a rigid body are finite-size
-particles (spheres or ellipsoids or line segments or triangles), then
-their contribution to the inertia tensor of the body is different than
-if they were point particles. This means the rotational dynamics of
-the rigid body will be different. Thus a model of a dimer is
-different if the dimer consists of two point masses versus two
-spheroids, even if the two particles have the same mass. Finite-size
-particles that experience torque due to their interaction with other
-particles will also impart that torque to a rigid body they are part
-of.
-
-See the "fix rigid" command for example of complex rigid-body models
-it is possible to define in LAMMPS.
-
-Note that the "fix shake"_fix_shake.html command can also be used to
-treat 2, 3, or 4 particles as a rigid body, but it always assumes the
-particles are point masses.
-
-Also note that body particles cannot be modeled with the "fix
-rigid"_fix_rigid.html command. Body particles are treated by LAMMPS
-as single particles, though they can store internal state, such as a
-list of sub-particles. Individual body partices are typically treated
-as rigid bodies, and their motion integrated with a command like "fix
-nve/body"_fix_nve_body.html. Interactions between pairs of body
-particles are computed via a command like "pair_style
-body"_pair_body.html.
-
-:line
-
-6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4
-
-There are four basic kinds of LAMMPS output:
-
-"Thermodynamic output"_thermo_style.html, which is a list
-of quantities printed every few timesteps to the screen and logfile. :ulb,l
-
-"Dump files"_dump.html, which contain snapshots of atoms and various
-per-atom values and are written at a specified frequency. :l
-
-Certain fixes can output user-specified quantities to files: "fix
-ave/time"_fix_ave_time.html for time averaging, "fix
-ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix
-print"_fix_print.html for single-line output of
-"variables"_variable.html. Fix print can also output to the
-screen. :l
-
-"Restart files"_restart.html. :l
-:ule
-
-A simulation prints one set of thermodynamic output and (optionally)
-restart files. It can generate any number of dump files and fix
-output files, depending on what "dump"_dump.html and "fix"_fix.html
-commands you specify.
-
-As discussed below, LAMMPS gives you a variety of ways to determine
-what quantities are computed and printed when the thermodynamics,
-dump, or fix commands listed above perform output. Throughout this
-discussion, note that users can also "add their own computes and fixes
-to LAMMPS"_Modify.html which can then generate values that can then be
-output with these commands.
-
-The following sub-sections discuss different LAMMPS command related
-to output and the kind of data they operate on and produce:
-
-"Global/per-atom/local data"_#global
-"Scalar/vector/array data"_#scalar
-"Thermodynamic output"_#thermo
-"Dump file output"_#dump
-"Fixes that write output files"_#fixoutput
-"Computes that process output quantities"_#computeoutput
-"Fixes that process output quantities"_#fixprocoutput
-"Computes that generate values to output"_#compute
-"Fixes that generate values to output"_#fix
-"Variables that generate values to output"_#variable
-"Summary table of output options and data flow between commands"_#table :ul
-
-Global/per-atom/local data :h4,link(global)
-
-Various output-related commands work with three different styles of
-data: global, per-atom, or local. A global datum is one or more
-system-wide values, e.g. the temperature of the system. A per-atom
-datum is one or more values per atom, e.g. the kinetic energy of each
-atom. Local datums are calculated by each processor based on the
-atoms it owns, but there may be zero or more per atom, e.g. a list of
-bond distances.
-
-Scalar/vector/array data :h4,link(scalar)
-
-Global, per-atom, and local datums can each come in three kinds: a
-single scalar value, a vector of values, or a 2d array of values. The
-doc page for a "compute" or "fix" or "variable" that generates data
-will specify both the style and kind of data it produces, e.g. a
-per-atom vector.
-
-When a quantity is accessed, as in many of the output commands
-discussed below, it can be referenced via the following bracket
-notation, where ID in this case is the ID of a compute. The leading
-"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
-
-c_ID | entire scalar, vector, or array
-c_ID\[I\] | one element of vector, one column of array
-c_ID\[I\]\[J\] | one element of array :tb(s=|)
-
-In other words, using one bracket reduces the dimension of the data
-once (vector -> scalar, array -> vector). Using two brackets reduces
-the dimension twice (array -> scalar). Thus a command that uses
-scalar values as input can typically also process elements of a vector
-or array.
-
-Thermodynamic output :h4,link(thermo)
-
-The frequency and format of thermodynamic output is set by the
-"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
-"thermo_modify"_thermo_modify.html commands. The
-"thermo_style"_thermo_style.html command also specifies what values
-are calculated and written out. Pre-defined keywords can be specified
-(e.g. press, etotal, etc). Three additional kinds of keywords can
-also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html
-or "fix"_fix.html or "variable"_variable.html provides the value to be
-output. In each case, the compute, fix, or variable must generate
-global values for input to the "thermo_style custom"_dump.html
-command.
-
-Note that thermodynamic output values can be "extensive" or
-"intensive". The former scale with the number of atoms in the system
-(e.g. total energy), the latter do not (e.g. temperature). The
-setting for "thermo_modify norm"_thermo_modify.html determines whether
-extensive quantities are normalized or not. Computes and fixes
-produce either extensive or intensive values; see their individual doc
-pages for details. "Equal-style variables"_variable.html produce only
-intensive values; you can include a division by "natoms" in the
-formula if desired, to make an extensive calculation produce an
-intensive result.
-
-Dump file output :h4,link(dump)
-
-Dump file output is specified by the "dump"_dump.html and
-"dump_modify"_dump_modify.html commands. There are several
-pre-defined formats (dump atom, dump xtc, etc).
-
-There is also a "dump custom"_dump.html format where the user
-specifies what values are output with each atom. Pre-defined atom
-attributes can be specified (id, x, fx, etc). Three additional kinds
-of keywords can also be specified (c_ID, f_ID, v_name), where a
-"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
-provides the values to be output. In each case, the compute, fix, or
-variable must generate per-atom values for input to the "dump
-custom"_dump.html command.
-
-There is also a "dump local"_dump.html format where the user specifies
-what local values to output. A pre-defined index keyword can be
-specified to enumerate the local values. Two additional kinds of
-keywords can also be specified (c_ID, f_ID), where a
-"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
-provides the values to be output. In each case, the compute or fix
-must generate local values for input to the "dump local"_dump.html
-command.
-
-Fixes that write output files :h4,link(fixoutput)
-
-Several fixes take various quantities as input and can write output
-files: "fix ave/time"_fix_ave_time.html, "fix
-ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
-"fix ave/correlate"_fix_ave_correlate.html, and "fix
-print"_fix_print.html.
-
-The "fix ave/time"_fix_ave_time.html command enables direct output to
-a file and/or time-averaging of global scalars or vectors. The user
-specifies one or more quantities as input. These can be global
-"compute"_compute.html values, global "fix"_fix.html values, or
-"variables"_variable.html of any style except the atom style which
-produces per-atom values. Since a variable can refer to keywords used
-by the "thermo_style custom"_thermo_style.html command (like temp or
-press) and individual per-atom values, a wide variety of quantities
-can be time averaged and/or output in this way. If the inputs are one
-or more scalar values, then the fix generate a global scalar or vector
-of output. If the inputs are one or more vector values, then the fix
-generates a global vector or array of output. The time-averaged
-output of this fix can also be used as input to other output commands.
-
-The "fix ave/chunk"_fix_ave_chunk.html command enables direct output
-to a file of chunk-averaged per-atom quantities like those output in
-dump files. Chunks can represent spatial bins or other collections of
-atoms, e.g. individual molecules. The per-atom quantities can be atom
-density (mass or number) or atom attributes such as position,
-velocity, force. They can also be per-atom quantities calculated by a
-"compute"_compute.html, by a "fix"_fix.html, or by an atom-style
-"variable"_variable.html. The chunk-averaged output of this fix can
-also be used as input to other output commands.
-
-The "fix ave/histo"_fix_ave_histo.html command enables direct output
-to a file of histogrammed quantities, which can be global or per-atom
-or local quantities. The histogram output of this fix can also be
-used as input to other output commands.
-
-The "fix ave/correlate"_fix_ave_correlate.html command enables direct
-output to a file of time-correlated quantities, which can be global
-values. The correlation matrix output of this fix can also be used as
-input to other output commands.
-
-The "fix print"_fix_print.html command can generate a line of output
-written to the screen and log file or to a separate file, periodically
-during a running simulation. The line can contain one or more
-"variable"_variable.html values for any style variable except the
-vector or atom styles). As explained above, variables themselves can
-contain references to global values generated by "thermodynamic
-keywords"_thermo_style.html, "computes"_compute.html,
-"fixes"_fix.html, or other "variables"_variable.html, or to per-atom
-values for a specific atom. Thus the "fix print"_fix_print.html
-command is a means to output a wide variety of quantities separate
-from normal thermodynamic or dump file output.
-
-Computes that process output quantities :h4,link(computeoutput)
-
-The "compute reduce"_compute_reduce.html and "compute
-reduce/region"_compute_reduce.html commands take one or more per-atom
-or local vector quantities as inputs and "reduce" them (sum, min, max,
-ave) to scalar quantities. These are produced as output values which
-can be used as input to other output commands.
-
-The "compute slice"_compute_slice.html command take one or more global
-vector or array quantities as inputs and extracts a subset of their
-values to create a new vector or array. These are produced as output
-values which can be used as input to other output commands.
-
-The "compute property/atom"_compute_property_atom.html command takes a
-list of one or more pre-defined atom attributes (id, x, fx, etc) and
-stores the values in a per-atom vector or array. These are produced
-as output values which can be used as input to other output commands.
-The list of atom attributes is the same as for the "dump
-custom"_dump.html command.
-
-The "compute property/local"_compute_property_local.html command takes
-a list of one or more pre-defined local attributes (bond info, angle
-info, etc) and stores the values in a local vector or array. These
-are produced as output values which can be used as input to other
-output commands.
-
-Fixes that process output quantities :h4,link(fixprocoutput)
-
-The "fix vector"_fix_vector.html command can create global vectors as
-output from global scalars as input, accumulating them one element at
-a time.
-
-The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
-of per-atom vectors. The per-atom quantities can be atom attributes
-such as position, velocity, force. They can also be per-atom
-quantities calculated by a "compute"_compute.html, by a
-"fix"_fix.html, or by an atom-style "variable"_variable.html. The
-time-averaged per-atom output of this fix can be used as input to
-other output commands.
-
-The "fix store/state"_fix_store_state.html command can archive one or
-more per-atom attributes at a particular time, so that the old values
-can be used in a future calculation or output. The list of atom
-attributes is the same as for the "dump custom"_dump.html command,
-including per-atom quantities calculated by a "compute"_compute.html,
-by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
-The output of this fix can be used as input to other output commands.
-
-Computes that generate values to output :h4,link(compute)
-
-Every "compute"_compute.html in LAMMPS produces either global or
-per-atom or local values. The values can be scalars or vectors or
-arrays of data. These values can be output using the other commands
-described in this section. The doc page for each compute command
-describes what it produces. Computes that produce per-atom or local
-values have the word "atom" or "local" in their style name. Computes
-without the word "atom" or "local" produce global values.
-
-Fixes that generate values to output :h4,link(fix)
-
-Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
-local values which can be accessed by other commands. The values can
-be scalars or vectors or arrays of data. These values can be output
-using the other commands described in this section. The doc page for
-each fix command tells whether it produces any output quantities and
-describes them.
-
-Variables that generate values to output :h4,link(variable)
-
-"Variables"_variable.html defined in an input script can store one or
-more strings. But equal-style, vector-style, and atom-style or
-atomfile-style variables generate a global scalar value, global vector
-or values, or a per-atom vector, respectively, when accessed. The
-formulas used to define these variables can contain references to the
-thermodynamic keywords and to global and per-atom data generated by
-computes, fixes, and other variables. The values generated by
-variables can be used as input to and thus output by the other
-commands described in this section.
-
-Summary table of output options and data flow between commands :h4,link(table)
-
-This table summarizes the various commands that can be used for
-generating output from LAMMPS. Each command produces output data of
-some kind and/or writes data to a file. Most of the commands can take
-data from other commands as input. Thus you can link many of these
-commands together in pipeline form, where data produced by one command
-is used as input to another command and eventually written to the
-screen or to a file. Note that to hook two commands together the
-output and input data types must match, e.g. global/per-atom/local
-data and scalar/vector/array data.
-
-Also note that, as described above, when a command takes a scalar as
-input, that could be an element of a vector or array. Likewise a
-vector input could be a column of an array.
-
-Command: Input: Output:
-"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
-"dump custom"_dump.html: per-atom vectors: dump file:
-"dump local"_dump.html: local vectors: dump file:
-"fix print"_fix_print.html: global scalar from variable: screen, file:
-"print"_print.html: global scalar from variable: screen:
-"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
-"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array:
-"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector:
-"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector:
-"compute slice"_compute_slice.html: global vectors/arrays: global vector/array:
-"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
-"compute property/local"_compute_property_local.html: local vectors: local vector/array:
-"fix vector"_fix_vector.html: global scalars: global vector:
-"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
-"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
-"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file:
-"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file:
-"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file:
-"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:)
-
-:line
-
-6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4
-
-Thermostatting means controlling the temperature of particles in an MD
-simulation. Barostatting means controlling the pressure. Since the
-pressure includes a kinetic component due to particle velocities, both
-these operations require calculation of the temperature. Typically a
-target temperature (T) and/or pressure (P) is specified by the user,
-and the thermostat or barostat attempts to equilibrate the system to
-the requested T and/or P.
-
-Temperature is computed as kinetic energy divided by some number of
-degrees of freedom (and the Boltzmann constant). Since kinetic energy
-is a function of particle velocity, there is often a need to
-distinguish between a particle's advection velocity (due to some
-aggregate motion of particles) and its thermal velocity. The sum of
-the two is the particle's total velocity, but the latter is often what
-is wanted to compute a temperature.
-
-LAMMPS has several options for computing temperatures, any of which
-can be used in thermostatting and barostatting. These "compute
-commands"_compute.html calculate temperature, and the "compute
-pressure"_compute_pressure.html command calculates pressure.
-
-"compute temp"_compute_temp.html
-"compute temp/sphere"_compute_temp_sphere.html
-"compute temp/asphere"_compute_temp_asphere.html
-"compute temp/com"_compute_temp_com.html
-"compute temp/deform"_compute_temp_deform.html
-"compute temp/partial"_compute_temp_partial.html
-"compute temp/profile"_compute_temp_profile.html
-"compute temp/ramp"_compute_temp_ramp.html
-"compute temp/region"_compute_temp_region.html :ul
-
-All but the first 3 calculate velocity biases directly (e.g. advection
-velocities) that are removed when computing the thermal temperature.
-"Compute temp/sphere"_compute_temp_sphere.html and "compute
-temp/asphere"_compute_temp_asphere.html compute kinetic energy for
-finite-size particles that includes rotational degrees of freedom.
-They both allow for velocity biases indirectly, via an optional extra
-argument, another temperature compute that subtracts a velocity bias.
-This allows the translational velocity of spherical or aspherical
-particles to be adjusted in prescribed ways.
-
-Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
-case by a pair style. Several thermostatting fixes are available:
-Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling
-(temp/rescale). Dissipative particle dynamics (DPD) thermostatting
-can be invoked via the {dpd/tstat} pair style:
-
-"fix nvt"_fix_nh.html
-"fix nvt/sphere"_fix_nvt_sphere.html
-"fix nvt/asphere"_fix_nvt_asphere.html
-"fix nvt/sllod"_fix_nvt_sllod.html
-"fix temp/berendsen"_fix_temp_berendsen.html
-"fix temp/csvr"_fix_temp_csvr.html
-"fix langevin"_fix_langevin.html
-"fix temp/rescale"_fix_temp_rescale.html
-"pair_style dpd/tstat"_pair_dpd.html :ul
-
-"Fix nvt"_fix_nh.html only thermostats the translational velocity of
-particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
-that it subtracts out a velocity bias due to a deforming box and
-integrates the SLLOD equations of motion. See the "NEMD
-simulations"_#howto_13 section of this page for further details. "Fix
-nvt/sphere"_fix_nvt_sphere.html and "fix
-nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
-velocities but also rotational velocities for spherical and aspherical
-particles.
-
-DPD thermostatting alters pairwise interactions in a manner analogous
-to the per-particle thermostatting of "fix
-langevin"_fix_langevin.html.
-
-Any of the thermostatting fixes can use temperature computes that
-remove bias which has two effects. First, the current calculated
-temperature, which is compared to the requested target temperature, is
-calculated with the velocity bias removed. Second, the thermostat
-adjusts only the thermal temperature component of the particle's
-velocities, which are the velocities with the bias removed. The
-removed bias is then added back to the adjusted velocities. See the
-doc pages for the individual fixes and for the
-"fix_modify"_fix_modify.html command for instructions on how to assign
-a temperature compute to a thermostatting fix. For example, you can
-apply a thermostat to only the x and z components of velocity by using
-it in conjunction with "compute
-temp/partial"_compute_temp_partial.html. Of you could thermostat only
-the thermal temperature of a streaming flow of particles without
-affecting the streaming velocity, by using "compute
-temp/profile"_compute_temp_profile.html.
-
-NOTE: Only the nvt fixes perform time integration, meaning they update
-the velocities and positions of particles due to forces and velocities
-respectively. The other thermostat fixes only adjust velocities; they
-do NOT perform time integration updates. Thus they should be used in
-conjunction with a constant NVE integration fix such as these:
-
-"fix nve"_fix_nve.html
-"fix nve/sphere"_fix_nve_sphere.html
-"fix nve/asphere"_fix_nve_asphere.html :ul
-
-Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two
-barosttating methods are currently available: Nose-Hoover (npt and
-nph) and Berendsen:
-
-"fix npt"_fix_nh.html
-"fix npt/sphere"_fix_npt_sphere.html
-"fix npt/asphere"_fix_npt_asphere.html
-"fix nph"_fix_nh.html
-"fix press/berendsen"_fix_press_berendsen.html :ul
-
-The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
-and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
-it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
-press/berendsen"_fix_press_berendsen.html can be used in conjunction
-with any of the thermostatting fixes.
-
-As with the thermostats, "fix npt"_fix_nh.html and "fix
-nph"_fix_nh.html only use translational motion of the particles in
-computing T and P and performing thermo/barostatting. "Fix
-npt/sphere"_fix_npt_sphere.html and "fix
-npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
-translation velocities but also rotational velocities for spherical
-and aspherical particles.
-
-All of the barostatting fixes use the "compute
-pressure"_compute_pressure.html compute to calculate a current
-pressure. By default, this compute is created with a simple "compute
-temp"_compute_temp.html (see the last argument of the "compute
-pressure"_compute_pressure.html command), which is used to calculated
-the kinetic component of the pressure. The barostatting fixes can
-also use temperature computes that remove bias for the purpose of
-computing the kinetic component which contributes to the current
-pressure. See the doc pages for the individual fixes and for the
-"fix_modify"_fix_modify.html command for instructions on how to assign
-a temperature or pressure compute to a barostatting fix.
-
-NOTE: As with the thermostats, the Nose/Hoover methods ("fix
-npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
-"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
-be used with one of the constant NVE fixes or with one of the NVT
-fixes.
-
-Finally, thermodynamic output, which can be setup via the
-"thermo_style"_thermo_style.html command, often includes temperature
-and pressure values. As explained on the doc page for the
-"thermo_style"_thermo_style.html command, the default T and P are
-setup by the thermo command itself. They are NOT the ones associated
-with any thermostatting or barostatting fix you have defined or with
-any compute that calculates a temperature or pressure. Thus if you
-want to view these values of T and P, you need to specify them
-explicitly via a "thermo_style custom"_thermo_style.html command. Or
-you can use the "thermo_modify"_thermo_modify.html command to
-re-define what temperature or pressure compute is used for default
-thermodynamic output.
-
-:line
-
-6.17 Walls :link(howto_17),h4
-
-Walls in an MD simulation are typically used to bound particle motion,
-i.e. to serve as a boundary condition.
-
-Walls in LAMMPS can be of rough (made of particles) or idealized
-surfaces. Ideal walls can be smooth, generating forces only in the
-normal direction, or frictional, generating forces also in the
-tangential direction.
-
-Rough walls, built of particles, can be created in various ways. The
-particles themselves can be generated like any other particle, via the
-"lattice"_lattice.html and "create_atoms"_create_atoms.html commands,
-or read in via the "read_data"_read_data.html command.
-
-Their motion can be constrained by many different commands, so that
-they do not move at all, move together as a group at constant velocity
-or in response to a net force acting on them, move in a prescribed
-fashion (e.g. rotate around a point), etc. Note that if a time
-integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html
-is not used with the group that contains wall particles, their
-positions and velocities will not be updated.
-
-"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together
-"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0
-"fix freeze"_fix_freeze.html - freeze particles for use as granular walls
-"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force
-"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul
-
-The "fix move"_fix_move.html command offers the most generality, since
-the motion of individual particles can be specified with
-"variable"_variable.html formula which depends on time and/or the
-particle position.
-
-For rough walls, it may be useful to turn off pairwise interactions
-between wall particles via the "neigh_modify
-exclude"_neigh_modify.html command.
-
-Rough walls can also be created by specifying frozen particles that do
-not move and do not interact with mobile particles, and then tethering
-other particles to the fixed particles, via a "bond"_bond_style.html.
-The bonded particles do interact with other mobile particles.
-
-Idealized walls can be specified via several fix commands. "Fix
-wall/gran"_fix_wall_gran.html creates frictional walls for use with
-granular particles; all the other commands create smooth walls.
-
-"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls
-"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential
-"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
-"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
-"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
-"fix wall/region"_fix_wall_region.html - use region surface as wall
-"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
-
-The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
-flat walls to move with a constant velocity, or oscillate in time.
-The "fix wall/region"_fix_wall_region.html command offers the most
-generality, since the region surface is treated as a wall, and the
-geometry of the region can be a simple primitive volume (e.g. a
-sphere, or cube, or plane), or a complex volume made from the union
-and intersection of primitive volumes. "Regions"_region.html can also
-specify a volume "interior" or "exterior" to the specified primitive
-shape or {union} or {intersection}. "Regions"_region.html can also be
-"dynamic" meaning they move with constant velocity, oscillate, or
-rotate.
-
-The only frictional idealized walls currently in LAMMPS are flat or
-curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html
-command. At some point we plan to allow regoin surfaces to be used as
-frictional walls, as well as triangulated surfaces.
-
-:line
-
-6.18 Elastic constants :link(howto_18),h4
-
-Elastic constants characterize the stiffness of a material. The formal
-definition is provided by the linear relation that holds between the
-stress and strain tensors in the limit of infinitesimal deformation.
-In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
-the repeated indices imply summation. s_ij are the elements of the
-symmetric stress tensor. e_kl are the elements of the symmetric strain
-tensor. C_ijkl are the elements of the fourth rank tensor of elastic
-constants. In three dimensions, this tensor has 3^4=81 elements. Using
-Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
-is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
-derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
-most 7*6/2 = 21 distinct elements.
-
-At zero temperature, it is easy to estimate these derivatives by
-deforming the simulation box in one of the six directions using the
-"change_box"_change_box.html command and measuring the change in the
-stress tensor. A general-purpose script that does this is given in the
-examples/elastic directory described on the "Examples"_Examples.html
-doc page.
-
-Calculating elastic constants at finite temperature is more
-challenging, because it is necessary to run a simulation that perfoms
-time averages of differential properties. One way to do this is to
-measure the change in average stress tensor in an NVT simulations when
-the cell volume undergoes a finite deformation. In order to balance
-the systematic and statistical errors in this method, the magnitude of
-the deformation must be chosen judiciously, and care must be taken to
-fully equilibrate the deformed cell before sampling the stress
-tensor. Another approach is to sample the triclinic cell fluctuations
-that occur in an NPT simulation. This method can also be slow to
-converge and requires careful post-processing "(Shinoda)"_#Shinoda1
-
-:line
-
-6.19 Library interface to LAMMPS :link(howto_19),h4
-
-As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
-be built as a library, so that it can be called by another code, used
-in a "coupled manner"_Section_howto.html#howto_10 with other codes, or
-driven through a "Python interface"_Python.html.
-
-All of these methodologies use a C-style interface to LAMMPS that is
-provided in the files src/library.cpp and src/library.h. The
-functions therein have a C-style argument list, but contain C++ code
-you could write yourself in a C++ application that was invoking LAMMPS
-directly. The C++ code in the functions illustrates how to invoke
-internal LAMMPS operations. Note that LAMMPS classes are defined
-within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
-application.
-
-The examples/COUPLE and python/examples directories have example C++
-and C and Python codes which show how a driver code can link to LAMMPS
-as a library, run LAMMPS on a subset of processors, grab data from
-LAMMPS, change it, and put it back into LAMMPS.
-
-The file src/library.cpp contains the following functions for creating
-and destroying an instance of LAMMPS and sending it commands to
-execute. See the documentation in the src/library.cpp file for
-details.
-
-NOTE: You can write code for additional functions as needed to define
-how your code talks to LAMMPS and add them to src/library.cpp and
-src/library.h, as well as to the "Python interface"_Python.html. The
-added functions can access or change any internal LAMMPS data you
-wish.
-
-void lammps_open(int, char **, MPI_Comm, void **)
-void lammps_open_no_mpi(int, char **, void **)
-void lammps_close(void *)
-int lammps_version(void *)
-void lammps_file(void *, char *)
-char *lammps_command(void *, char *)
-void lammps_commands_list(void *, int, char **)
-void lammps_commands_string(void *, char *)
-void lammps_free(void *) :pre
-
-The lammps_open() function is used to initialize LAMMPS, passing in a
-list of strings as if they were "command-line
-arguments"_Section_start.html#start_6 when LAMMPS is run in
-stand-alone mode from the command line, and a MPI communicator for
-LAMMPS to run under. It returns a ptr to the LAMMPS object that is
-created, and which is used in subsequent library calls. The
-lammps_open() function can be called multiple times, to create
-multiple instances of LAMMPS.
-
-LAMMPS will run on the set of processors in the communicator. This
-means the calling code can run LAMMPS on all or a subset of
-processors. For example, a wrapper script might decide to alternate
-between LAMMPS and another code, allowing them both to run on all the
-processors. Or it might allocate half the processors to LAMMPS and
-half to the other code and run both codes simultaneously before
-syncing them up periodically. Or it might instantiate multiple
-instances of LAMMPS to perform different calculations.
-
-The lammps_open_no_mpi() function is similar except that no MPI
-communicator is passed from the caller. Instead, MPI_COMM_WORLD is
-used to instantiate LAMMPS, and MPI is initialized if necessary.
-
-The lammps_close() function is used to shut down an instance of LAMMPS
-and free all its memory.
-
-The lammps_version() function can be used to determined the specific
-version of the underlying LAMMPS code. This is particularly useful
-when loading LAMMPS as a shared library via dlopen(). The code using
-the library interface can than use this information to adapt to
-changes to the LAMMPS command syntax between versions. The returned
-LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
-20150902) that grows with every new LAMMPS version.
-
-The lammps_file(), lammps_command(), lammps_commands_list(), and
-lammps_commands_string() functions are used to pass one or more
-commands to LAMMPS to execute, the same as if they were coming from an
-input script.
-
-Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
-interface to setup a problem and then run it in stages. The caller
-can interleave the command function calls with operations it performs,
-calls to extract information from or set information within LAMMPS, or
-calls to another code's library.
-
-The lammps_file() function passes the filename of an input script.
-The lammps_command() function passes a single command as a string.
-The lammps_commands_list() function passes multiple commands in a
-char** list. In both lammps_command() and lammps_commands_list(),
-individual commands may or may not have a trailing newline. The
-lammps_commands_string() function passes multiple commands
-concatenated into one long string, separated by newline characters.
-In both lammps_commands_list() and lammps_commands_string(), a single
-command can be spread across multiple lines, if the last printable
-character of all but the last line is "&", the same as if the lines
-appeared in an input script.
-
-The lammps_free() function is a clean-up function to free memory that
-the library allocated previously via other function calls. See
-comments in src/library.cpp file for which other functions need this
-clean-up.
-
-The file src/library.cpp also contains these functions for extracting
-information from LAMMPS and setting value within LAMMPS. Again, see
-the documentation in the src/library.cpp file for details, including
-which quantities can be queried by name:
-
-int lammps_extract_setting(void *, char *)
-void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *,
- double *, double *, double *, int *, int *)
-void *lammps_extract_atom(void *, char *)
-void *lammps_extract_compute(void *, char *, int, int)
-void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *) :pre
-
-The extract_setting() function returns info on the size
-of data types (e.g. 32-bit or 64-bit atom IDs) used
-by the LAMMPS executable (a compile-time choice).
-
-The other extract functions return a pointer to various global or
-per-atom quantities stored in LAMMPS or to values calculated by a
-compute, fix, or variable. The pointer returned by the
-extract_global() function can be used as a permanent reference to a
-value which may change. For the extract_atom() method, see the
-extract() method in the src/atom.cpp file for a list of valid per-atom
-properties. New names could easily be added if the property you want
-is not listed. For the other extract functions, the underlying
-storage may be reallocated as LAMMPS runs, so you need to re-call the
-function to assure a current pointer or returned value(s).
-
-double lammps_get_thermo(void *, char *)
-int lammps_get_natoms(void *) :pre
-
-int lammps_set_variable(void *, char *, char *)
-void lammps_reset_box(void *, double *, double *, double, double, double) :pre
-
-The lammps_get_thermo() function returns the current value of a thermo
-keyword as a double precision value.
-
-The lammps_get_natoms() function returns the total number of atoms in
-the system and can be used by the caller to allocate memory for the
-lammps_gather_atoms() and lammps_scatter_atoms() functions.
-
-The lammps_set_variable() function can set an existing string-style
-variable to a new string value, so that subsequent LAMMPS commands can
-access the variable.
-
-The lammps_reset_box() function resets the size and shape of the
-simulation box, e.g. as part of restoring a previously extracted and
-saved state of a simulation.
-
-void lammps_gather_atoms(void *, char *, int, int, void *)
-void lammps_gather_atoms_concat(void *, char *, int, int, void *)
-void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
-void lammps_scatter_atoms(void *, char *, int, int, void *)
-void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
-
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
- imageint *, int) :pre
-
-The gather functions collect peratom info of the requested type (atom
-coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
-functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
-
-The lammps_gather_atoms() function does this for all N atoms in the
-system, ordered by atom ID, from 1 to N. The
-lammps_gather_atoms_concat() function does it for all N atoms, but
-simply concatenates the subset of atoms owned by each processor. The
-resulting vector is not ordered by atom ID. Atom IDs can be requetsed
-by the same function if the caller needs to know the ordering. The
-lammps_gather_subset() function allows the caller to request values
-for only a subset of atoms (identified by ID).
-For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
-If the count is specified as 1, they are returned
-in a packed format with all three image flags stored in a single integer.
-If the count is specified as 3, the values are unpacked into xyz flags
-by the library before returning them.
-
-The lammps_scatter_atoms() function takes a list of values for all N
-atoms in the system, ordered by atom ID, from 1 to N, and assigns
-those values to each atom in the system. The
-lammps_scatter_atoms_subset() function takes a subset of IDs as an
-argument and only scatters those values to the owning atoms.
-
-The lammps_create_atoms() function takes a list of N atoms as input
-with atom types and coords (required), an optionally atom IDs and
-velocities and image flags. It uses the coords of each atom to assign
-it as a new atom to the processor that owns it. This function is
-useful to add atoms to a simulation or (in tandem with
-lammps_reset_box()) to restore a previously extracted and saved state
-of a simulation. Additional properties for the new atoms can then be
-assigned via the lammps_scatter_atoms() or lammps_extract_atom()
-functions.
-
-:line
-
-6.20 Calculating thermal conductivity :link(howto_20),h4
-
-The thermal conductivity kappa of a material can be measured in at
-least 4 ways using various options in LAMMPS. See the examples/KAPPA
-directory for scripts that implement the 4 methods discussed here for
-a simple Lennard-Jones fluid model. Also, see "this
-section"_Section_howto.html#howto_21 of the manual for an analogous
-discussion for viscosity.
-
-The thermal conductivity tensor kappa is a measure of the propensity
-of a material to transmit heat energy in a diffusive manner as given
-by Fourier's law
-
-J = -kappa grad(T)
-
-where J is the heat flux in units of energy per area per time and
-grad(T) is the spatial gradient of temperature. The thermal
-conductivity thus has units of energy per distance per time per degree
-K and is often approximated as an isotropic quantity, i.e. as a
-scalar.
-
-The first method is to setup two thermostatted regions at opposite
-ends of a simulation box, or one in the middle and one at the end of a
-periodic box. By holding the two regions at different temperatures
-with a "thermostatting fix"_Section_howto.html#howto_13, the energy
-added to the hot region should equal the energy subtracted from the
-cold region and be proportional to the heat flux moving between the
-regions. See the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji
-and "Wirnsberger et al"_#howto-Wirnsberger for details of this idea.
-Note that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix
-langevin"_fix_langevin.html, and "fix
-temp/rescale"_fix_temp_rescale.html store the cumulative energy they
-add/subtract.
-
-Alternatively, as a second method, the "fix heat"_fix_heat.html or
-"fix ehex"_fix_ehex.html commands can be used in place of thermostats
-on each of two regions to add/subtract specified amounts of energy to
-both regions. In both cases, the resulting temperatures of the two
-regions can be monitored with the "compute temp/region" command and
-the temperature profile of the intermediate region can be monitored
-with the "fix ave/chunk"_fix_ave_chunk.html and "compute
-ke/atom"_compute_ke_atom.html commands.
-
-The third method is to perform a reverse non-equilibrium MD simulation
-using the "fix thermal/conductivity"_fix_thermal_conductivity.html
-command which implements the rNEMD algorithm of Muller-Plathe.
-Kinetic energy is swapped between atoms in two different layers of the
-simulation box. This induces a temperature gradient between the two
-layers which can be monitored with the "fix
-ave/chunk"_fix_ave_chunk.html and "compute
-ke/atom"_compute_ke_atom.html commands. The fix tallies the
-cumulative energy transfer that it performs. See the "fix
-thermal/conductivity"_fix_thermal_conductivity.html command for
-details.
-
-The fourth method is based on the Green-Kubo (GK) formula which
-relates the ensemble average of the auto-correlation of the heat flux
-to kappa. The heat flux can be calculated from the fluctuations of
-per-atom potential and kinetic energies and per-atom stress tensor in
-a steady-state equilibrated simulation. This is in contrast to the
-two preceding non-equilibrium methods, where energy flows continuously
-between hot and cold regions of the simulation box.
-
-The "compute heat/flux"_compute_heat_flux.html command can calculate
-the needed heat flux and describes how to implement the Green_Kubo
-formalism using additional LAMMPS commands, such as the "fix
-ave/correlate"_fix_ave_correlate.html command to calculate the needed
-auto-correlation. See the doc page for the "compute
-heat/flux"_compute_heat_flux.html command for an example input script
-that calculates the thermal conductivity of solid Ar via the GK
-formalism.
-
-:line
-
-6.21 Calculating viscosity :link(howto_21),h4
-
-The shear viscosity eta of a fluid can be measured in at least 5 ways
-using various options in LAMMPS. See the examples/VISCOSITY directory
-for scripts that implement the 5 methods discussed here for a simple
-Lennard-Jones fluid model. Also, see "this
-section"_Section_howto.html#howto_20 of the manual for an analogous
-discussion for thermal conductivity.
-
-Eta is a measure of the propensity of a fluid to transmit momentum in
-a direction perpendicular to the direction of velocity or momentum
-flow. Alternatively it is the resistance the fluid has to being
-sheared. It is given by
-
-J = -eta grad(Vstream)
-
-where J is the momentum flux in units of momentum per area per time.
-and grad(Vstream) is the spatial gradient of the velocity of the fluid
-moving in another direction, normal to the area through which the
-momentum flows. Viscosity thus has units of pressure-time.
-
-The first method is to perform a non-equilibrium MD (NEMD) simulation
-by shearing the simulation box via the "fix deform"_fix_deform.html
-command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
-thermostat the fluid via the SLLOD equations of motion.
-Alternatively, as a second method, one or more moving walls can be
-used to shear the fluid in between them, again with some kind of
-thermostat that modifies only the thermal (non-shearing) components of
-velocity to prevent the fluid from heating up.
-
-In both cases, the velocity profile setup in the fluid by this
-procedure can be monitored by the "fix
-ave/chunk"_fix_ave_chunk.html command, which determines
-grad(Vstream) in the equation above. E.g. the derivative in the
-y-direction of the Vx component of fluid motion or grad(Vstream) =
-dVx/dy. The Pxy off-diagonal component of the pressure or stress
-tensor, as calculated by the "compute pressure"_compute_pressure.html
-command, can also be monitored, which is the J term in the equation
-above. See "this section"_Section_howto.html#howto_13 of the manual
-for details on NEMD simulations.
-
-The third method is to perform a reverse non-equilibrium MD simulation
-using the "fix viscosity"_fix_viscosity.html command which implements
-the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
-swapped between atoms in two different layers of the simulation box in
-a different dimension. This induces a velocity gradient which can be
-monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
-The fix tallies the cumulative momentum transfer that it performs.
-See the "fix viscosity"_fix_viscosity.html command for details.
-
-The fourth method is based on the Green-Kubo (GK) formula which
-relates the ensemble average of the auto-correlation of the
-stress/pressure tensor to eta. This can be done in a fully
-equilibrated simulation which is in contrast to the two preceding
-non-equilibrium methods, where momentum flows continuously through the
-simulation box.
-
-Here is an example input script that calculates the viscosity of
-liquid Ar via the GK formalism:
-
-# Sample LAMMPS input script for viscosity of liquid Ar :pre
-
-units real
-variable T equal 86.4956
-variable V equal vol
-variable dt equal 4.0
-variable p equal 400 # correlation length
-variable s equal 5 # sample interval
-variable d equal $p*$s # dump interval :pre
-
-# convert from LAMMPS real units to SI :pre
-
-variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann
-variable atm2Pa equal 101325.0
-variable A2m equal 1.0e-10
-variable fs2s equal 1.0e-15
-variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre
-
-# setup problem :pre
-
-dimension 3
-boundary p p p
-lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
-region box block 0 4 0 4 0 4
-create_box 1 box
-create_atoms 1 box
-mass 1 39.948
-pair_style lj/cut 13.0
-pair_coeff * * 0.2381 3.405
-timestep $\{dt\}
-thermo $d :pre
-
-# equilibration and thermalization :pre
-
-velocity all create $T 102486 mom yes rot yes dist gaussian
-fix NVT all nvt temp $T $T 10 drag 0.2
-run 8000 :pre
-
-# viscosity calculation, switch to NVE if desired :pre
-
-#unfix NVT
-#fix NVE all nve :pre
-
-reset_timestep 0
-variable pxy equal pxy
-variable pxz equal pxz
-variable pyz equal pyz
-fix SS all ave/correlate $s $p $d &
- v_pxy v_pxz v_pyz type auto file S0St.dat ave running
-variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\}
-variable v11 equal trap(f_SS\[3\])*$\{scale\}
-variable v22 equal trap(f_SS\[4\])*$\{scale\}
-variable v33 equal trap(f_SS\[5\])*$\{scale\}
-thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
-run 100000
-variable v equal (v_v11+v_v22+v_v33)/3.0
-variable ndens equal count(all)/vol
-print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre
-
-The fifth method is related to the above Green-Kubo method,
-but uses the Einstein formulation, analogous to the Einstein
-mean-square-displacement formulation for self-diffusivity. The
-time-integrated momentum fluxes play the role of Cartesian
-coordinates, whose mean-square displacement increases linearly
-with time at sufficiently long times.
-
-:line
-
-6.22 Calculating a diffusion coefficient :link(howto_22),h4
-
-The diffusion coefficient D of a material can be measured in at least
-2 ways using various options in LAMMPS. See the examples/DIFFUSE
-directory for scripts that implement the 2 methods discussed here for
-a simple Lennard-Jones fluid model.
-
-The first method is to measure the mean-squared displacement (MSD) of
-the system, via the "compute msd"_compute_msd.html command. The slope
-of the MSD versus time is proportional to the diffusion coefficient.
-The instantaneous MSD values can be accumulated in a vector via the
-"fix vector"_fix_vector.html command, and a line fit to the vector to
-compute its slope via the "variable slope"_variable.html function, and
-thus extract D.
-
-The second method is to measure the velocity auto-correlation function
-(VACF) of the system, via the "compute vacf"_compute_vacf.html
-command. The time-integral of the VACF is proportional to the
-diffusion coefficient. The instantaneous VACF values can be
-accumulated in a vector via the "fix vector"_fix_vector.html command,
-and time integrated via the "variable trap"_variable.html function,
-and thus extract D.
-
-:line
-
-6.23 Using chunks to calculate system properties :link(howto_23),h4
-
-In LAMMS, "chunks" are collections of atoms, as defined by the
-"compute chunk/atom"_compute_chunk_atom.html command, which assigns
-each atom to a chunk ID (or to no chunk at all). The number of chunks
-and the assignment of chunk IDs to atoms can be static or change over
-time. Examples of "chunks" are molecules or spatial bins or atoms
-with similar values (e.g. coordination number or potential energy).
-
-The per-atom chunk IDs can be used as input to two other kinds of
-commands, to calculate various properties of a system:
-
-"fix ave/chunk"_fix_ave_chunk.html
-any of the "compute */chunk"_compute.html commands :ul
-
-Here, each of the 3 kinds of chunk-related commands is briefly
-overviewed. Then some examples are given of how to compute different
-properties with chunk commands.
-
-Compute chunk/atom command: :h4
-
-This compute can assign atoms to chunks of various styles. Only atoms
-in the specified group and optional specified region are assigned to a
-chunk. Here are some possible chunk definitions:
-
-atoms in same molecule | chunk ID = molecule ID |
-atoms of same atom type | chunk ID = atom type |
-all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
-atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
-atoms in same spatial bin | chunk ID = bin ID |
-atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
-atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
-atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
-
-Note that chunk IDs are integer values, so for atom properties or
-computes that produce a floating point value, they will be truncated
-to an integer. You could also use the compute in a variable that
-scales the floating point value to spread it across multiple integers.
-
-Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
-pencils, 3d bins = boxes, spherical bins, cylindrical bins.
-
-This compute also calculates the number of chunks {Nchunk}, which is
-used by other commands to tally per-chunk data. {Nchunk} can be a
-static value or change over time (e.g. the number of clusters). The
-chunk ID for an individual atom can also be static (e.g. a molecule
-ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
-
-Note that this compute allows the per-atom output of other
-"computes"_compute.html, "fixes"_fix.html, and
-"variables"_variable.html to be used to define chunk IDs for each
-atom. This means you can write your own compute or fix to output a
-per-atom quantity to use as chunk ID. See the "Modify"_Modify.html
-doc page for how to do this. You can also define a "per-atom
-variable"_variable.html in the input script that uses a formula to
-generate a chunk ID for each atom.
-
-Fix ave/chunk command: :h4
-
-This fix takes the ID of a "compute
-chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
-it then sums one or more specified per-atom values over the atoms in
-each chunk. The per-atom values can be any atom property, such as
-velocity, force, charge, potential energy, kinetic energy, stress,
-etc. Additional keywords are defined for per-chunk properties like
-density and temperature. More generally any per-atom value generated
-by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
-variables"_variable.html, can be summed over atoms in each chunk.
-
-Similar to other averaging fixes, this fix allows the summed per-chunk
-values to be time-averaged in various ways, and output to a file. The
-fix produces a global array as output with one row of values per
-chunk.
-
-Compute */chunk commands: :h4
-
-Currently the following computes operate on chunks of atoms to produce
-per-chunk values.
-
-"compute com/chunk"_compute_com_chunk.html
-"compute gyration/chunk"_compute_gyration_chunk.html
-"compute inertia/chunk"_compute_inertia_chunk.html
-"compute msd/chunk"_compute_msd_chunk.html
-"compute property/chunk"_compute_property_chunk.html
-"compute temp/chunk"_compute_temp_chunk.html
-"compute torque/chunk"_compute_vcm_chunk.html
-"compute vcm/chunk"_compute_vcm_chunk.html :ul
-
-They each take the ID of a "compute
-chunk/atom"_compute_chunk_atom.html command as input. As their names
-indicate, they calculate the center-of-mass, radius of gyration,
-moments of inertia, mean-squared displacement, temperature, torque,
-and velocity of center-of-mass for each chunk of atoms. The "compute
-property/chunk"_compute_property_chunk.html command can tally the
-count of atoms in each chunk and extract other per-chunk properties.
-
-The reason these various calculations are not part of the "fix
-ave/chunk command"_fix_ave_chunk.html, is that each requires a more
-complicated operation than simply summing and averaging over per-atom
-values in each chunk. For example, many of them require calculation
-of a center of mass, which requires summing mass*position over the
-atoms and then dividing by summed mass.
-
-All of these computes produce a global vector or global array as
-output, wih one or more values per chunk. They can be used
-in various ways:
-
-As input to the "fix ave/time"_fix_ave_time.html command, which can
-write the values to a file and optionally time average them. :ulb,l
-
-As input to the "fix ave/histo"_fix_ave_histo.html command to
-histogram values across chunks. E.g. a histogram of cluster sizes or
-molecule diffusion rates. :l
-
-As input to special functions of "equal-style
-variables"_variable.html, like sum() and max(). E.g. to find the
-largest cluster or fastest diffusing molecule. :l
-:ule
-
-Example calculations with chunks :h4
-
-Here are examples using chunk commands to calculate various
-properties:
-
-(1) Average velocity in each of 1000 2d spatial bins:
-
-compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
-fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
-
-(2) Temperature in each spatial bin, after subtracting a flow
-velocity:
-
-compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
-compute vbias all temp/profile 1 0 0 y 10
-fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
-
-(3) Center of mass of each molecule:
-
-compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
-
-(4) Total force on each molecule and ave/max across all molecules:
-
-compute cc1 all chunk/atom molecule
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_1\[2\])
-variable xmax equal max(f_1\[2\])
-thermo 1000
-thermo_style custom step temp v_xave v_xmax :pre
-
-(5) Histogram of cluster sizes:
-
-compute cluster all cluster/atom 1.0
-compute cc1 all chunk/atom c_cluster compress yes
-compute size all property/chunk cc1 count
-fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
-
-:line
-
-6.24 Setting parameters for the "kspace_style pppm/disp"_kspace_style.html command :link(howto_24),h4
-
-The PPPM method computes interactions by splitting the pair potential
-into two parts, one of which is computed in a normal pairwise fashion,
-the so-called real-space part, and one of which is computed using the
-Fourier transform, the so called reciprocal-space or kspace part. For
-both parts, the potential is not computed exactly but is approximated.
-Thus, there is an error in both parts of the computation, the
-real-space and the kspace error. The just mentioned facts are true
-both for the PPPM for Coulomb as well as dispersion interactions. The
-deciding difference - and also the reason why the parameters for
-pppm/disp have to be selected with more care - is the impact of the
-errors on the results: The kspace error of the PPPM for Coulomb and
-dispersion interaction and the real-space error of the PPPM for
-Coulomb interaction have the character of noise. In contrast, the
-real-space error of the PPPM for dispersion has a clear physical
-interpretation: the underprediction of cohesion. As a consequence, the
-real-space error has a much stronger effect than the kspace error on
-simulation results for pppm/disp. Parameters must thus be chosen in a
-way that this error is much smaller than the kspace error.
-
-When using pppm/disp and not making any specifications on the PPPM
-parameters via the kspace modify command, parameters will be tuned
-such that the real-space error and the kspace error are equal. This
-will result in simulations that are either inaccurate or slow, both of
-which is not desirable. For selecting parameters for the pppm/disp
-that provide fast and accurate simulations, there are two approaches,
-which both have their up- and downsides.
-
-The first approach is to set desired real-space an kspace accuracies
-via the {kspace_modify force/disp/real} and {kspace_modify
-force/disp/kspace} commands. Note that the accuracies have to be
-specified in force units and are thus dependent on the chosen unit
-settings. For real units, 0.0001 and 0.002 seem to provide reasonable
-accurate and efficient computations for the real-space and kspace
-accuracies. 0.002 and 0.05 work well for most systems using lj
-units. PPPM parameters will be generated based on the desired
-accuracies. The upside of this approach is that it usually provides a
-good set of parameters and will work for both the {kspace_modify diff
-ad} and {kspace_modify diff ik} options. The downside of the method
-is that setting the PPPM parameters will take some time during the
-initialization of the simulation.
-
-The second approach is to set the parameters for the pppm/disp
-explicitly using the {kspace_modify mesh/disp}, {kspace_modify
-order/disp}, and {kspace_modify gewald/disp} commands. This approach
-requires a more experienced user who understands well the impact of
-the choice of parameters on the simulation accuracy and
-performance. This approach provides a fast initialization of the
-simulation. However, it is sensitive to errors: A combination of
-parameters that will perform well for one system might result in
-far-from-optimal conditions for other simulations. For example,
-parameters that provide accurate and fast computations for
-all-atomistic force fields can provide insufficient accuracy or
-united-atomistic force fields (which is related to that the latter
-typically have larger dispersion coefficients).
-
-To avoid inaccurate or inefficient simulations, the pppm/disp stops
-simulations with an error message if no action is taken to control the
-PPPM parameters. If the automatic parameter generation is desired and
-real-space and kspace accuracies are desired to be equal, this error
-message can be suppressed using the {kspace_modify disp/auto yes}
-command.
-
-A reasonable approach that combines the upsides of both methods is to
-make the first run using the {kspace_modify force/disp/real} and
-{kspace_modify force/disp/kspace} commands, write down the PPPM
-parameters from the outut, and specify these parameters using the
-second approach in subsequent runs (which have the same composition,
-force field, and approximately the same volume).
-
-Concerning the performance of the pppm/disp there are two more things
-to consider. The first is that when using the pppm/disp, the cutoff
-parameter does no longer affect the accuracy of the simulation
-(subject to that gewald/disp is adjusted when changing the cutoff).
-The performance can thus be increased by examining different values
-for the cutoff parameter. A lower bound for the cutoff is only set by
-the truncation error of the repulsive term of pair potentials.
-
-The second is that the mixing rule of the pair style has an impact on
-the computation time when using the pppm/disp. Fastest computations
-are achieved when using the geometric mixing rule. Using the
-arithmetic mixing rule substantially increases the computational cost.
-The computational overhead can be reduced using the {kspace_modify
-mix/disp geom} and {kspace_modify splittol} commands. The first
-command simply enforces geometric mixing of the dispersion
-coefficients in kspace computations. This introduces some error in
-the computations but will also significantly speed-up the
-simulations. The second keyword sets the accuracy with which the
-dispersion coefficients are approximated using a matrix factorization
-approach. This may result in better accuracy then using the first
-command, but will usually also not provide an equally good increase of
-efficiency.
-
-Finally, pppm/disp can also be used when no mixing rules apply.
-This can be achieved using the {kspace_modify mix/disp none} command.
-Note that the code does not check automatically whether any mixing
-rule is fulfilled. If mixing rules do not apply, the user will have
-to specify this command explicitly.
-
-:line
-
-6.25 Polarizable models :link(howto_25),h4
-
-In polarizable force fields the charge distributions in molecules and
-materials respond to their electrostatic environments. Polarizable
-systems can be simulated in LAMMPS using three methods:
-
-the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
-package, :ulb,l
-the adiabatic core-shell method, implemented in the
-"CORESHELL"_#howto_26 package, :l
-the thermalized Drude dipole method, implemented in the
-"USER-DRUDE"_#howto_27 package. :l
-:ule
-
-The fluctuating charge method calculates instantaneous charges on
-interacting atoms based on the electronegativity equalization
-principle. It is implemented in the "fix qeq"_fix_qeq.html which is
-available in several variants. It is a relatively efficient technique
-since no additional particles are introduced. This method allows for
-charge transfer between molecules or atom groups. However, because the
-charges are located at the interaction sites, off-plane components of
-polarization cannot be represented in planar molecules or atom groups.
-
-The two other methods share the same basic idea: polarizable atoms are
-split into one core atom and one satellite particle (called shell or
-Drude particle) attached to it by a harmonic spring. Both atoms bear
-a charge and they represent collectively an induced electric dipole.
-These techniques are computationally more expensive than the QEq
-method because of additional particles and bonds. These two
-charge-on-spring methods differ in certain features, with the
-core-shell model being normally used for ionic/crystalline materials,
-whereas the so-called Drude model is normally used for molecular
-systems and fluid states.
-
-The core-shell model is applicable to crystalline materials where the
-high symmetry around each site leads to stable trajectories of the
-core-shell pairs. However, bonded atoms in molecules can be so close
-that a core would interact too strongly or even capture the Drude
-particle of a neighbor. The Drude dipole model is relatively more
-complex in order to remediate this and other issues. Specifically, the
-Drude model includes specific thermostating of the core-Drude pairs
-and short-range damping of the induced dipoles.
-
-The three polarization methods can be implemented through a
-self-consistent calculation of charges or induced dipoles at each
-timestep. In the fluctuating charge scheme this is done by the matrix
-inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell
-or Drude-dipoles the relaxed-dipoles technique would require an slow
-iterative procedure. These self-consistent solutions yield accurate
-trajectories since the additional degrees of freedom representing
-polarization are massless. An alternative is to attribute a mass to
-the additional degrees of freedom and perform time integration using
-an extended Lagrangian technique. For the fluctuating charge scheme
-this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
-charge-on-spring models by the methods outlined in the next two
-sections. The assignment of masses to the additional degrees of
-freedom can lead to unphysical trajectories if care is not exerted in
-choosing the parameters of the polarizable models and the simulation
-conditions.
-
-In the core-shell model the vibration of the shells is kept faster
-than the ionic vibrations to mimic the fast response of the
-polarizable electrons. But in molecular systems thermalizing the
-core-Drude pairs at temperatures comparable to the rest of the
-simulation leads to several problems (kinetic energy transfer, too
-short a timestep, etc.) In order to avoid these problems the relative
-motion of the Drude particles with respect to their cores is kept
-"cold" so the vibration of the core-Drude pairs is very slow,
-approaching the self-consistent regime. In both models the
-temperature is regulated using the velocities of the center of mass of
-core+shell (or Drude) pairs, but in the Drude model the actual
-relative core-Drude particle motion is thermostated separately as
-well.
-
-:line
-
-6.26 Adiabatic core/shell model :link(howto_26),h4
-
-The adiabatic core-shell model by "Mitchell and
-Fincham"_#MitchellFincham is a simple method for adding
-polarizability to a system. In order to mimic the electron shell of
-an ion, a satellite particle is attached to it. This way the ions are
-split into a core and a shell where the latter is meant to react to
-the electrostatic environment inducing polarizability.
-
-Technically, shells are attached to the cores by a spring force f =
-k*r where k is a parametrized spring constant and r is the distance
-between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). This
-setup introduces the ion polarizability (alpha) given by
-alpha = q(shell)^2 / k. In a
-similar fashion the mass of the ion is distributed on the core and the
-shell with the core having the larger mass.
-
-To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
-be used since atom charge and bonds are needed. Each kind of
-core/shell pair requires two atom types and a bond type. The core and
-shell of a core/shell pair should be bonded to each other with a
-harmonic bond that provides the spring force. For example, a data file
-for NaCl, as found in examples/coreshell, has this format:
-
-432 atoms # core and shell atoms
-216 bonds # number of core/shell springs :pre
-
-4 atom types # 2 cores and 2 shells for Na and Cl
-2 bond types :pre
-
-0.0 24.09597 xlo xhi
-0.0 24.09597 ylo yhi
-0.0 24.09597 zlo zhi :pre
-
-Masses # core/shell mass ratio = 0.1 :pre
-
-1 20.690784 # Na core
-2 31.90500 # Cl core
-3 2.298976 # Na shell
-4 3.54500 # Cl shell :pre
-
-Atoms :pre
-
-1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
-2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
-3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
-4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
-(...) :pre
-
-Bonds # Bond topology for spring forces :pre
-
-1 2 1 2 # spring for core/shell pair 1
-2 2 3 4 # spring for core/shell pair 2
-(...) :pre
-
-Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
-defined between the shells. Coulombic interactions are defined
-between all cores and shells. If desired, additional bonds can be
-specified between cores.
-
-The "special_bonds"_special_bonds.html command should be used to
-turn-off the Coulombic interaction within core/shell pairs, since that
-interaction is set by the bond spring. This is done using the
-"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
-which is the default value. It needs to be considered whether one has
-to adjust the "special_bonds"_special_bonds.html weighting according
-to the molecular topology since the interactions of the shells are
-bypassed over an extra bond.
-
-Note that this core/shell implementation does not require all ions to
-be polarized. One can mix core/shell pairs and ions without a
-satellite particle if desired.
-
-Since the core/shell model permits distances of r = 0.0 between the
-core and shell, a pair style with a "cs" suffix needs to be used to
-implement a valid long-range Coulombic correction. Several such pair
-styles are provided in the CORESHELL package. See "this doc
-page"_pair_cs.html for details. All of the core/shell enabled pair
-styles require the use of a long-range Coulombic solver, as specified
-by the "kspace_style"_kspace_style.html command. Either the PPPM or
-Ewald solvers can be used.
-
-For the NaCL example problem, these pair style and bond style settings
-are used:
-
-pair_style born/coul/long/cs 20.0 20.0
-pair_coeff * * 0.0 1.000 0.00 0.00 0.00
-pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
-pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
-pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
-
-bond_style harmonic
-bond_coeff 1 63.014 0.0
-bond_coeff 2 25.724 0.0 :pre
-
-When running dynamics with the adiabatic core/shell model, the
-following issues should be considered. The relative motion of
-the core and shell particles corresponds to the polarization,
-hereby an instantaneous relaxation of the shells is approximated
-and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation.
-Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to
-its electrostatic environment.
-Therefore it is typically desirable to decouple the relative motion of
-the core/shell pair, which is an imaginary degree of freedom, from the
-real physical system. To do that, the "compute
-temp/cs"_compute_temp_cs.html command can be used, in conjunction with
-any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
-langevin"_fix_langevin. This compute uses the center-of-mass velocity
-of the core/shell pairs to calculate a temperature, and insures that
-velocity is what is rescaled for thermostatting purposes. This
-compute also works for a system with both core/shell pairs and
-non-polarized ions (ions without an attached satellite particle). The
-"compute temp/cs"_compute_temp_cs.html command requires input of two
-groups, one for the core atoms, another for the shell atoms.
-Non-polarized ions which might also be included in the treated system
-should not be included into either of these groups, they are taken
-into account by the {group-ID} (2nd argument) of the compute. The
-groups can be defined using the "group {type}"_group.html command.
-Note that to perform thermostatting using this definition of
-temperature, the "fix modify temp"_fix_modify.html command should be
-used to assign the compute to the thermostat fix. Likewise the
-"thermo_modify temp"_thermo_modify.html command can be used to make
-this temperature be output for the overall system.
-
-For the NaCl example, this can be done as follows:
-
-group cores type 1 2
-group shells type 3 4
-compute CSequ all temp/cs cores shells
-fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
-fix thermostatequ all nve # integrator as needed for the berendsen thermostat
-fix_modify thermoberendsen temp CSequ
-thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
-
-The pressure for the core/shell system is computed via the regular
-LAMMPS convention by "treating the cores and shells as individual
-particles"_#MitchellFincham2. For the thermo output of the pressure
-as well as for the application of a barostat, it is necessary to
-use an additional "pressure"_compute_pressure compute based on the
-default "temperature"_compute_temp and specifying it as a second
-argument in "fix modify"_fix_modify.html and
-"thermo_modify"_thermo_modify.html resulting in:
-
-(...)
-compute CSequ all temp/cs cores shells
-compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles
-thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure
-fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
-fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre
-
-If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
-relative motion of the core and the shell should in theory be
-stable. However numerical fluctuation can introduce a small
-momentum to the system, which is noticable over long trajectories.
-Therefore it is recommendable to use the "fix
-momentum"_fix_momentum.html command in combination with "compute
-temp/cs"_compute_temp_cs.html when equilibrating the system to
-prevent any drift.
-
-When initializing the velocities of a system with core/shell pairs, it
-is also desirable to not introduce energy into the relative motion of
-the core/shell particles, but only assign a center-of-mass velocity to
-the pairs. This can be done by using the {bias} keyword of the
-"velocity create"_velocity.html command and assigning the "compute
-temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
-"velocity"_velocity.html command, e.g.
-
-velocity all create 1427 134 bias yes temp CSequ
-velocity all scale 1427 temp CSequ :pre
-
-To maintain the correct polarizability of the core/shell pairs, the
-kinetic energy of the internal motion shall remain nearly constant.
-Therefore the choice of spring force and mass ratio need to ensure
-much faster relative motion of the 2 atoms within the core/shell pair
-than their center-of-mass velocity. This allows the shells to
-effectively react instantaneously to the electrostatic environment and
-limits energy transfer to or from the core/shell oscillators.
-This fast movement also dictates the timestep that can be used.
-
-The primary literature of the adiabatic core/shell model suggests that
-the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment.
-The mentioned energy transfer will typically lead to a small drift
-in total energy over time. This internal energy can be monitored
-using the "compute chunk/atom"_compute_chunk_atom.html and "compute
-temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
-energies of each core/shell pair can then be summed using the sum()
-special function of the "variable"_variable.html command. Or they can
-be time/averaged and output using the "fix ave/time"_fix_ave_time.html
-command. To use these commands, each core/shell pair must be defined
-as a "chunk". If each core/shell pair is defined as its own molecule,
-the molecule ID can be used to define the chunks. If cores are bonded
-to each other to form larger molecules, the chunks can be identified
-by the "fix property/atom"_fix_property_atom.html via assigning a
-core/shell ID to each atom using a special field in the data file read
-by the "read_data"_read_data.html command. This field can then be
-accessed by the "compute property/atom"_compute_property_atom.html
-command, to use as input to the "compute
-chunk/atom"_compute_chunk_atom.html command to define the core/shell
-pairs as chunks.
-
-For example if core/shell pairs are the only molecules:
-
-read_data NaCl_CS_x0.1_prop.data
-compute prop all property/atom molecule
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
-
-For example if core/shell pairs and other molecules are present:
-
-fix csinfo all property/atom i_CSID # property/atom command
-read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
-compute prop all property/atom i_CSID
-(...) :pre
-
-The additional section in the date file would be formatted like this:
-
-CS-Info # header of additional section :pre
-
-1 1 # column 1 = atom ID, column 2 = core/shell ID
-2 1
-3 2
-4 2
-5 3
-6 3
-7 4
-8 4
-(...) :pre
-
-:line
-
-6.27 Drude induced dipoles :link(howto_27),h4
-
-The thermalized Drude model, similarly to the "core-shell"_#howto_26
-model, represents induced dipoles by a pair of charges (the core atom
-and the Drude particle) connected by a harmonic spring. The Drude
-model has a number of features aimed at its use in molecular systems
-("Lamoureux and Roux"_#howto-Lamoureux):
-
-Thermostating of the additional degrees of freedom associated with the
-induced dipoles at very low temperature, in terms of the reduced
-coordinates of the Drude particles with respect to their cores. This
-makes the trajectory close to that of relaxed induced dipoles. :ulb,l
-
-Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
-pair represents a single (polarizable) atom, so the special screening
-factors in a covalent structure should be the same for the core and
-the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4
-special neighbor relations from their respective cores. :l
-
-Stabilization of the interactions between induced dipoles. Drude
-dipoles on covalently bonded atoms interact too strongly due to the
-short distances, so an atom may capture the Drude particle of a
-neighbor, or the induced dipoles within the same molecule may align
-too much. To avoid this, damping at short range can be done by Thole
-functions (for which there are physical grounds). This Thole damping
-is applied to the point charges composing the induced dipole (the
-charge of the Drude particle and the opposite charge on the core, not
-to the total charge of the core atom). :l
-:ule
-
-A detailed tutorial covering the usage of Drude induced dipoles in
-LAMMPS is "available here"_tutorial_drude.html.
-
-As with the core-shell model, the cores and Drude particles should
-appear in the data file as standard atoms. The same holds for the
-springs between them, which are described by standard harmonic bonds.
-The nature of the atoms (core, Drude particle or non-polarizable) is
-specified via the "fix drude"_fix_drude.html command. The special
-list of neighbors is automatically refactored to account for the
-equivalence of core and Drude particles as regards special 1-2 to 1-4
-screening. It may be necessary to use the {extra/special/per/atom}
-keyword of the "read_data"_read_data.html command. If using "fix
-shake"_fix_shake.html, make sure no Drude particle is in this fix
-group.
-
-There are two ways to thermostat the Drude particles at a low
-temperature: use either "fix langevin/drude"_fix_langevin_drude.html
-for a Langevin thermostat, or "fix
-drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
-thermostat. The former requires use of the command "comm_modify vel
-yes"_comm_modify.html. The latter requires two separate integration
-fixes like {nvt} or {npt}. The correct temperatures of the reduced
-degrees of freedom can be calculated using the "compute
-temp/drude"_compute_temp_drude.html. This requires also to use the
-command {comm_modify vel yes}.
-
-Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the "pair style
-thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
-with a Coulomb pair style. It may be useful to use {coul/long/cs} or
-similar from the CORESHELL package if the core and Drude particle come
-too close, which can cause numerical issues.
-
-:line
-
-6.28 Magnetic spins :link(howto_28),h4
-
-Classical magnetic spin simualtions can be performed via the SPIN
-package. The algrorithmic and implementation details are described in
-"Tranchida"_#Tranchida7.
-
-The model representents the simulation of atomic magnetic spins
-coupled to lattice vibrations. The dynamics of those magnetic spins
-can be used to simulate a broad range a phenomena related to
-magneto-elasticity, or or to study the influence of defects on the
-magnetic properties of materials.
-
-The magnetic spins are interacting with each others and with the
-lattice via pair interactions. Typically, the magnetic exchange
-interaction can be defined using the
-"pair/spin/exchange"_pair_spin_exchange.html command. This exchange
-applies a magnetic torque to a given spin, considering the orientation
-of its neighboring spins and their relative distances.
-It also applies a force on the atoms as a function of the spin
-orientations and their associated inter-atomic distances.
-
-The command "fix precession/spin"_fix_precession_spin.html allows to
-apply a constant magnetic torque on all the spins in the system. This
-torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy.
-
-A Langevin thermostat can be applied to those magnetic spins using
-"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
-can be coupled to another Langevin thermostat applied to the atoms
-using "fix langevin"_fix_langevin.html in order to simulate
-thermostated spin-lattice system.
-
-The magnetic Gilbert damping can also be applied using "fix
-langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
-the thermal energy of the Langevin thermostat, or to perform a
-relaxation of the magnetic configuration toward an equilibrium state.
-
-All the computed magnetic properties can be outputed by two main
-commands. The first one is "compute spin"_compute_spin.html, that
-enables to evaluate magnetic averaged quantities, such as the total
-magnetization of the system along x, y, or z, the spin temperature, or
-the magnetic energy. The second command is "compute
-property/atom"_compute_property_atom.html. It enables to output all the
-per atom magnetic quantities. Typically, the orientation of a given
-magnetic spin, or the magnetic force acting on this spin.
-
-:line
-:line
-
-:link(howto-Berendsen)
-[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
-6269-6271 (1987).
-
-:link(howto-Cornell)
-[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
-Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
-
-:link(Horn)
-[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
-J Chem Phys, 120, 9665 (2004).
-
-:link(howto-Ikeshoji)
-[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
-(1994).
-
-:link(howto-Wirnsberger)
-[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
-(2015).
-
-:link(howto-MacKerell)
-[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
-Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
-
-:link(howto-Mayo)
-[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).
-
-:link(Jorgensen1)
-[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
-Phys, 79, 926 (1983).
-
-:link(Price1)
-[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
-
-:link(Shinoda1)
-[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
-
-:link(MitchellFincham)
-[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
-5, 1031-1038 (1993).
-
-:link(MitchellFincham2)
-[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
-6, 393-404 (1994).
-
-:link(howto-Lamoureux)
-[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
-
-:link(Tranchida7)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
deleted file mode 100644
index c7cf5bf8d2..0000000000
--- a/doc/src/Section_intro.txt
+++ /dev/null
@@ -1,550 +0,0 @@
-"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_start.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-1. Introduction :h2
-
-This section provides an overview of what LAMMPS can and can't do,
-describes what it means for LAMMPS to be an open-source code, and
-acknowledges the funding and people who have contributed to LAMMPS
-over the years.
-
-1.1 "What is LAMMPS"_#intro_1
-1.2 "LAMMPS features"_#intro_2
-1.3 "LAMMPS non-features"_#intro_3
-1.4 "Open source distribution"_#intro_4
-1.5 "Acknowledgments and citations"_#intro_5 :all(b)
-
-:line
-:line
-
-1.1 What is LAMMPS :link(intro_1),h4
-
-LAMMPS is a classical molecular dynamics code that models an ensemble
-of particles in a liquid, solid, or gaseous state. It can model
-atomic, polymeric, biological, metallic, granular, and coarse-grained
-systems using a variety of force fields and boundary conditions.
-
-For examples of LAMMPS simulations, see the Publications page of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS runs efficiently on single-processor desktop or laptop
-machines, but is designed for parallel computers. It will run on any
-parallel machine that compiles C++ and supports the "MPI"_mpi
-message-passing library. This includes distributed- or shared-memory
-parallel machines and Beowulf-style clusters.
-
-:link(mpi,http://www-unix.mcs.anl.gov/mpi)
-
-LAMMPS can model systems with only a few particles up to millions or
-billions. See "Section 8"_Section_perf.html for information on
-LAMMPS performance and scalability, or the Benchmarks section of the
-"LAMMPS WWW Site"_lws.
-
-LAMMPS is a freely-available open-source code, distributed under the
-terms of the "GNU Public License"_gnu, which means you can use or
-modify the code however you wish. See "this section"_#intro_4 for a
-brief discussion of the open-source philosophy.
-
-:link(gnu,http://www.gnu.org/copyleft/gpl.html)
-
-LAMMPS is designed to be easy to modify or extend with new
-capabilities, such as new force fields, atom types, boundary
-conditions, or diagnostics. See the "Modify"_Modify.html doc page for
-more details.
-
-The current version of LAMMPS is written in C++. Earlier versions
-were written in F77 and F90. See
-"Section 13"_Section_history.html for more information on
-different versions. All versions can be downloaded from the "LAMMPS
-WWW Site"_lws.
-
-LAMMPS was originally developed under a US Department of Energy CRADA
-(Cooperative Research and Development Agreement) between two DOE labs
-and 3 companies. It is distributed by "Sandia National Labs"_snl.
-See "this section"_#intro_5 for more information on LAMMPS funding and
-individuals who have contributed to LAMMPS.
-
-:link(snl,http://www.sandia.gov)
-
-In the most general sense, LAMMPS integrates Newton's equations of
-motion for collections of atoms, molecules, or macroscopic particles
-that interact via short- or long-range forces with a variety of
-initial and/or boundary conditions. For computational efficiency
-LAMMPS uses neighbor lists to keep track of nearby particles. The
-lists are optimized for systems with particles that are repulsive at
-short distances, so that the local density of particles never becomes
-too large. On parallel machines, LAMMPS uses spatial-decomposition
-techniques to partition the simulation domain into small 3d
-sub-domains, one of which is assigned to each processor. Processors
-communicate and store "ghost" atom information for atoms that border
-their sub-domain. LAMMPS is most efficient (in a parallel sense) for
-systems whose particles fill a 3d rectangular box with roughly uniform
-density. Papers with technical details of the algorithms used in
-LAMMPS are listed in "this section"_#intro_5.
-
-:line
-
-1.2 LAMMPS features :link(intro_2),h4
-
-This section highlights LAMMPS features, with pointers to specific
-commands which give more details. If LAMMPS doesn't have your
-favorite interatomic potential, boundary condition, or atom type, see
-the "Modify"_Modify.html doc page, which describes how you can add it
-to LAMMPS.
-
-General features :h4
-
- runs on a single processor or in parallel
- distributed-memory message-passing parallelism (MPI)
- spatial-decomposition of simulation domain for parallelism
- open-source distribution
- highly portable C++
- optional libraries used: MPI and single-processor FFT
- GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features
- easy to extend with new features and functionality
- runs from an input script
- syntax for defining and using variables and formulas
- syntax for looping over runs and breaking out of loops
- run one or multiple simulations simultaneously (in parallel) from one script
- build as library, invoke LAMMPS thru library interface or provided Python wrapper
- couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
-
-Particle and model types :h4
-("atom style"_atom_style.html command)
-
- atoms
- coarse-grained particles (e.g. bead-spring polymers)
- united-atom polymers or organic molecules
- all-atom polymers, organic molecules, proteins, DNA
- metals
- granular materials
- coarse-grained mesoscale models
- finite-size spherical and ellipsoidal particles
- finite-size line segment (2d) and triangle (3d) particles
- point dipole particles
- rigid collections of particles
- hybrid combinations of these :ul
-
-Force fields :h4
-("pair style"_pair_style.html, "bond style"_bond_style.html,
-"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
-"improper style"_improper_style.html, "kspace style"_kspace_style.html
-commands)
-
- pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
- Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
- charged pairwise potentials: Coulombic, point-dipole
- manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
- embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \
- REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
- long-range interactions for charge, point-dipoles, and LJ dispersion: \
- Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
- polarization models: "QEq"_fix_qeq.html, \
- "core/shell model"_Section_howto.html#howto_26, \
- "Drude dipole model"_Section_howto.html#howto_27
- charge equilibration (QEq via dynamic, point, shielded, Slater methods)
- coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
- mesoscopic potentials: granular, Peridynamics, SPH
- electron force field (eFF, AWPMD)
- bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
- quartic (breakable)
- angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
- class 2 (COMPASS)
- dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
- class 2 (COMPASS), OPLS
- improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
- polymer potentials: all-atom, united-atom, bead-spring, breakable
- water potentials: TIP3P, TIP4P, SPC
- implicit solvent potentials: hydrodynamic lubrication, Debye
- force-field compatibility with common CHARMM, AMBER, DREIDING, \
- OPLS, GROMACS, COMPASS options
- access to "KIM archive"_http://openkim.org of potentials via \
- "pair kim"_pair_kim.html
- hybrid potentials: multiple pair, bond, angle, dihedral, improper \
- potentials can be used in one simulation
- overlaid potentials: superposition of multiple pair potentials :ul
-
-Atom creation :h4
-("read_data"_read_data.html, "lattice"_lattice.html,
-"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
-"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
-
- read in atom coords from files
- create atoms on one or more lattices (e.g. grain boundaries)
- delete geometric or logical groups of atoms (e.g. voids)
- replicate existing atoms multiple times
- displace atoms :ul
-
-Ensembles, constraints, and boundary conditions :h4
-("fix"_fix.html command)
-
- 2d or 3d systems
- orthogonal or non-orthogonal (triclinic symmetry) simulation domains
- constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
- thermostatting options for groups and geometric regions of atoms
- pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
- simulation box deformation (tensile and shear)
- harmonic (umbrella) constraint forces
- rigid body constraints
- SHAKE bond and angle constraints
- Monte Carlo bond breaking, formation, swapping
- atom/molecule insertion and deletion
- walls of various kinds
- non-equilibrium molecular dynamics (NEMD)
- variety of additional boundary conditions and constraints :ul
-
-Integrators :h4
-("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
-
- velocity-Verlet integrator
- Brownian dynamics
- rigid body integration
- energy minimization via conjugate gradient or steepest descent relaxation
- rRESPA hierarchical timestepping
- rerun command for post-processing of dump files :ul
-
-Diagnostics :h4
-
- see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
-
-Output :h4
-("dump"_dump.html, "restart"_restart.html commands)
-
- log file of thermodynamic info
- text dump files of atom coords, velocities, other per-atom quantities
- binary restart files
- parallel I/O of dump and restart files
- per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
- user-defined system-wide (log file) or per-atom (dump file) calculations
- spatial and time averaging of per-atom quantities
- time averaging of system-wide quantities
- atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
-
-Multi-replica models :h4
-
-"nudged elastic band"_neb.html
-"parallel replica dynamics"_prd.html
-"temperature accelerated dynamics"_tad.html
-"parallel tempering"_temper.html
-
-Pre- and post-processing :h4
-
-Various pre- and post-processing serial tools are packaged with
-LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l
-
-Our group has also written and released a separate toolkit called
-"Pizza.py"_pizza which provides tools for doing setup, analysis,
-plotting, and visualization for LAMMPS simulations. Pizza.py is
-written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza. :l
-:ule
-
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(python,http://www.python.org)
-
-Specialized features :h4
-
-LAMMPS can be built with optional packages which implement a variety
-of additional capabilities. An overview of all the packages is "given
-here"_Section_packages.html.
-
-These are some LAMMPS capabilities which you may not think of as
-typical classical molecular dynamics options:
-
-"static"_balance.html and "dynamic load-balancing"_fix_balance.html
-"generalized aspherical particles"_body.html
-"stochastic rotation dynamics (SRD)"_fix_srd.html
-"real-time visualization and interactive MD"_fix_imd.html
-calculate "virtual diffraction patterns"_compute_xrd.html
-"atom-to-continuum coupling"_fix_atc.html with finite elements
-coupled rigid body integration via the "POEMS"_fix_poems.html library
-"QM/MM coupling"_fix_qmmm.html
-"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
-Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html
-"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
-"Peridynamics mesoscale modeling"_pair_peri.html
-"Lattice Boltzmann fluid"_fix_lb_fluid.html
-"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
-"two-temperature electron model"_fix_ttm.html :ul
-
-:line
-
-1.3 LAMMPS non-features :link(intro_3),h4
-
-LAMMPS is designed to efficiently compute Newton's equations of motion
-for a system of interacting particles. Many of the tools needed to
-pre- and post-process the data for such simulations are not included
-in the LAMMPS kernel for several reasons:
-
-the desire to keep LAMMPS simple
-they are not parallel operations
-other codes already do them
-limited development resources :ul
-
-Specifically, LAMMPS itself does not:
-
-run thru a GUI
-build molecular systems
-assign force-field coefficients automagically
-perform sophisticated analyses of your MD simulation
-visualize your MD simulation
-plot your output data :ul
-
-A few tools for pre- and post-processing tasks are provided as part of
-the LAMMPS package; they are described on the "Tools"_Tools.html doc
-page. However, many people use other codes or write their own tools
-for these tasks.
-
-As noted above, our group has also written and released a separate
-toolkit called "Pizza.py"_pizza which addresses some of the listed
-bullets. It provides tools for doing setup, analysis, plotting, and
-visualization for LAMMPS simulations. Pizza.py is written in
-"Python"_python and is available for download from "the Pizza.py WWW
-site"_pizza.
-
-LAMMPS requires as input a list of initial atom coordinates and types,
-molecular topology information, and force-field coefficients assigned
-to all atoms and bonds. LAMMPS will not build molecular systems and
-assign force-field parameters for you.
-
-For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
-command which places atoms on solid-state lattices (fcc, bcc,
-user-defined, etc). Assigning small numbers of force field
-coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
-coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
-For molecular systems or more complicated simulation geometries, users
-typically use another code as a builder and convert its output to
-LAMMPS input format, or write their own code to generate atom
-coordinate and molecular topology for LAMMPS to read in.
-
-For complicated molecular systems (e.g. a protein), a multitude of
-topology information and hundreds of force-field coefficients must
-typically be specified. We suggest you use a program like
-"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
-such problems and dump its information to a file. You can then
-reformat the file as LAMMPS input. Some of the tools described on the
-"Tools"_Tools.html doc page can assist in this process.
-
-Similarly, LAMMPS creates output files in a simple format. Most users
-post-process these files with their own analysis tools or re-format
-them for input into other programs, including visualization packages.
-If you are convinced you need to compute something on-the-fly as
-LAMMPS runs, see the "Modify"_Modify.html doc page for a discussion of
-how you can use the "dump"_dump.html and "compute"_compute.html and
-"fix"_fix.html commands to print out data of your choosing. Keep in
-mind that complicated computations can slow down the molecular
-dynamics timestepping, particularly if the computations are not
-parallel, so it is often better to leave such analysis to
-post-processing codes.
-
-For high-quality visualization we recommend the
-following packages:
-
-"VMD"_http://www.ks.uiuc.edu/Research/vmd
-"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
-"OVITO"_http://www.ovito.org/
-"ParaView"_http://www.paraview.org/
-"PyMol"_http://www.pymol.org
-"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
-"RasMol"_http://www.openrasmol.org :ul
-
-Other features that LAMMPS does not yet (and may never) support are
-discussed in "Section 13"_Section_history.html.
-
-Finally, these are freely-available molecular dynamics codes, most of
-them parallel, which may be well-suited to the problems you want to
-model. They can also be used in conjunction with LAMMPS to perform
-complementary modeling tasks.
-
-"CHARMM"_charmm
-"AMBER"_amber
-"NAMD"_namd
-"NWCHEM"_nwchem
-"DL_POLY"_dlpoly
-"Tinker"_tinker :ul
-
-:link(charmm,http://www.charmm.org)
-:link(amber,http://ambermd.org)
-:link(namd,http://www.ks.uiuc.edu/Research/namd/)
-:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
-:link(tinker,http://dasher.wustl.edu/tinker)
-
-CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
-modeling biological molecules. CHARMM and AMBER use
-atom-decomposition (replicated-data) strategies for parallelism; NAMD
-and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
-Tinker is a serial code. DL_POLY includes potentials for a variety of
-biological and non-biological materials; both a replicated-data and
-spatial-decomposition version exist.
-
-:line
-
-1.4 Open source distribution :link(intro_4),h4
-
-LAMMPS comes with no warranty of any kind. As each source file states
-in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the "GNU Public License"_gnu (GPL). This
-is often referred to as open-source distribution - see
-"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
-details. The legal text of the GPL is in the LICENSE file that is
-included in the LAMMPS distribution.
-
-:link(gnuorg,http://www.gnu.org)
-:link(opensource,http://www.opensource.org)
-
-Here is a summary of what the GPL means for LAMMPS users:
-
-(1) Anyone is free to use, modify, or extend LAMMPS in any way they
-choose, including for commercial purposes.
-
-(2) If you distribute a modified version of LAMMPS, it must remain
-open-source, meaning you distribute it under the terms of the GPL.
-You should clearly annotate such a code as a derivative version of
-LAMMPS.
-
-(3) If you release any code that includes LAMMPS source code, then it
-must also be open-sourced, meaning you distribute it under the terms
-of the GPL.
-
-(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
-source file headers (including the copyright and GPL notices) should
-remain part of the code.
-
-In the spirit of an open-source code, these are various ways you can
-contribute to making LAMMPS better. You can send email to the
-"developers"_http://lammps.sandia.gov/authors.html on any of these
-items.
-
-Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
-talks or link to it from your WWW site. :ulb,l
-
-If you find an error or omission in this manual or on the "LAMMPS WWW
-Site"_lws, or have a suggestion for something to clarify or include,
-send an email to the
-"developers"_http://lammps.sandia.gov/authors.html. :l
-
-If you find a bug, the "Errors bugs"_Errors_bugs.html doc page
-describes how to report it. :l
-
-If you publish a paper using LAMMPS results, send the citation (and
-any cool pictures or movies if you like) to add to the Publications,
-Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
-and attributions back to you. :l
-
-Create a new Makefile.machine that can be added to the src/MAKE
-directory. :l
-
-The tools sub-directory of the LAMMPS distribution has various
-stand-alone codes for pre- and post-processing of LAMMPS data. More
-details are given on the "Tools"_Tools.html doc page. If you write a
-new tool that users will find useful, it can be added to the LAMMPS
-distribution. :l
-
-LAMMPS is designed to be easy to extend with new code for features
-like potentials, boundary conditions, diagnostic computations, etc.
-The "Modify"_Modify.html doc page gives details. If you add a feature
-of general interest, it can be added to the LAMMPS distribution. :l
-
-The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
-performance on various platforms. The files needed to run the
-benchmarks are part of the LAMMPS distribution. If your machine is
-sufficiently different from those listed, your timing data can be
-added to the page. :l
-
-You can send feedback for the User Comments page of the "LAMMPS WWW
-Site"_lws. It might be added to the page. No promises. :l
-
-Cash. Small denominations, unmarked bills preferred. Paper sack OK.
-Leave on desk. VISA also accepted. Chocolate chip cookies
-encouraged. :l
-:ule
-
-:line
-
-1.5 Acknowledgments and citations :h3,link(intro_5)
-
-LAMMPS development has been funded by the "US Department of
-Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
-programs and its "OASCR"_oascr and "OBER"_ober offices.
-
-Specifically, work on the latest version was funded in part by the US
-Department of Energy's Genomics:GTL program
-("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
-Sequestration in Synechococcus Sp.: From Molecular Machines to
-Hierarchical Modeling".
-
-:link(doe,http://www.doe.gov)
-:link(gtl,http://www.doegenomestolife.org)
-:link(ourgtl,http://www.genomes2life.org)
-:link(oascr,http://www.sc.doe.gov/ascr/home.html)
-:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
-
-The following paper describe the basic parallel algorithms used in
-LAMMPS. If you use LAMMPS results in your published work, please cite
-this paper and include a pointer to the "LAMMPS WWW Site"_lws
-(http://lammps.sandia.gov):
-
-S. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
-Dynamics], J Comp Phys, 117, 1-19 (1995).
-
-Other papers describing specific algorithms used in LAMMPS are listed
-under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of
-the LAMMPS WWW page.
-
-The "Publications link"_http://lammps.sandia.gov/papers.html on the
-LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
-not listed there for some reason, feel free to send us the info. If
-the simulations in your paper produced cool pictures or animations,
-we'll be pleased to add them to the
-"Pictures"_http://lammps.sandia.gov/pictures.html or
-"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
-site.
-
-The primary LAMMPS developers are at Sandia National Labs and Temple University:
-
-Steve Plimpton, sjplimp at sandia.gov
-Aidan Thompson, athomps at sandia.gov
-Stan Moore, stamoor at sandia.gov
-Axel Kohlmeyer, akohlmey at gmail.com :ul
-
-Past primary developers include Paul Crozier and Mark Stevens,
-both at Sandia, and Ray Shan, now at Materials Design.
-
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort. Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
-
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
-Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
-Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
-
-As discussed in "Section 13"_Section_history.html, LAMMPS
-originated as a cooperative project between DOE labs and industrial
-partners. Folks involved in the design and testing of the original
-version of LAMMPS were the following:
-
-John Carpenter (Mayo Clinic, formerly at Cray Research)
-Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
-Steve Lustig (Dupont)
-Jim Belak (LLNL) :ul
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index d8f340b179..19a798d5df 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_commands.html :c
+Section"_Commands.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,10 +119,11 @@ lower-case name of the package, e.g. replica or user-misc.
If you want to do one of the following:
-use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html)
-build with a package that requires an extra library
-build with an accelerator package that requires special compiler/linker settings
-run on a machine that has its own compilers, settings, or libraries :ul
+use a LAMMPS command that requires an extra library (e.g. "dump
+image"_dump_image.html) build with a package that requires an extra
+library build with an accelerator package that requires special
+compiler/linker settings run on a machine that has its own compilers,
+settings, or libraries :ul
then building LAMMPS is more complicated. You may need to find where
extra libraries exist on your machine or install them if they don't.
@@ -697,8 +698,8 @@ are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.
-"Section 4"_Section_packages.html in the manual has details about all
-the packages, which come in two flavors: [standard] and [user]
+The "Packages"_Packages.html doc pages has details about all the
+packages, which come in two flavors: [standard] and [user]
packages. It also has specific instructions for building LAMMPS with
any package which requires an extra library. General instructions are
below.
@@ -828,45 +829,47 @@ options.
Packages that require extra libraries :h4,link(start_3_3)
A few of the standard and user packages require extra libraries. See
-"Section 4"_Section_packages.html for two tables of packages which
-indicate which ones require libraries. For each such package, the
-Section 4 doc page gives details on how to build the extra library,
-including how to download it if necessary. The basic ideas are
-summarized here.
+the "Packages"_Packages.html doc pages for two tables of packages
+which indicate which ones require libraries. For each such package,
+the Section 4 doc page gives details on how to build the extra
+library, including how to download it if necessary. The basic ideas
+are summarized here.
[System libraries:]
-Packages in the tables "Section 4"_Section_packages.html with a "sys"
-in the last column link to system libraries that typically already
-exist on your machine. E.g. the python package links to a system
-Python library. If your machine does not have the required library,
-you will have to download and install it on your machine, in either
-the system or user space.
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with a "sys" in the last column
+link to system libraries that typically already exist on your machine.
+E.g. the python package links to a system Python library. If your
+machine does not have the required library, you will have to download
+and install it on your machine, in either the system or user space.
[Internal libraries:]
-Packages in the tables "Section 4"_Section_packages.html with an "int"
-in the last column link to internal libraries whose source code is
-included with LAMMPS, in the lib/name directory where name is the
-package name. You must first build the library in that directory
-before building LAMMPS with that package installed. E.g. the gpu
-package links to a library you build in the lib/gpu dir. You can
-often do the build in one step by typing "make lib-name args=..."
-from the src dir, with appropriate arguments. You can leave off the
-args to see a help message. See "Section 4"_Section_packages.html for
-details for each package.
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with an "int" in the last column
+link to internal libraries whose source code is included with LAMMPS,
+in the lib/name directory where name is the package name. You must
+first build the library in that directory before building LAMMPS with
+that package installed. E.g. the gpu package links to a library you
+build in the lib/gpu dir. You can often do the build in one step by
+typing "make lib-name args=..." from the src dir, with appropriate
+arguments. You can leave off the args to see a help message. See the
+"Packages details"_Packages_details.html doc page for details for each
+package.
[External libraries:]
-Packages in the tables "Section 4"_Section_packages.html with an "ext"
-in the last column link to external libraries whose source code is not
-included with LAMMPS. You must first download and install the library
-before building LAMMPS with that package installed. E.g. the voronoi
-package links to the freely available "Voro++ library"_voro_home2. You
-can often do the download/build in one step by typing "make lib-name
+Packages in the standard and user tables of the
+"Packages"_Packages.html doc pages with an "ext" in the last column
+link to external libraries whose source code is not included with
+LAMMPS. You must first download and install the library before
+building LAMMPS with that package installed. E.g. the voronoi package
+links to the freely available "Voro++ library"_voro_home2. You can
+often do the download/build in one step by typing "make lib-name
args=..." from the src dir, with appropriate arguments. You can leave
-off the args to see a help message. See "Section
-4"_Section_packages.html for details for each package.
+off the args to see a help message. See the "Packages
+details"_Packages_details.html doc page for details for each package.
:link(voro_home2,http://math.lbl.gov/voro++)
@@ -888,9 +891,9 @@ copied from a lib/name/Makefile.lammps.* file when the library is
built. If those settings are not correct for your machine you will
need to edit or create an appropriate Makefile.lammps file.
-Package-specific details for these steps are given in "Section
-4"_Section_packages.html an in README files in the lib/name
-directories.
+Package-specific details for these steps are given on the "Packages
+details"_Packages_details.html doc page and in README files in the
+lib/name directories.
[Compiler options needed for accelerator packages:]
@@ -901,14 +904,14 @@ these accelerator packages for optimal performance requires specific
settings in the Makefile.machine file you use.
A summary of the Makefile.machine settings needed for each of these
-packages is given in "Section 4"_Section_packages.html. More info is
-given on the doc pages that describe each package in detail:
+packages is given on the "Packages"_Packages.html doc pages. More
+info is given on the doc pages that describe each package in detail:
-5.3.1 "USER-INTEL package"_accelerate_intel.html
-5.3.2 "GPU package"_accelerate_intel.html
-5.3.3 "KOKKOS package"_accelerate_kokkos.html
-5.3.4 "USER-OMP package"_accelerate_omp.html
-5.3.5 "OPT package"_accelerate_opt.html :all(b)
+"USER-INTEL package"_Speed_intel.html
+"GPU package"_Speed_gpu.html
+"KOKKOS package"_Speed_kokkos.html
+"USER-OMP package"_Speed_omp.html
+"OPT package"_Speed_opt.html :all(b)
You can also use or examine the following machine Makefiles in
src/MAKE/OPTIONS, which include the settings. Note that the
@@ -931,9 +934,9 @@ Makefile.opt :ul
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
-"this section"_Section_howto.html#howto_10 for more info on coupling
-LAMMPS to other codes. See the "Python"_Python.html doc page for more
-info on wrapping and running LAMMPS from Python.
+the "Howto couple"_Howto_couple.html doc page for more info on
+coupling LAMMPS to other codes. See the "Python"_Python.html doc page
+for more info on wrapping and running LAMMPS from Python.
Static library :h4
@@ -1036,16 +1039,16 @@ src/library.cpp and src/library.h.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
-There are other examples as well in the COUPLE directory which are
-discussed in "Section 6.10"_Section_howto.html#howto_10 of the manual.
-See the "Python"_Python.html doc page for a description of the Python
-wrapper provided with LAMMPS that operates through the LAMMPS library
-interface.
+There are other examples as well in the COUPLE directory which use
+coupling ideas discussed on the "Howto couple"_Howto_couple.html doc
+page. See the "Python"_Python.html doc page for a description of the
+Python wrapper provided with LAMMPS that operates through the LAMMPS
+library interface.
The files src/library.cpp and library.h define the C-style API for
-using LAMMPS as a library. See "Section
-6.19"_Section_howto.html#howto_19 of the manual for a description of the
-interface and how to extend it for your needs.
+using LAMMPS as a library. See the "Howto library"_Howto_library.html
+doc page for a description of the interface and how to extend it for
+your needs.
:line
@@ -1067,7 +1070,7 @@ the '-in' command-line switch, e.g.
lmp_linux -in in.file :pre
-"This section"_Section_commands.html describes how input scripts are
+The "Commands"_Commands.html doc page describes how input scripts are
structured and what commands they contain.
You can test LAMMPS on any of the sample inputs provided in the
@@ -1276,8 +1279,8 @@ Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
-settings to use on different platforms is given in "Section
-5.3"_Section_accelerate.html#acc_3.
+settings to use on different platforms is given on the "Speed
+kokkos"_Speed_kokkos.html doc page.
d or device
g or gpus
@@ -1388,16 +1391,16 @@ processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
-Running with multiple partitions can e useful for running
-"multi-replica simulations"_Section_howto.html#howto_5, where each
-replica runs on on one or a few processors. Note that with MPI
-installed on a machine (e.g. your desktop), you can run on more
-(virtual) processors than you have physical processors.
+Running with multiple partitions can be useful for running
+"multi-replica simulations"_Howto_replica.html, where each replica
+runs on on one or a few processors. Note that with MPI installed on a
+machine (e.g. your desktop), you can run on more (virtual) processors
+than you have physical processors.
To run multiple independent simulations from one input script, using
-multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
-of the manual. World- and universe-style "variables"_variable.html
-are useful in this context.
+multiple partitions, see the "Howto multiple"_Howto_multiple.html doc
+page. World- and universe-style "variables"_variable.html are useful
+in this context.
-plog file :pre
@@ -1461,8 +1464,7 @@ cores within each node are ranked in a desired order. Or when using
the "run_style verlet/split"_run_style.html command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
-See the "Section 5"_Section_accelerate.html doc pages for
-more details.
+See the "Speed tips"_Speed_tips.html doc page for more details.
If the keyword {nth} is used with a setting {N}, then it means every
Nth processor will be moved to the end of the ranking. This is useful
@@ -1613,9 +1615,9 @@ value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
-defining index and other kinds of variables and "this
-section"_Section_commands.html#cmd_2 for more info on using variables
-in input scripts.
+defining index and other kinds of variables and the "Commands
+parse"_Commands_parse.html page for more info on using variables in
+input scripts.
NOTE: Currently, the command-line parser looks for arguments that
start with "-" to indicate new switches. Thus you cannot specify
@@ -1785,11 +1787,13 @@ communication, roughly 75% in the example above.
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
-in "Section 13"_Section_history.html. The F90 and F77 versions
-(2001 and 99) are also freely distributed as open-source codes; check
-the "LAMMPS WWW Site"_lws for distribution information if you prefer
-those versions. The 99 and 2001 versions are no longer under active
-development; they do not have all the features of C++ LAMMPS.
+on the "History page"_http://lammps.sandia.gov/history.html of the
+LAMMPS website. The F90 and F77 versions (2001 and 99) are also
+freely distributed as open-source codes; check the "History
+page"_http://lammps.sandia.gov/history.html of the LAMMPS website for
+info about those versions. The 99 and 2001 versions are no longer
+under active development; they do not have all the features of C++
+LAMMPS.
If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
new file mode 100644
index 0000000000..091657082a
--- /dev/null
+++ b/doc/src/Speed.txt
@@ -0,0 +1,64 @@
+"Previous Section"_Package.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Howto.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Accelerate performance :h2
+
+This section describes various methods for improving LAMMPS
+performance for different classes of problems running on different
+kinds of machines.
+
+There are two thrusts to the discussion that follows. The first is
+using code options that implement alternate algorithms that can
+speed-up a simulation. The second is to use one of the several
+accelerator packages provided with LAMMPS that contain code optimized
+for certain kinds of hardware, including multi-core CPUs, GPUs, and
+Intel Xeon Phi coprocessors.
+
+The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
+web site gives performance results for the various accelerator
+packages discussed on the "Speed packages"_Speed_packages.html doc
+page, for several of the standard LAMMPS benchmark problems, as a
+function of problem size and number of compute nodes, on different
+hardware platforms.
+
+<!-- RST
+
+.. toctree::
+
+ Speed_bench
+ Speed_measure
+
+.. toctree::
+
+ Speed_tips
+
+.. toctree::
+
+ Speed_packages
+ Speed_compare
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Benchmarks"_Speed_bench.html
+"Measuring performance"_Speed_measure.html :all(b)
+
+"General tips"_Speed_tips.html :all(b)
+
+"Accelerator packages"_Speed_packages.html
+"GPU package"_Speed_gpu.html
+"USER-INTEL package"_Speed_intel.html
+"KOKKOS package"_Speed_kokkos.html
+"USER-OMP package"_Speed_omp.html
+"OPT package"_Speed_opt.html
+"Comparison of accelerator packages"_Speed_compare.html :all(b)
+
+<!-- END_HTML_ONLY -->
diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt
similarity index 86%
rename from doc/src/Section_perf.txt
rename to doc/src/Speed_bench.txt
index f320780129..8e407d14ea 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Speed_bench.txt
@@ -1,19 +1,18 @@
-"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html
-:c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-8. Performance & scalability :h2
+Benchmarks :h3
-Current LAMMPS performance is discussed on the Benchmarks page of the
-"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are
-listed. The page has several sections, which are briefly described
-below:
+Current LAMMPS performance is discussed on the "Benchmarks
+page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
+where timings and parallel efficiencies are listed. The page has
+several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
GPU and Xeon Phi performance on same and related problems
@@ -53,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
and bench/KEPLER dirs have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those dirs and the
-"Section 5.3"_Section_accelerate.html#acc_3 doc pages for
-instructions on how to build LAMMPS and run on that kind of hardware.
+"Speed packages"_Speed_packages.html doc pages for instructions on how
+to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the
table of results on the
diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt
new file mode 100644
index 0000000000..1a17b39c79
--- /dev/null
+++ b/doc/src/Speed_compare.txt
@@ -0,0 +1,73 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Comparison of various accelerator packages :h3
+
+NOTE: this section still needs to be re-worked with additional KOKKOS
+and USER-INTEL information.
+
+The next section compares and contrasts the various accelerator
+options, since there are multiple ways to perform OpenMP threading,
+run on GPUs, and run on Intel Xeon Phi coprocessors.
+
+All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
+hardware, but they do it in different ways.
+
+As a consequence, for a particular simulation on specific hardware,
+one package may be faster than the other. We give guidelines below,
+but the best way to determine which package is faster for your input
+script is to try both of them on your machine. See the benchmarking
+section below for examples where this has been done.
+
+[Guidelines for using each package optimally:]
+
+The GPU package allows you to assign multiple CPUs (cores) to a single
+GPU (a common configuration for "hybrid" nodes that contain multicore
+CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
+
+The GPU package moves per-atom data (coordinates, forces)
+back-and-forth between the CPU and GPU every timestep. The
+KOKKOS/CUDA package only does this on timesteps when a CPU calculation
+is required (e.g. to invoke a fix or compute that is non-GPU-ized).
+Hence, if you can formulate your input script to only use GPU-ized
+fixes and computes, and avoid doing I/O too often (thermo output, dump
+file snapshots, restart files), then the data transfer cost of the
+KOKKOS/CUDA package can be very low, causing it to run faster than the
+GPU package. :l
+
+The GPU package is often faster than the KOKKOS/CUDA package, if the
+number of atoms per GPU is smaller. The crossover point, in terms of
+atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
+strongly on the pair style. For example, for a simple Lennard Jones
+system the crossover (in single precision) is often about 50K-100K
+atoms per GPU. When performing double precision calculations the
+crossover point can be significantly smaller. :l
+
+Both packages compute bonded interactions (bonds, angles, etc) on the
+CPU. If the GPU package is running with several MPI processes
+assigned to one GPU, the cost of computing the bonded interactions is
+spread across more CPUs and hence the GPU package can run faster. :l
+
+When using the GPU package with multiple CPUs assigned to one GPU, its
+performance depends to some extent on high bandwidth between the CPUs
+and the GPU. Hence its performance is affected if full 16 PCIe lanes
+are not available for each GPU. In HPC environments this can be the
+case if S2050/70 servers are used, where two devices generally share
+one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
+full 16 lanes to each of the PCIe 2.0 16x slots. :l
+:ule
+
+[Differences between the two packages:]
+
+The GPU package accelerates only pair force, neighbor list, and PPPM
+calculations. :ulb,l
+
+The GPU package requires neighbor lists to be built on the CPU when using
+exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+:ule
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt
similarity index 96%
rename from doc/src/accelerate_gpu.txt
rename to doc/src/Speed_gpu.txt
index 816a31c788..ab8ec7e9d1 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.1 GPU package :h5
+GPU package :h3
The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
@@ -72,10 +70,9 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
[Building LAMMPS with the GPU package:]
This requires two steps (a,b): build the GPU library, then build
-LAMMPS with the GPU package.
-
-You can do both these steps in one line as described in
-"Section 4"_Section_packages.html of the manual.
+LAMMPS with the GPU package. You can do both these steps in one line
+as described on the "Packages details"_Packages_details.html#GPU doc
+page.
Or you can follow these two (a,b) steps:
diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt
similarity index 97%
rename from doc/src/accelerate_intel.txt
rename to doc/src/Speed_intel.txt
index 71f5185b15..20f49672e0 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.2 USER-INTEL package :h5
+USER-INTEL package :h3
The USER-INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,
@@ -188,8 +186,8 @@ can start running so that the CPU pipeline is still being used
efficiently. Although benefits can be seen by launching a MPI task
for every hardware thread, for multinode simulations, we recommend
that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
-"KOKKOS package"_accelerate_kokkos.html. In the example above, up
+USER-INTEL package, "USER-OMP package"_Speed_omp.html, or
+"KOKKOS package"_Speed_kokkos.html. In the example above, up
to 36X speedups can be observed by using all 36 physical cores with
LAMMPS. By using all 72 hardware threads, an additional 10-30%
performance gain can be achieved.
@@ -233,9 +231,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
-Alternatively this can be done as a single command with
-suitable make command invocations. This is discussed in "Section
-4"_Section_packages.html of the manual.
+Alternatively this can be done as a single command with suitable make
+command invocations, as described on the "Packages
+details"_Packages_details.html#USER-INTEL doc page.
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
@@ -391,8 +389,8 @@ performance and/or scalability for simple 2-body potentials such as
lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
-the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html. Of course,
+the USER-INTEL package with styles from the "OPT"_Speed_opt.html
+package or the "USER-OMP package"_Speed_omp.html. Of course,
this requires that these packages were installed at build time. This
can performed automatically by using "-sf hybrid intel opt" or
"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/Speed_kokkos.txt
similarity index 59%
rename from doc/src/accelerate_kokkos.txt
rename to doc/src/Speed_kokkos.txt
index 0c9178d6e4..14f4103aed 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -1,38 +1,41 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.3 KOKKOS package :h5
+KOKKOS package :h3
Kokkos is a templated C++ library that provides abstractions to allow
-a single implementation of an application kernel (e.g. a pair style) to run efficiently on
-different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
-CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
-The Kokkos library also provides data abstractions to adjust (at
-compile time) the memory layout of data structures like 2d and
-3d arrays to optimize performance on different hardware. For more information on Kokkos, see
-"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
-Christian Trott, and Dan Sunderland (all Sandia).
-
-The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
-that use data structures and macros provided by the Kokkos library,
-which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
-and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
-Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+a single implementation of an application kernel (e.g. a pair style)
+to run efficiently on different kinds of hardware, such as GPUs, Intel
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
+different backend languages such as CUDA, OpenMP, or Pthreads. The
+Kokkos library also provides data abstractions to adjust (at compile
+time) the memory layout of data structures like 2d and 3d arrays to
+optimize performance on different hardware. For more information on
+Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
+of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
+library was written primarily by Carter Edwards, Christian Trott, and
+Dan Sunderland (all Sandia).
+
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
+styles that use data structures and macros provided by the Kokkos
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
+package was developed primarily by Christian Trott (Sandia) and Stan
+Moore (Sandia) with contributions of various styles by others,
+including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
+(Sandia). For more information on developing using Kokkos abstractions
see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
Kokkos currently provides support for 3 modes of execution (per MPI
-task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
-for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
-produce an executable compatible with specific hardware.
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
+GPUs). You choose the mode at build time to produce an executable
+compatible with specific hardware.
[Building LAMMPS with the KOKKOS package:]
@@ -40,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
Clang 3.5.2 or later is required.
-The recommended method of building the KOKKOS package is to start with the provided Kokkos
-Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
-to match your specific hardware. For example:
+The recommended method of building the KOKKOS package is to start with
+the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
+modify the KOKKOS_ARCH variable in the Makefile to match your specific
+hardware. For example:
for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
for Broadwell CPUs, set KOKKOS_ARCH=BWD
for K80 GPUs, set KOKKOS_ARCH=Kepler37
for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
-See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
+See the [Advanced Kokkos Options] section below for a listing of all
+KOKKOS_ARCH options.
[Compile for CPU-only (MPI only, no threading):]
@@ -63,11 +68,12 @@ make kokkos_mpi_only :pre
[Compile for CPU-only (MPI plus OpenMP threading):]
-NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
-OpenMP interface. You should have one or more multi-core CPUs so that
-multiple threads can be launched by each MPI task running on a CPU.
+NOTE: To build with Kokkos support for OpenMP threading, your compiler
+must support the OpenMP interface. You should have one or more
+multi-core CPUs so that multiple threads can be launched by each MPI
+task running on a CPU.
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the
following:
@@ -85,14 +91,14 @@ make kokkos_phi :pre
[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
-NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
-version 7.5 or later must be installed on your system. See the
-discussion for the "GPU"_accelerate_gpu.html package for details of
-how to check and do this.
+NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
+software version 7.5 or later must be installed on your system. See
+the discussion for the "GPU package"_Speed_gpu.html for details of how
+to check and do this.
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
-above. Then do the following:
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
+described above. Then do the following:
cd lammps/src
make yes-kokkos
@@ -106,24 +112,24 @@ on the make command line. For example:
make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre
-Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
-make command line requires a GNU-compatible make command. Try
-"gmake" if your system's standard make complains.
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
+command line requires a GNU-compatible make command. Try "gmake" if
+your system's standard make complains.
NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
-or "make clean-machine" before each build. This is to force all the
-KOKKOS-dependent files to be re-compiled with the new options.
+with different KOKKOS options and the *same* target, then you *must*
+perform a "make clean-all" or "make clean-machine" before each
+build. This is to force all the KOKKOS-dependent files to be
+re-compiled with the new options.
[Running LAMMPS with the KOKKOS package:]
-All Kokkos operations occur within the
-context of an individual MPI task running on a single node of the
-machine. The total number of MPI tasks used by LAMMPS (one or
-multiple per compute node) is set in the usual manner via the mpirun
-or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
-command in OpenMPI does this via its
--np and -npernode switches. Ditto for MPICH via -np and -ppn.
+All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+-npernode switches. Ditto for MPICH via -np and -ppn.
[Running on a multi-core CPU:]
@@ -135,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI
mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
-To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
-You must use the "-k on" "command-line
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
+kokkos" "command-line switches"_Section_start.html#start_7 in your
+mpirun command. You must use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package. It
takes additional arguments for hardware settings appropriate to your
system. Those arguments are "documented
@@ -144,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use:
-k on t Nt :pre
-The "t Nt" option specifies how many OpenMP threads per MPI
-task to use with a node. The default is Nt = 1, which is MPI-only mode.
-Note that the product of MPI tasks * OpenMP
-threads/task should not exceed the physical number of cores (on a
-node), otherwise performance will suffer. If hyperthreading is enabled, then
-the product of MPI tasks * OpenMP threads/task should not exceed the
-physical number of cores * hardware threads.
-The "-k on" switch also issues a "package kokkos" command (with no
-additional arguments) which sets various KOKKOS options to default
-values, as discussed on the "package"_package.html command doc page.
-
-The "-sf kk" "command-line switch"_Section_start.html#start_7
-will automatically append the "/kk" suffix to styles that support it.
-In this manner no modification to the input script is needed. Alternatively,
-one can run with the KOKKOS package by editing the input script as described below.
-
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+The "t Nt" option specifies how many OpenMP threads per MPI task to
+use with a node. The default is Nt = 1, which is MPI-only mode. Note
+that the product of MPI tasks * OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer. If hyperthreading is enabled, then the product of MPI tasks *
+OpenMP threads/task should not exceed the physical number of cores *
+hardware threads. The "-k on" switch also issues a "package kokkos"
+command (with no additional arguments) which sets various KOKKOS
+options to default values, as discussed on the "package"_package.html
+command doc page.
+
+The "-sf kk" "command-line switch"_Section_start.html#start_7 will
+automatically append the "/kk" suffix to styles that support it. In
+this manner no modification to the input script is
+needed. Alternatively, one can run with the KOKKOS package by editing
+the input script as described below.
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. However, when running on CPUs, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
-styles. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+styles. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
@@ -178,9 +186,9 @@ script, it can also override the Newton flag defaults.
[Core and Thread Affinity:]
-When using multi-threading, it is important for
-performance to bind both MPI tasks to physical cores, and threads to
-physical cores, so they do not migrate during a simulation.
+When using multi-threading, it is important for performance to bind
+both MPI tasks to physical cores, and threads to physical cores, so
+they do not migrate during a simulation.
If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
@@ -191,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :
For binding threads with KOKKOS OpenMP, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable
-OMP_PROC_BIND=true should be sufficient. In general, for best performance
-with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
-For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
-as described below.
+OMP_PROC_BIND=true should be sufficient. In general, for best
+performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
+OMP_PLACES=threads. For binding threads with the KOKKOS pthreads
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
[Running on Knight's Landing (KNL) Intel Xeon Phi:]
-Here is a quick overview of how to use the KOKKOS package
-for the Intel Knight's Landing (KNL) Xeon Phi:
+Here is a quick overview of how to use the KOKKOS package for the
+Intel Knight's Landing (KNL) Xeon Phi:
-KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
-are reserved for the OS, and only 64 or 66 cores are used. Each core
-has 4 hyperthreads,so there are effectively N = 256 (4*64) or
-N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
-otherwise performance will suffer. Note that with the KOKKOS package you do not need to
-specify how many KNLs there are per node; each
-KNL is simply treated as running some number of MPI tasks.
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
+hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+cores to run on. The product of MPI tasks * OpenMP threads/task should
+not exceed this limit, otherwise performance will suffer. Note that
+with the KOKKOS package you do not need to specify how many KNLs there
+are per node; each KNL is simply treated as running some number of MPI
+tasks.
Examples of mpirun commands that follow these rules are shown below.
@@ -223,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
threads/task as Nt. The product of these two values should be N, i.e.
256 or 264.
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. When running on KNL, this
-will typically be best for pair-wise potentials. For manybody potentials,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this will
+typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the Newton flag to "on" may be
+faster. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
-NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
+NOTE: MPI tasks and threads should be bound to cores as described
+above for CPUs.
-NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
-system must be configured to use them in "native" mode, not "offload"
-mode like the USER-INTEL package supports.
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
+such as Knight's Corner (KNC), your system must be configured to use
+them in "native" mode, not "offload" mode like the USER-INTEL package
+supports.
[Running on GPUs:]
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting
-of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node.
-You can assign multiple MPI tasks to the same GPU with the
-KOKKOS package, but this is usually only faster if significant portions
-of the input script have not been ported to use Kokkos. Using CUDA MPS
-is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
-of physical cores/node, then the number of MPI tasks/node should not exceed N.
+Use the "-k" "command-line switch"_Section_start.html#start_7 to
+specify the number of GPUs per node. Typically the -np setting of the
+mpirun command should set the number of MPI tasks/node to be equal to
+the # of physical GPUs on the node. You can assign multiple MPI tasks
+to the same GPU with the KOKKOS package, but this is usually only
+faster if significant portions of the input script have not been
+ported to use Kokkos. Using CUDA MPS is recommended in this
+scenario. As above for multi-core CPUs (and no GPU), if N is the
+number of physical cores/node, then the number of MPI tasks/node
+should not exceed N.
-k on g Ng :pre
-Here are examples of how to use the KOKKOS package for GPUs,
-assuming one or more nodes, each with two GPUs:
+Here are examples of how to use the KOKKOS package for GPUs, assuming
+one or more nodes, each with two GPUs:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions, along with threaded communication.
-When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
-equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+When running on Maxwell or Kepler GPUs, this will typically be
+best. For Pascal GPUs, using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the
+neighbor binsize equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
+to change the default "package kokkos"_package.html options. See its
+doc page for details and default settings. Experimenting with its
+options can provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -301,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the "package kokkos"_package.html or "suffix
kk"_suffix.html commands to your input script.
-The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
-appropriate thread are the same.
+The discussion above for building LAMMPS with the KOKKOS package, the
+mpirun/mpiexec command, and setting appropriate thread are the same.
You must still use the "-k on" "command-line
switch"_Section_start.html#start_7 to enable the KOKKOS package, and
@@ -320,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on"
[Using OpenMP threading and CUDA together (experimental):]
-With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
-together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
-include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
+used together in a few special cases. In the Makefile, the
+KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
+the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
KOKKOS_DEVICES=Cuda,OpenMP :pre
The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
-using the "-sf kk" in the command line gives the default CUDA version everywhere.
-However, if the "/kk/host" suffix is added to a specific style in the input
-script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
-Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+using the "-sf kk" in the command line gives the default CUDA version
+everywhere. However, if the "/kk/host" suffix is added to a specific
+style in the input script, the Kokkos OpenMP (CPU) version of that
+specific style will be used instead. Set the number of OpenMP threads
+as "t Nt" and the number of GPUs as "g Ng"
-k on t Nt g Ng :pre
@@ -338,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
-Conversely, if the "-sf kk/host" is used in the command line and then the
-"/kk" or "/kk/device" suffix is added to a specific style in your input script,
-then only that specific style will run on the GPU while everything else will
-run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
-styles will NOT overlap, except for a special case:
-
-A kspace style and/or molecular topology (bonds, angles, etc.) running on
-the host CPU can overlap with a pair style running on the GPU. First compile
-with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
-Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
-in the input file and the "kk" suffix (equal to "kk/device") on the command line.
-Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+Conversely, if the "-sf kk/host" is used in the command line and then
+the "/kk" or "/kk/device" suffix is added to a specific style in your
+input script, then only that specific style will run on the GPU while
+everything else will run on the CPU in OpenMP mode. Note that the
+execution of the CPU and GPU styles will NOT overlap, except for a
+special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running
+on the host CPU can overlap with a pair style running on the
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
+in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
+suffix for kspace and bonds, angles, etc. in the input file and the
+"kk" suffix (equal to "kk/device") on the command line. Also make
+sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
so CPU/GPU overlap can occur.
[Speed-ups to expect:]
@@ -386,9 +401,8 @@ hardware.
There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line
or in Makefile.machine. This is the full list of options, including
-those discussed above. Each takes a value shown below. The
-default value is listed, which is set in the
-/lib/kokkos/Makefile.kokkos file.
+those discussed above. Each takes a value shown below. The default
+value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
@@ -434,8 +448,8 @@ migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
-threads to hardware cores. More info on binding threads to cores is
-given in "Section 5.3"_Section_accelerate.html#acc_3.
+threads to hardware cores. More info on binding threads to cores is
+given on the "Speed omp"_Speed_omp.html doc page.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all
@@ -446,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
debugging information that can be useful. It also enables runtime
bounds checking on Kokkos data structures.
-KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
+building LAMMPS.
-KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
-with the {enable_lambda} option when using GPUs.
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
+package must be compiled with the {enable_lambda} option when using
+GPUs.
[Restrictions:]
-Currently, there are no precision options with the KOKKOS
-package. All compilation and computation is performed in double
-precision.
+Currently, there are no precision options with the KOKKOS package. All
+compilation and computation is performed in double precision.
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
new file mode 100644
index 0000000000..78dc220088
--- /dev/null
+++ b/doc/src/Speed_measure.txt
@@ -0,0 +1,55 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Measuring performance :h3
+
+Before trying to make your simulation run faster, you should
+understand how it currently performs and where the bottlenecks are.
+
+The best way to do this is run the your system (actual number of
+atoms) for a modest number of timesteps (say 100 steps) on several
+different processor counts, including a single processor if possible.
+Do this for an equilibrium version of your system, so that the
+100-step timings are representative of a much longer run. There is
+typically no need to run for 1000s of timesteps to get accurate
+timings; you can simply extrapolate from short runs.
+
+For the set of runs, look at the timing data printed to the screen and
+log file at the end of each LAMMPS run. "This
+section"_Section_start.html#start_7 of the manual has an overview.
+
+Running on one (or a few processors) should give a good estimate of
+the serial performance and what portions of the timestep are taking
+the most time. Running the same problem on a few different processor
+counts should give an estimate of parallel scalability. I.e. if the
+simulation runs 16x faster on 16 processors, its 100% parallel
+efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
+
+The most important data to look at in the timing info is the timing
+breakdown and relative percentages. For example, trying different
+options for speeding up the long-range solvers will have little impact
+if they only consume 10% of the run time. If the pairwise time is
+dominating, you may want to look at GPU or OMP versions of the pair
+style, as discussed below. Comparing how the percentages change as
+you increase the processor count gives you a sense of how different
+operations within the timestep are scaling. Note that if you are
+running with a Kspace solver, there is additional output on the
+breakdown of the Kspace time. For PPPM, this includes the fraction
+spent on FFTs, which can be communication intensive.
+
+Another important detail in the timing info are the histograms of
+atoms counts and neighbor counts. If these vary widely across
+processors, you have a load-imbalance issue. This often results in
+inaccurate relative timing data, because processors have to wait when
+communication occurs for other processors to catch up. Thus the
+reported times for "Communication" or "Other" may be higher than they
+really are, due to load-imbalance. If this is an issue, you can
+uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+LAMMPS, to obtain synchronized timings.
+
diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt
similarity index 95%
rename from doc/src/accelerate_omp.txt
rename to doc/src/Speed_omp.txt
index fa7bef1a52..bcfc406902 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section 5 overview"_Section_accelerate.html
-
-5.3.4 USER-OMP package :h5
+USER-OMP package :h3
The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
@@ -39,7 +37,8 @@ each MPI task running on a CPU.
The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the "make" command. Or how to do it with
-one command as described in "Section 4"_Section_packages.html of the manual.
+one command as described on the "Packages
+details"_Packages_details.html#USER-OMP doc page.
Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
include "-fopenmp". Likewise, if you use an Intel compiler, the
@@ -100,7 +99,7 @@ task, versus running standard LAMMPS with its standard un-accelerated
styles (in serial or all-MPI parallelization with 1 task/core). This
is because many of the USER-OMP styles contain similar optimizations
to those used in the OPT package, described in "Section
-5.3.5"_accelerate_opt.html.
+5.3.5"_Speed_opt.html.
With multiple threads/task, the optimal choice of number of MPI
tasks/node and OpenMP threads/task can vary a lot and should always be
diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt
similarity index 85%
rename from doc/src/accelerate_opt.txt
rename to doc/src/Speed_opt.txt
index 845264b522..676a5d8418 100644
--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -1,15 +1,13 @@
-"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
-"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
-"Return to Section accelerate overview"_Section_accelerate.html
-
-5.3.5 OPT package :h5
+OPT package :h3
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@@ -34,7 +32,8 @@ None.
The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the "make" command. Or how to do it with one command
-as described in "Section 4"_Section_packages.html of the manual.
+as described on the "Packages details"_Packages_details.html#OPT doc
+page.
Note that if you use an Intel compiler to build with the OPT package,
the CCFLAGS setting in your Makefile.machine must include "-restrict".
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
new file mode 100644
index 0000000000..f463ed91b8
--- /dev/null
+++ b/doc/src/Speed_packages.txt
@@ -0,0 +1,192 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Accelerator packages :h3
+
+Accelerated versions of various "pair_style"_pair_style.html,
+"fixes"_fix.html, "computes"_compute.html, and other commands have
+been added to LAMMPS, which will typically run faster than the
+standard non-accelerated versions. Some require appropriate hardware
+to be present on your system, e.g. GPUs or Intel Xeon Phi
+coprocessors.
+
+All of these commands are in packages provided with LAMMPS. An
+overview of packages is give on the "Packages"_Packages.html doc
+pages.
+
+These are the accelerator packages currently in LAMMPS, either as
+standard or user packages:
+
+"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support
+"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi
+"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
+"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations
+"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:)
+
+<!-- RST
+
+.. toctree::
+ :maxdepth: 1
+ :hidden:
+
+ Speed_gpu
+ Speed_intel
+ Speed_kokkos
+ Speed_omp
+ Speed_opt
+
+END_RST -->
+
+Inverting this list, LAMMPS currently has acceleration support for
+three kinds of hardware, via the listed packages:
+
+Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages
+NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages
+Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:)
+
+Which package is fastest for your hardware may depend on the size
+problem you are running and what commands (accelerated and
+non-accelerated) are invoked by your input script. While these doc
+pages include performance guidelines, there is no substitute for
+trying out the different packages appropriate to your hardware.
+
+Any accelerated style has the same name as the corresponding standard
+style, except that a suffix is appended. Otherwise, the syntax for
+the command that uses the style is identical, their functionality is
+the same, and the numerical results it produces should also be the
+same, except for precision and round-off effects.
+
+For example, all of these styles are accelerated variants of the
+Lennard-Jones "pair_style lj/cut"_pair_lj.html:
+
+"pair_style lj/cut/gpu"_pair_lj.html
+"pair_style lj/cut/intel"_pair_lj.html
+"pair_style lj/cut/kk"_pair_lj.html
+"pair_style lj/cut/omp"_pair_lj.html
+"pair_style lj/cut/opt"_pair_lj.html :ul
+
+To see what accelerate styles are currently available for a particular
+style, find the style name in the "Commands_all"_Commands_all.html
+style pages (fix,compute,pair,etc) and see what suffixes are listed
+(g,i,k,o,t) with it. The doc pages for individual commands
+(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list
+any accelerated variants available for that style.
+
+To use an accelerator package in LAMMPS, and one or more of the styles
+it provides, follow these general steps. Details vary from package to
+package and are explained in the individual accelerator doc pages,
+listed above:
+
+build the accelerator library |
+ only for GPU package |
+install the accelerator package |
+ make yes-opt, make yes-user-intel, etc |
+add compile/link flags to Makefile.machine in src/MAKE |
+ only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
+re-build LAMMPS |
+ make machine |
+prepare and test a regular LAMMPS simulation |
+ lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+ only needed for KOKKOS package |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+ only if defaults need to be changed |
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+:tb(c=2,s=|)
+
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed on the
+"Packages"_Packages.html doc pages, and its use is illustrated in the
+individual accelerator sections. Typically these steps only need to
+be done once, to create an executable that uses one or more
+accelerator packages.
+
+The last 4 steps can all be done from the command-line when LAMMPS is
+launched, without changing your input script, as illustrated in the
+individual accelerator sections. Or you can add
+"package"_package.html and "suffix"_suffix.html commands to your input
+script.
+
+NOTE: With a few exceptions, you can build a single LAMMPS executable
+with all its accelerator packages installed. Note however that the
+USER-INTEL and KOKKOS packages require you to choose one of their
+hardware options when building for a specific platform. I.e. CPU or
+Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
+option for the KOKKOS package.
+
+These are the exceptions. You cannot build a single executable with:
+
+both the USER-INTEL Phi and KOKKOS Phi options
+the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
+
+See the examples/accelerate/README and make.list files for sample
+Make.py commands that build LAMMPS with any or all of the accelerator
+packages. As an example, here is a command that builds with all the
+GPU related packages installed (GPU, KOKKOS with Cuda), including
+settings to build the needed auxiliary GPU libraries for Kepler GPUs:
+
+Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
+ -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
+
+The examples/accelerate directory also has input scripts that can be
+used with all of the accelerator packages. See its README file for
+details.
+
+Likewise, the bench directory has FERMI and KEPLER and PHI
+sub-directories with Make.py commands and input scripts for using all
+the accelerator packages on various machines. See the README files in
+those dirs.
+
+As mentioned above, the "Benchmark
+page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
+performance results for the various accelerator packages for several
+of the standard LAMMPS benchmark problems, as a function of problem
+size and number of compute nodes, on different hardware platforms.
+
+Here is a brief summary of what the various packages provide. Details
+are in the individual accelerator sections.
+
+Styles with a "gpu" suffix are part of the GPU package, and can be run
+on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
+factors, discussed in the accelerator sections. :ulb,l
+
+Styles with an "intel" suffix are part of the USER-INTEL
+package. These styles support vectorized single and mixed precision
+calculations, in addition to full double precision. In extreme cases,
+this can provide speedups over 3.5x on CPUs. The package also
+supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
+coprocessors. This can result in additional speedup over 2x depending
+on the hardware configuration. :l
+
+Styles with a "kk" suffix are part of the KOKKOS package, and can be
+run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
+Xeon Phi in "native" mode. The speed-up depends on a variety of
+factors, as discussed on the KOKKOS accelerator page. :l
+
+Styles with an "omp" suffix are part of the USER-OMP package and allow
+a pair-style to be run in multi-threaded mode using OpenMP. This can
+be useful on nodes with high-core counts when using less MPI processes
+than cores is advantageous, e.g. when running with PPPM so that FFTs
+are run on fewer MPI processors or when the many MPI tasks would
+overload the available bandwidth for communication. :l
+
+Styles with an "opt" suffix are part of the OPT package and typically
+speed-up the pairwise calculations of your simulation by 5-25% on a
+CPU. :l
+:ule
+
+The individual accelerator package doc pages explain:
+
+what hardware and software the accelerated package requires
+how to build LAMMPS with the accelerated package
+how to run with the accelerated package either via command-line switches or modifying the input script
+speed-ups to expect
+guidelines for best performance
+restrictions :ul
+
diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt
new file mode 100644
index 0000000000..7c950779d5
--- /dev/null
+++ b/doc/src/Speed_tips.txt
@@ -0,0 +1,63 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+General tips :h3
+
+NOTE: this section 5.2 is still a work in progress
+
+Here is a list of general ideas for improving simulation performance.
+Most of them are only applicable to certain models and certain
+bottlenecks in the current performance, so let the timing data you
+generate be your guide. It is hard, if not impossible, to predict how
+much difference these options will make, since it is a function of
+problem size, number of processors used, and your machine. There is
+no substitute for identifying performance bottlenecks, and trying out
+various options.
+
+make individual pages for these, or one for PPPM
+one for timestepping, etc
+one for balancing
+or proc layout
+
+rRESPA
+2-FFT PPPM
+Staggered PPPM
+single vs double PPPM
+partial charge PPPM
+verlet/split run style
+processor command for proc layout and numa layout
+load-balancing: balance and fix balance :ul
+
+2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
+2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
+PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
+achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
+cost is the performance bottleneck (typically large problems running
+on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
+
+Staggered PPPM performs calculations using two different meshes, one
+shifted slightly with respect to the other. This can reduce force
+aliasing errors and increase the accuracy of the method, but also
+doubles the amount of work required. For high relative accuracy, using
+staggered PPPM allows one to half the mesh size in each dimension as
+compared to regular PPPM, which can give around a 4x speedup in the
+kspace time. However, for low relative accuracy, using staggered PPPM
+gives little benefit and can be up to 2x slower in the kspace
+time. For example, the rhodopsin benchmark was run on a single
+processor, and results for kspace time vs. relative accuracy for the
+different methods are shown in the figure below. For this system,
+staggered PPPM (using ik differentiation) becomes useful when using a
+relative accuracy of slightly greater than 1e-5 and above.
+
+:c,image(JPG/rhodo_staggered.jpg)
+
+NOTE: Using staggered PPPM may not give the same increase in accuracy
+of energy and pressure as it does in forces, so some caution must be
+used if energy and/or pressure are quantities of interest, such as
+when using a barostat.
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 4c5fbbd453..85ee531cfd 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
+"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Modify.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -142,8 +142,8 @@ The syntax for running the tool is
chain < def.chain > data.file :pre
See the def.chain or def.chain.ab files in the tools directory for
-examples of definition files. This tool was used to create the
-system for the "chain benchmark"_Section_perf.html.
+examples of definition files. This tool was used to create the system
+for the "chain benchmark"_Speed_bench.html.
:line
@@ -249,9 +249,9 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
emacs tool :h4,link(emacs)
-The tools/emacs directory contains a Lips add-on file for Emacs that
-enables a lammps-mode for editing of input scripts when using Emacs,
-with various highlighting options setup.
+The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
+that enables a lammps-mode for editing input scripts when using GNU Emacs,
+with various highlighting options set up.
These tools were provided by Aidan Thompson at Sandia
(athomps at sandia.gov).
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index 7ff7ef8fd4..f72f086234 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index d4330139c9..3e5445d3a3 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,10 +83,9 @@ same value from the Ea formula.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -98,8 +97,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt
index 37298ba145..4c217bae7d 100644
--- a/doc/src/angle_coeff.txt
+++ b/doc/src/angle_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+angle styles is on the "Commands bond"_Commands_bond.html#angle doc
+page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index c0ce3c9301..5a1fe91c83 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,9 @@ K (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 7182ffecc8..63a451b763 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index 830fd6db58..b6ac0ed818 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ internally.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index b5c53b1b0f..c5b184e0b4 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -21,10 +21,10 @@ angle_coeff * 75.0 1 6 :pre
[Description:]
The {cosine/periodic} angle style uses the following potential, which
-is commonly used in the "DREIDING"_Section_howto.html#howto_4 force
-field, particularly for organometallic systems where {n} = 4 might be
-used for an octahedral complex and {n} = 3 might be used for a
-trigonal center:
+is commonly used in the "DREIDING"_Howto_bioFF.html force field,
+particularly for organometallic systems where {n} = 4 might be used
+for an octahedral complex and {n} = 3 might be used for a trigonal
+center:
:c,image(Eqs/angle_cosine_periodic.jpg)
@@ -51,10 +51,9 @@ geometry.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 6ed9fe2150..90ac61fe23 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ theta (angle) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index 44a68c1087..f1c4c93c42 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ A (real number) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index 065cdad542..ba5fd9d413 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ internally.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index 34cc8c153c..c001d9d920 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -71,10 +71,9 @@ gamma0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index da39e7cf32..e0e32c1eed 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,10 +39,9 @@ C2 (real) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -54,8 +53,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 5adda6cb32..3c50536a2c 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,9 @@ n (real) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 4c74763964..76c7a491e8 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index bdd3707ccb..2646903421 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt
index a4a9b07c78..1eca5cbbec 100644
--- a/doc/src/angle_none.txt
+++ b/doc/src/angle_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index f7640bdfbc..294be330b1 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 0cc535e543..9c5630ef3a 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index f687e9286c..63295faf26 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+angle styles are is on the "Commands bond"_Commands_bond.html#angle
+doc page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style zero"_angle_zero.html - topology but no interactions
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index bd6e167bd8..31ab532be1 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -124,10 +124,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -139,8 +138,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt
index b8e8ebf953..c6c1958ec8 100644
--- a/doc/src/angle_zero.txt
+++ b/doc/src/angle_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 1dc0fa6bfb..c882d1b0ba 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -3,7 +3,7 @@ Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 442bb5ac70..abf05885a3 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -20,7 +20,7 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{body} args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
- see the "body"_body.html doc page for details
+ see the "Howto body"_Howto_body.html doc page for details
{tdpd} arg = Nspecies
Nspecies = # of chemical species
{template} arg = template-ID
@@ -106,9 +106,9 @@ output the custom values.
All of the above styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
-{body} styles, which define finite-size particles. See "Section
-6.14"_Section_howto.html#howto_14 for an overview of using finite-size
-particle models with LAMMPS.
+{body} styles, which define finite-size particles. See the "Howto
+spherical"_Howto_spherical.html doc page for an overview of using
+finite-size particle models with LAMMPS.
All of the point-particle styles assign mass to particles on a
per-type basis, using the "mass"_mass.html command, The finite-size
@@ -224,15 +224,16 @@ the {bstyle} argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
-The "body"_body.html doc page describes the body styles LAMMPS
-currently supports, and provides more details as to the kind of body
-particles they represent. For all styles, each body particle stores
-moments of inertia and a quaternion 4-vector, so that its orientation
-and position can be time integrated due to forces and torques.
+The "Howto body"_Howto_body.html doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent. For all styles, each body particle
+stores moments of inertia and a quaternion 4-vector, so that its
+orientation and position can be time integrated due to forces and
+torques.
Note that there may be additional arguments required along with the
{bstyle} specification, in the atom_style body command. These
-arguments are described in the "body"_body.html doc page.
+arguments are described on the "Howto body"_Howto_body.html doc page.
:line
@@ -261,10 +262,10 @@ styles; see the "Modify"_Modify.html doc page.
Styles with a {kk} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+run faster, depending on your available hardware, as discussed in on
+the "Speed packages"_Speed_packages.html doc page. The accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
@@ -279,8 +280,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index da6f59900d..06c4eca491 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 9687a63168..3d8d5007ba 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,10 +44,9 @@ K4 (energy/distance^4) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt
index d93c0b223b..7485fa3d8d 100644
--- a/doc/src/bond_coeff.txt
+++ b/doc/src/bond_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that here are also additional bond styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index 9050c3bf5c..e16307a710 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,10 +47,9 @@ sigma (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -62,8 +61,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index ff687444a9..8edd325885 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,10 +50,9 @@ delta (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index cc3ff75878..275036a421 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index c18a7e0fd4..e4b2015fed 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -42,10 +42,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -57,8 +56,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index bf3b3c115a..b6dc18a5fd 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ rc (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index 1918ce00b6..b3054437d8 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,9 @@ rc (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 400c3e0be4..140fb72378 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 4f6a32e341..9b64e8c5c1 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ r0 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt
index 8cb262a50f..cace1919e1 100644
--- a/doc/src/bond_none.txt
+++ b/doc/src/bond_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 434af62506..08109bc699 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ lamda (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index 927fea6403..a0e14a123a 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 4dc7ad4a36..87a21eff02 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -76,10 +76,9 @@ delete_bonds all bond 0 remove :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -91,8 +90,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 3bd8afda19..41fa1cabb2 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Note that there are also additional bond styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style zero"_bond_zero.html - topology but no interactions
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index 906d3e5d76..e53cbdfa9f 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -121,10 +121,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -136,8 +135,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt
index 4797d06cb1..711bd2c296 100644
--- a/doc/src/bond_write.txt
+++ b/doc/src/bond_write.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt
index b599f291b4..554f26e7f0 100644
--- a/doc/src/bond_zero.txt
+++ b/doc/src/bond_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt
index ce638f11b3..f9685433b2 100644
--- a/doc/src/boundary.txt
+++ b/doc/src/boundary.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,9 +82,9 @@ and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
[Restrictions:]
diff --git a/doc/src/box.txt b/doc/src/box.txt
index a6207ae993..38c874fb78 100644
--- a/doc/src/box.txt
+++ b/doc/src/box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,9 +30,9 @@ For triclinic (non-orthogonal) simulation boxes, the {tilt} keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the "create_box"_create_box.html or
"read_data"_read_data.html commands. Tilt factors determine how
-skewed the triclinic box is; see "this
-section"_Section_howto.html#howto_12 of the manual for a discussion of
-triclinic boxes in LAMMPS.
+skewed the triclinic box is; see the "Howto
+triclinic"_Howto_triclinic.html doc page for a discussion of triclinic
+boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st
diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt
index 2c7a890d4c..adc5d6bdcb 100644
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,9 +75,9 @@ The "create_box"_create_box.html, "read data"_read_data.html, and
simulation box is orthogonal or triclinic and their doc pages explain
the meaning of the xy,xz,yz tilt factors.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
The keywords used in this command are applied sequentially to the
@@ -140,8 +140,8 @@ transformation in the sequence. If skew is exceeded before the final
transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box
-skew see the discussion on triclinic boxes on "this
-page"_Section_howto.html#howto_12.
+skew see the discussion on triclinic boxes on "Howto
+triclinic"_Howto_triclinic.html doc page.
:line
@@ -258,9 +258,7 @@ command.
:line
The {ortho} and {triclinic} keywords convert the simulation box to be
-orthogonal or triclinic (non-orthogonal). See "this
-section"_Section_howto#howto_13 for a discussion of how non-orthogonal
-boxes are represented in LAMMPS.
+orthogonal or triclinic (non-orthogonal).
The simulation box is defined as either orthogonal or triclinic when
it is created via the "create_box"_create_box.html,
@@ -271,8 +269,8 @@ These keywords allow you to toggle the existing simulation box from
orthogonal to triclinic and vice versa. For example, an initial
equilibration simulation can be run in an orthogonal box, the box can
be toggled to triclinic, and then a "non-equilibrium MD (NEMD)
-simulation"_Section_howto.html#howto_13 can be run with deformation
-via the "fix deform"_fix_deform.html command.
+simulation"_Howto_nemd.html can be run with deformation via the "fix
+deform"_fix_deform.html command.
If the simulation box is currently triclinic and has non-zero tilt in
xy, yz, or xz, then it cannot be converted to an orthogonal box.
diff --git a/doc/src/clear.txt b/doc/src/clear.txt
index 7ac4da5c8d..c4ad4c4030 100644
--- a/doc/src/clear.txt
+++ b/doc/src/clear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt
index 3e8d0eca4f..489278523b 100644
--- a/doc/src/comm_modify.txt
+++ b/doc/src/comm_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt
index 8248d654d3..39eb1d4ef5 100644
--- a/doc/src/comm_style.txt
+++ b/doc/src/comm_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 532a5414e3..7d9e443e7d 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
-See this "howto section"_Section_howto.html#howto_15 for a summary of
+See the "Howto output"_Howto_output.html doc page for a summary of
various LAMMPS output options, many of which involve computes.
The ID of a compute can only contain alphanumeric characters and
@@ -161,13 +161,19 @@ calculations accessed in the various ways described above.
Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
-available in LAMMPS. They are also given in more compact form in the
-Compute section of "this page"_Section_commands.html#cmd_5.
+available in LAMMPS. They are also listed in more compact form on the
+"Commands compute"_Commands_compute.html doc page.
There are also additional compute styles (not listed here) submitted
-by users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the compute
-section of "this page"_Section_commands.html#cmd_5.
+by users which are included in the LAMMPS distribution. The full list
+of all compute styles is on the "Commands
+compute"_Commands_compute.html doc page.
+
+There are also additional accelerated compute styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands
+compute"_Commands_compute.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle/local"_compute_bond_local.html - theta and energy of each angle
@@ -243,16 +249,6 @@ section of "this page"_Section_commands.html#cmd_5.
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
-There are also additional compute styles submitted by users which are
-included in the LAMMPS distribution. The list of these with links to
-the individual styles are given in the compute section of "this
-page"_Section_commands.html#cmd_5.
-
-There are also additional accelerated compute styles included in the
-LAMMPS distribution for faster performance on CPUs and GPUs. The list
-of these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
-
[Restrictions:] none
[Related commands:]
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index 3fd838d957..485c191313 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,7 +60,7 @@ which computes this quantity.-
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
[Restrictions:]
diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt
index 2c363ce8f6..64eb2f4bb1 100644
--- a/doc/src/compute_angle.txt
+++ b/doc/src/compute_angle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "angle_style
hybrid"_angle_style.html command, which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt
index 0ee1d32d7d..3a321965ef 100644
--- a/doc/src/compute_angle_local.txt
+++ b/doc/src/compute_angle_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,8 +70,8 @@ array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {theta} will be in degrees. The output for {eng} will
diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt
index 813da15eea..7e49ff3024 100644
--- a/doc/src/compute_angmom_chunk.txt
+++ b/doc/src/compute_angmom_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the angular momentum
vector for each chunk, due to the velocity/momentum of the individual
@@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular momentum for each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index b59a3fd4c8..067a020c35 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,9 +46,8 @@ in examples/USER/misc/basal.
This compute calculates a per-atom array with 3 columns, which can be
accessed by indices 1-3 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom vector values are unitless since the 3 columns represent
components of a unit vector.
diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt
index 12ce218853..8ac3f00c55 100644
--- a/doc/src/compute_body_local.txt
+++ b/doc/src/compute_body_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Define a computation that calculates properties of individual body
sub-particles. The number of datums generated, aggregated across all
processors, equals the number of body sub-particles plus the number of
non-body particles in the system, modified by the group parameter as
-explained below. See "Section 6.14"_Section_howto.html#howto_14
-of the manual and the "body"_body.html doc page for more details on
-using body particles.
+explained below. See the "Howto body"_Howto_body.html doc page for
+more details on using body particles.
The local data stored by this command is generated by looping over all
the atoms. An atom will only be included if it is in the group. If
@@ -58,8 +57,8 @@ group.
For a body particle, the {integer} keywords refer to fields calculated
by the body style for each sub-particle. The body style, as specified
by the "atom_style body"_atom_style.html, determines how many fields
-exist and what they are. See the "body"_body.html doc page for
-details of the different styles.
+exist and what they are. See the "Howto_body"_Howto_body.html doc
+page for details of the different styles.
Here is an example of how to output body information using the "dump
local"_dump.html command with this compute. If fields 1,2,3 for the
@@ -78,9 +77,9 @@ array is the number of datums as described above. If a single keyword
is specified, a local vector is produced. If two or more keywords are
specified, a local array is produced where the number of columns = the
number of keywords. The vector or array can be accessed by any
-command that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+command that uses local values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The "units"_units.html for output values depend on the body style.
diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt
index 6c4384b080..a87c510538 100644
--- a/doc/src/compute_bond.txt
+++ b/doc/src/compute_bond.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "bond_style
hybrid"_bond_style.html command, which can be accessed by indices 1-N.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt
index 58d96f9ee4..c3dc1cc4af 100644
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The
diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt
index 4e4b03d167..183537690f 100644
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a
By default, this compute calculates the centrosymmetry value for each
atom as a per-atom vector, which can be accessed by any command that
-uses per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
If the {axes} keyword setting is {yes}, then a per-atom array is
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index 00a75f50c4..95e6e6c010 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,14 +101,13 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix
ave/chunk"_fix_ave_chunk.html command to sum and time average a
variety of per-atom properties over the atoms in each chunk. Or they
can simply be accessed by any command that uses per-atom values from a
-compute as input, as discussed in "Section
-6.15"_Section_howto.html#howto_15.
+compute as input, as discussed on the "Howto output"_Howto_output.html
+doc page.
-See "Section 6.23"_Section_howto.html#howto_23 for an overview of
-how this compute can be used with a variety of other commands to
-tabulate properties of a simulation. The howto section gives several
-examples of input script commands that can be used to calculate
-interesting properties.
+See the "Howto chunk"_Howto_chunk.html doc page for an overview of how
+this compute can be used with a variety of other commands to tabulate
+properties of a simulation. The page gives several examples of input
+script commands that can be used to calculate interesting properties.
Conceptually it is important to realize that this compute does two
simple things. First, it sets the value of {Nchunk} = the number of
@@ -167,11 +166,11 @@ or the bounds specified by the optional {bounds} keyword.
For orthogonal simulation boxes, the bins are layers, pencils, or
boxes aligned with the xyz coordinate axes. For triclinic
(non-orthogonal) simulation boxes, the bin faces are parallel to the
-tilted faces of the simulation box. See "this
-section"_Section_howto.html#howto_12 of the manual for a discussion of
-the geometry of triclinic boxes in LAMMPS. As described there, a
-tilted simulation box has edge vectors a,b,c. In that nomenclature,
-bins in the x dimension have faces with normals in the "b" cross "c"
+tilted faces of the simulation box. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a discussion of the
+geometry of triclinic boxes in LAMMPS. As described there, a tilted
+simulation box has edge vectors a,b,c. In that nomenclature, bins in
+the x dimension have faces with normals in the "b" cross "c"
direction. Bins in y have faces normal to the "a" cross "c"
direction. And bins in z have faces normal to the "a" cross "b"
direction. Note that in order to define the size and position of
@@ -626,7 +625,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values are unitless chunk IDs, ranging from 1 to
diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt
index 94113de5f2..e6138fe1e8 100644
--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -84,7 +84,7 @@ the neighbor list.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.
diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt
index 23289b0132..d69c5e9c46 100644
--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be a number from 0 to 5, as explained
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 16a51f5241..44a77d23ca 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -78,7 +78,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be real positive numbers. Some typical CNP
diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt
index b0e0c14e42..fdc631a263 100644
--- a/doc/src/compute_com.txt
+++ b/doc/src/compute_com.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,9 +41,8 @@ image"_set.html command.
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
distance "units"_units.html.
diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt
index d497585cb0..b982f0d901 100644
--- a/doc/src/compute_com_chunk.txt
+++ b/doc/src/compute_com_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the center-of-mass
for each chunk, which includes all effects due to atoms passing thru
@@ -71,9 +70,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the x,y,z center-of-mass coordinates of each chunk. These
values can be accessed by any command that uses global array values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
distance "units"_units.html.
diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt
index f0bd62f4e8..efe524263a 100644
--- a/doc/src/compute_contact_atom.txt
+++ b/doc/src/compute_contact_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,7 +36,7 @@ specified compute group.
This compute calculates a per-atom vector, whose values can be
accessed by any command that uses per-atom values from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index a88f7ec729..66eecd195d 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,9 +109,8 @@ array, with N columns.
For {cstyle} orientorder, this compute calculates a per-atom vector.
These values can be accessed by any command that uses per-atom values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-atom vector or array values will be a number >= 0.0, as
explained above.
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 918fbf65ef..74939e2280 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,7 +44,7 @@ group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values are unitless numbers (damage) >= 0.0.
diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt
index a3c3dff8d6..aa25f9dd10 100644
--- a/doc/src/compute_dihedral.txt
+++ b/doc/src/compute_dihedral.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "dihedral_style
hybrid"_dihedral_style.html command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt
index 865e86fddb..77812699d3 100644
--- a/doc/src/compute_dihedral_local.txt
+++ b/doc/src/compute_dihedral_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,8 +62,8 @@ array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {phi} will be in degrees.
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index ce00f7f12a..498110cf99 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,8 +47,9 @@ compute group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-Section_howto 15 for an overview of LAMMPS output options.
+any command that uses per-atom values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-atom vector values are unitless numbers (theta) >= 0.0.
diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt
index 75131ffbb1..d45fde9af2 100644
--- a/doc/src/compute_dipole_chunk.txt
+++ b/doc/src/compute_dipole_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,10 +32,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z coordinates of the dipole vector
and the total dipole moment for each chunk, which includes all effects
@@ -76,8 +75,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
4 for the x,y,z dipole vector components and the total dipole of each
chunk. These values can be accessed by any command that uses global
-array values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 00e5f696c1..669ab9f7ca 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -118,9 +118,8 @@ would be empty.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom array values will be in distance "units"_units.html.
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index 0e43feb9d2..1721456e35 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,9 +40,9 @@ where N is the number of particles in the system
[Output info:]
This compute calculates a global vector of length 5 (U_cond, U_mech,
-U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
-output options.
+U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The vector values will be in energy and temperature "units"_units.html.
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index 0532fc60c6..8e502d4a60 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,9 +34,9 @@ particles.
[Output info:]
This compute calculates a per-particle array with 4 columns (u_cond,
-u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command
-that uses per-particle values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any
+command that uses per-particle values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle array values will be in energy (u_cond, u_mech, u_chem)
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index 5b8c8ebd67..f33398e03d 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,9 @@ For more details please see "(Espanol1997)"_#Espanol1997 and
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+any command that uses per-atom values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in temperature "units"_units.html.
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index f7e7b8a667..9c45fd2870 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -98,8 +98,8 @@ compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
By default, this compute calculates the pair entropy value for each
atom as a per-atom vector, which can be accessed by any command that
-uses per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The pair entropy values have units of the Boltzmann constant. They are
diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt
index b9a486c32e..5cdc099782 100644
--- a/doc/src/compute_erotate_asphere.txt
+++ b/doc/src/compute_erotate_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ will be the same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index dec0939a43..5b9077870e 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,9 +41,9 @@ calculation.
This compute calculates a global scalar (the summed rotational energy
of all the rigid bodies). This value can be used by any command that
-uses a global scalar value from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+uses a global scalar value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt
index 41e80b0154..d0c176b50e 100644
--- a/doc/src/compute_erotate_sphere.txt
+++ b/doc/src/compute_erotate_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,7 +35,7 @@ as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt
index a0081ff6a8..fdd609a0e6 100644
--- a/doc/src/compute_erotate_sphere_atom.txt
+++ b/doc/src/compute_erotate_sphere_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius =
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 5e3a0c8599..561ded35c0 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,7 +43,7 @@ local atom displacements and may generate "false positives."
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 9bbae7b20f..8b4a92e16e 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these
are used in the simulation.
These output results can be used by any command that uses a global
-scalar or vector from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+scalar or vector from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options. For example, the computed values can be averaged using "fix
ave/time"_fix_ave_time.html.
diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt
index 28b4aa2461..a26dba72b0 100644
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,7 +67,7 @@ this command. This command will then assign the global chunk value to
each atom in the chunk, producing a per-atom vector or per-atom array
as output. The per-atom values can then be output to a dump file or
used by any command that uses per-atom values from a compute as input,
-as discussed in "Section 6.15"_Section_howto.html#howto_15.
+as discussed on the "Howto output"_Howto_output.html doc page.
As a concrete example, these commands will calculate the displacement
of each atom from the center-of-mass of the molecule it is in, and
@@ -203,7 +203,7 @@ vector. If multiple inputs are specified, this compute produces a
per-atom array values, where the number of columns is equal to the
number of inputs specified. These values can be used by any command
that uses per-atom vector or array values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector or array values will be in whatever units the
diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt
index f10547339d..cff3687354 100644
--- a/doc/src/compute_group_group.txt
+++ b/doc/src/compute_group_group.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -123,8 +123,8 @@ group-group calculations are performed.
This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
Both the scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt
index dd71431527..4dc883ad0b 100644
--- a/doc/src/compute_gyration.txt
+++ b/doc/src/compute_gyration.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -55,8 +55,8 @@ using the "set image"_set.html command.
This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
-vector values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt
index 3e338213cf..dcbfc65393 100644
--- a/doc/src/compute_gyration_chunk.txt
+++ b/doc/src/compute_gyration_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the radius of gyration Rg for each chunk,
which includes all effects due to atoms passing thru periodic
@@ -93,8 +92,8 @@ calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword
is specified, the global array has 6 columns. The vector or array can
be accessed by any command that uses global values from a compute as
-input. See "this section"_Section_howto.html#howto_15 for an overview
-of LAMMPS output options.
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
All the vector or array values calculated by this compute are
"intensive". The vector or array values will be in distance
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
index 39a1470201..81a2a3f517 100644
--- a/doc/src/compute_heat_flux.txt
+++ b/doc/src/compute_heat_flux.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,9 @@ or to calculate a thermal conductivity using the equilibrium
Green-Kubo formalism.
For other non-equilibrium ways to compute a thermal conductivity, see
-"this section"_Section_howto.html#howto_20. These include use of the
-"fix thermal/conductivity"_fix_thermal_conductivity.html command for
-the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
+the "Howto kappa"_Howto_kappa.html doc page.. These include use of
+the "fix thermal/conductivity"_fix_thermal_conductivity.html command
+for the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
which can add or subtract heat from groups of atoms.
The compute takes three arguments which are IDs of other
@@ -99,8 +99,8 @@ result should be: average conductivity ~0.29 in W/mK.
This compute calculates a global vector of length 6 (total heat flux
vector, followed by convective heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
-uses global vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses global vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values calculated by this compute are "extensive", meaning
diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt
index cdf47e0894..082a3cad7a 100644
--- a/doc/src/compute_hexorder_atom.txt
+++ b/doc/src/compute_hexorder_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -95,10 +95,9 @@ This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts {qn}, a complex number restricted to the
unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 .
-These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+These values can be accessed by any command that uses per-atom values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:] none
diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt
index f0d2fa400e..867dd48cc1 100644
--- a/doc/src/compute_improper.txt
+++ b/doc/src/compute_improper.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the
number of sub_styles defined by the "improper_style
hybrid"_improper_style.html command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt
index 0c289fbf07..f340d5a03f 100644
--- a/doc/src/compute_improper_local.txt
+++ b/doc/src/compute_improper_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,8 +63,8 @@ array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {chi} will be in degrees.
diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt
index b0dbb12aea..d6cdb3fe79 100644
--- a/doc/src/compute_inertia_chunk.txt
+++ b/doc/src/compute_inertia_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 6 components of the symmetric inertia
tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The
@@ -72,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
6 for the 6 components of the inertia tensor for each chunk, ordered
as listed above. These values can be accessed by any command that
-uses global array values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses global array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt
index caee897162..64ab83db48 100644
--- a/doc/src/compute_ke.txt
+++ b/doc/src/compute_ke.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc).
This compute calculates a global scalar (the summed KE). This value
can be used by any command that uses a global scalar value from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt
index f5431f0569..d288ab0236 100644
--- a/doc/src/compute_ke_atom.txt
+++ b/doc/src/compute_ke_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,7 +34,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index 8228e13f07..f665f35055 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,9 @@ electrons) not in the specified compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom computes as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+accessed by any command that uses per-atom computes as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index ac8d7e6c01..d6d7fdb10f 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
-input. See "Section 6.15"_Section_howto.html#howto_15 for an
+input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index f79696a77a..45ba2673b0 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,8 +40,8 @@ calculation.
This compute calculates a global scalar (the summed KE of all the
rigid bodies). This value can be used by any command that uses a
-global scalar value from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+global scalar value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "extensive". The
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 4e621b4301..9a9c7fae11 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index a017424dd0..30b1142b6c 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in mass/volume "units"_units.html.
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index 9e81b038f4..ab92f05018 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in temperature "units"_units.html.
diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt
index 9a2480ec0a..192ea0bc9e 100644
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt
index f806c5e292..b54e05bc64 100644
--- a/doc/src/compute_msd.txt
+++ b/doc/src/compute_msd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,9 +93,8 @@ instead of many, which will change the values of msd somewhat.
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
distance^2 "units"_units.html.
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 7f31b61ed0..264f38d5fd 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
@@ -106,7 +105,7 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
4 for dx,dy,dz and the total displacement. These values can be
accessed by any command that uses global array values from a compute
-as input. See "this section"_Section_howto.html#howto_15 for an
+as input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index 198da999e0..814159121d 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,8 @@ NOTEs, which also apply to this compute.
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The first vector value will be in
distance^2 "units"_units.html, the second is in distance^4 units, and
diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt
index 46c72d3dcb..84b25ac6f2 100644
--- a/doc/src/compute_omega_chunk.txt
+++ b/doc/src/compute_omega_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the angular velocity
vector for each chunk, via the formula L = Iw where L is the angular
@@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the angular velocity for each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt
index adf11dcfcf..7327a7b1d3 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -115,10 +115,9 @@ Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This
way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
columns.
-These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+These values can be accessed by any command that uses per-atom values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:] none
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index 0602dab81b..a2c25fcc8d 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,9 +62,8 @@ This compute calculates a global scalar which is {epair} or {evdwl} or
{ecoul}. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. These values
can be used by any command that uses global scalar or vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are
"extensive".
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index 16aaba4667..7588e92527 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,8 +119,8 @@ array is the number of pairs. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The
diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt
index 15f27a8eff..37655dfd48 100644
--- a/doc/src/compute_pe.txt
+++ b/doc/src/compute_pe.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,9 +64,8 @@ See the "thermo_style" command for more details.
This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt
index c312c886a6..400621f8df 100644
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,7 +81,7 @@ global system energy.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 788213fc65..50a51d9937 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,8 +41,9 @@ compute group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-Section_howto 15 for an overview of LAMMPS output options.
+any command that uses per-atom values from a compute as input. See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-atom vector values are unitless numbers (lambda) >= 0.0.
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index f0691ad207..dea0a7f05b 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,10 +105,9 @@ where "thermo_temp" is the ID of a similarly defined compute of style
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -130,8 +129,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
-or vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+or vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 5b252b369d..61cc85ad80 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index c0970d5121..512009093c 100644
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,11 +93,11 @@ compute 3 all property/atom sp spx spy spz :pre
Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
-"output commands"_Section_howto.html#howto_15 that take computes as
-inputs. See for example, the "compute reduce"_compute_reduce.html,
-"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html,
-"fix ave/chunk"_fix_ave_chunk.html, and "atom-style
-variable"_variable.html commands.
+"output commands"_Howto_output.html that take computes as inputs. See
+for example, the "compute reduce"_compute_reduce.html, "fix
+ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix
+ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html
+commands.
The list of possible attributes is the same as that used by the "dump
custom"_dump.html command, which describes their meaning, with some
@@ -149,8 +149,8 @@ on the number of input values. If a single input is specified, a
per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
-per-atom values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values will be in whatever "units"_units.html the
diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt
index b9d4944b30..a30b5a1f0a 100644
--- a/doc/src/compute_property_chunk.txt
+++ b/doc/src/compute_property_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,15 +36,14 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates and stores the specified attributes of chunks
as global data so they can be accessed by other "output
-commands"_Section_howto.html#howto_15 and used in conjunction with
-other commands that generate per-chunk data, such as "compute
+commands"_Howto_output.html and used in conjunction with other
+commands that generate per-chunk data, such as "compute
com/chunk"_compute_com_chunk.html or "compute
msd/chunk"_compute_msd_chunk.html.
@@ -103,8 +102,8 @@ single input is specified, a global vector is produced. If two or
more inputs are specified, a global array is produced where the number
of columns = the number of inputs. The vector or array can be
accessed by any command that uses global values from a compute as
-input. See "this section"_Section_howto.html#howto_15 for an overview
-of LAMMPS output options.
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The vector or array values are "intensive". The values will be
unitless or in the units discussed above.
diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt
index 39106a39c8..b0ec088cf7 100644
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,10 @@ compute 1 all property/local atype aatom2 :pre
Define a computation that stores the specified attributes as local
data so it can be accessed by other "output
-commands"_Section_howto.html#howto_15. If the input attributes refer
-to bond information, then the number of datums generated, aggregated
-across all processors, equals the number of bonds in the system.
-Ditto for pairs, angles, etc.
+commands"_Howto_output.html. If the input attributes refer to bond
+information, then the number of datums generated, aggregated across
+all processors, equals the number of bonds in the system. Ditto for
+pairs, angles, etc.
If multiple attributes are specified then they must all generate the
same amount of information, so that the resulting local array has the
@@ -140,8 +140,8 @@ the array is the number of bonds, angles, etc. If a single input is
specified, a local vector is produced. If two or more inputs are
specified, a local array is produced where the number of columns = the
number of inputs. The vector or array can be accessed by any command
-that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+that uses local values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values will be integers that correspond to the
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index e462e85fc0..04b38682cc 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -152,7 +152,7 @@ coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of {itypeN} versus
{jtypeN} interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".
diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt
index 48115a0886..ef3c7c6489 100644
--- a/doc/src/compute_reduce.txt
+++ b/doc/src/compute_reduce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 077ad57d81..b5e6954ab9 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,8 +49,8 @@ Define a computation that simply stores rigid body attributes for
rigid bodies defined by the "fix rigid/small"_fix_rigid.html command
or one of its NVE, NVT, NPT, NPH variants. The data is stored as
local data so it can be accessed by other "output
-commands"_Section_howto.html#howto_15 that process local data, such as
-the "compute reduce"_compute_reduce.html or "dump local"_dump.html
+commands"_Howto_output.html that process local data, such as the
+"compute reduce"_compute_reduce.html or "dump local"_dump.html
commands.
Note that this command only works with the "fix
@@ -154,9 +154,9 @@ array is the number of rigid bodies. If a single keyword is
specified, a local vector is produced. If two or more keywords are
specified, a local array is produced where the number of columns = the
number of keywords. The vector or array can be accessed by any
-command that uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+command that uses local values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The vector or array values will be in whatever "units"_units.html the
corresponding attribute is in:
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 020f72f565..8c17a30fca 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,10 +143,9 @@ the number of reciprocal lattice nodes that are explored by the mesh.
The entries of the global vector are the computed diffraction
intensities as described above.
-The vector can be accessed by any command that uses global values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+The vector can be accessed by any command that uses global values from
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive".
diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt
index 13f40ecf92..51031aeab3 100644
--- a/doc/src/compute_slice.txt
+++ b/doc/src/compute_slice.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,8 +94,8 @@ specified or a global array with N columns where N is the number of
inputs. The length of the vector or the number of rows in the array
is equal to the number of values extracted from each input vector.
These values can be used by any command that uses global vector or
-array values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The vector or array values calculated by this compute are simply
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index 69fe453343..cd13816047 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ specified compute group.
[Output info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle vector values will be in distance "units"_units.html.
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index b6c75a3b20..afabe23d7c 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -28,10 +28,10 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in
[Output Info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values are dimensionless an in the range of zero to one.
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index a15b79e64e..13fd20a589 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,10 +37,10 @@ Mach Dynamics in LAMMPS.
[Output Info:]
-This compute calculates a per-particle vector, which can be accessed by
-any command that uses per-particle values from a compute as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed
+by any command that uses per-particle values from a compute as input.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will are dimensionless. See
"units"_units.html.
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index bc6f9e0f20..6585c3429f 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of energy.
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index af5b164453..fb3c5c9138 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given dimensionless. See "units"_units.html.
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index ba7b3176db..b913ae9097 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index ae50526725..a1ee1d9c5b 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,8 +33,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be in "units"_units.html of mass over volume.
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index 68b5dffa1c..1663c84f65 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS.
This compute outputss a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-particle vector values will be given dimensionless. See
"units"_units.html. The per-particle vector has 10 entries. The first
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index 560a9b6fd8..c714f3266b 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,8 +37,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values will be given in "units"_units.html of time.
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index 0420d1903d..af5b0741db 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle values are dimensionless. See "units"_units.html.
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index 02bd0c50dd..927cd7c7ae 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,9 +33,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors, which can be
accessed by any command that uses per-particle values from a compute
-as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+as input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The per-particle vector has 7 entries. The first three entries
correspond to the lengths of the ellipsoid's axes and have units of
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index f25d1b77db..4536f26c8e 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The per-particle tensor values will be given dimensionless. See
"units"_units.html.
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index 13ca57ac4d..ae2883e4bb 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "How-to discussions, section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index 5d707d4c2f..50d6b7f434 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,11 +29,10 @@ Mach Dynamics in LAMMPS.
[Output info:]
-This compute calculates a per-particle vector of vectors (tensors), which can be
-accessed by any command that uses per-particle values from a compute
-as input. See
-"How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+This compute calculates a per-particle vector of vectors (tensors),
+which can be accessed by any command that uses per-particle values
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 5b0f0afc4c..9e167924d1 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,9 +31,9 @@ Mach Dynamics in LAMMPS.
[Output info:]
This compute returns a per-particle vector of vectors, which can be
-accessed by any command that uses per-particle values from a compute as
-input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15
-for an overview of LAMMPS output options.
+accessed by any command that uses per-particle values from a compute
+as input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and
(x3/y3/z3) corresponding to the first, second, and third vertex of
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index adece93343..202b8f15e1 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS.
This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle values will be given dimensionless, see "units"_units.html.
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index b7d425b12b..76c47162a5 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle tensor, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+See the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
The per-particle vector has 6 entries, corresponding to the xx, yy,
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index e2c349c265..c851e767b3 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of one over time.
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index 47f903d3b8..a5692b2412 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,9 +30,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
which can be accessed by any command that uses per-particle values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The values will be given in "units"_units.html of pressure.
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index fc736a5bf5..fc4871d6f3 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector, which can be accessed
by any command that uses per-particle values from a compute as input.
-See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for
-an overview of LAMMPS output options.
+See the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
The per-particle vector values will be given in "units"_units.html of
volume.
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 268e23ac28..3b302a0a71 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -244,9 +244,8 @@ So the nesting order from inside to outside is bispectrum component,
linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
-from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
[Restrictions:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index fcc764c14c..792706ecdf 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
index 83b1df68e3..222513da61 100644
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -142,9 +142,8 @@ global system pressure.
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The per-atom array values will be in pressure*volume
"units"_units.html as discussed above.
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 95ef4a553b..23fac43093 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index a6a12dc52c..9ee4d3da34 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,9 +33,9 @@ details see "(Li2015)"_#Li2015a.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
-any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
+any command that uses per-atom values from a compute as input. See the
+"Howto output"_Howto_output.html doc page for an overview of LAMMPS
+output options.
The per-atom vector values will be in the units of chemical species
per unit mass.
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index b88be79e20..9f3a1ca906 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,8 +58,8 @@ compute thermo_temp all temp :pre
See the "thermo_style" command for more details.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -67,10 +67,9 @@ thermostatting.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -82,8 +81,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -92,8 +91,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 495366b345..6766729ae0 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,8 +93,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -122,8 +122,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index f72b886cc4..4e3ce3e77f 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,8 +75,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -104,8 +104,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt
index f877f6ece8..de8c850a70 100644
--- a/doc/src/compute_temp_chunk.txt
+++ b/doc/src/compute_temp_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -52,10 +52,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
The temperature is calculated by the formula KE = DOF/2 k T, where KE =
total kinetic energy of all atoms assigned to chunks (sum of 1/2 m
@@ -200,8 +199,8 @@ molecule.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
This compute also optionally calculates a global array, if one or more
@@ -210,9 +209,8 @@ of the optional values are specified. The number of rows in the array
"compute chunk/atom"_compute_chunk_atom.html command. The number of
columns is the number of specified values (1 or more). These values
can be accessed by any command that uses global array values from a
-compute as input. Again, see "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+compute as input. Again, see the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt
index c7cc5ec4e2..12df694e38 100644
--- a/doc/src/compute_temp_com.txt
+++ b/doc/src/compute_temp_com.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -74,8 +74,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt
index 561b787df6..0236319f54 100644
--- a/doc/src/compute_temp_cs.txt
+++ b/doc/src/compute_temp_cs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -28,9 +28,9 @@ Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See
-"Section 6.25"_Section_howto.html#howto_25 of the manual for an
-overview of the model as implemented in LAMMPS. Specifically, this
-compute enables correct temperature calculation and thermostatting of
+the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
+the model as implemented in LAMMPS. Specifically, this compute
+enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
@@ -83,8 +83,9 @@ langevin"_fix_langevin.html.
The internal energy of core/shell pairs can be calculated by the
"compute temp/chunk"_compute_temp_chunk.html command, if chunks are
-defined as core/shell pairs. See "Section
-6.25"_Section_howto.html#howto_25 for more discussion on how to do this.
+defined as core/shell pairs. See the "Howto
+coreshell"_Howto_coreshell.html doc page doc page for more discussion
+on how to do this.
[Output info:]
diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt
index 168b0b3880..26d322589e 100644
--- a/doc/src/compute_temp_deform.txt
+++ b/doc/src/compute_temp_deform.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -104,8 +104,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -113,8 +113,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index d09a0ace2f..876d492f34 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,8 +48,8 @@ component of the electrons is not affected.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt
index 169b8d5880..20d9a5c056 100644
--- a/doc/src/compute_temp_drude.txt
+++ b/doc/src/compute_temp_drude.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -22,10 +22,10 @@ compute TDRUDE all temp/drude :pre
[Description:]
Define a computation that calculates the temperatures of core-Drude
-pairs. This compute is designed to be used with the
-"thermalized Drude oscillator model"_tutorial_drude.html. Polarizable
-models in LAMMPS are described in "this
-Section"_Section_howto.html#howto_25.
+pairs. This compute is designed to be used with the "thermalized Drude
+oscillator model"_Howto_drude.html. Polarizable models in LAMMPS
+are described on the "Howto polarizable"_Howto_polarizable.html doc
+page.
Drude oscillators consist of a core particle and a Drude particle
connected by a harmonic bond, and the relative motion of these Drude
@@ -57,8 +57,8 @@ kinetic energy of the centers of mass (energy units)
kinetic energy of the dipoles (energy units) :ol
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
Both the scalar value and the first two values of the vector
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 409319edcb..35ddb75b12 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,8 +69,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index fe2420b4e4..2769246532 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -74,10 +74,9 @@ thermostatting.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -89,8 +88,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -99,8 +98,8 @@ more instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt
index 64a6abd283..4ed04ca67e 100644
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -122,8 +122,8 @@ degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the {extra} option, which is applied to each bin.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting. Using this compute in conjunction with a
thermostatting fix, as explained there, will effectively implement a
profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1.
@@ -145,8 +145,8 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
indices are numbered from 1 to 10 in each dimension.
These values can be used by any command that uses global scalar or
-vector or array values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector or array values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt
index bc9283469c..15cad9c0cb 100644
--- a/doc/src/compute_temp_ramp.txt
+++ b/doc/src/compute_temp_ramp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,8 +83,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -92,8 +92,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt
index 3e4a80db8d..f23901af98 100644
--- a/doc/src/compute_temp_region.txt
+++ b/doc/src/compute_temp_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,8 +81,8 @@ If needed the number of subtracted degrees-of-freedom can be set
explicitly using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -90,8 +90,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 8baf2dd46c..95892eb257 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -39,8 +39,8 @@ temp/eff"_compute_temp_eff.html command.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 34feca7b6f..189246d3e4 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,8 +64,8 @@ atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
@@ -73,8 +73,8 @@ thermostatting.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt
index 9e9dff2cb6..5a55126d12 100644
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -79,8 +79,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
:line
@@ -108,8 +108,8 @@ rotational degrees of freedom.
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
-vector values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
+vector values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index acd3a6218d..a94d5db8ed 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index 733954d146..e79b594e3f 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,9 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike.
This compute calculates a global scalar, namely dUs/dlambda. This
value can be used by any command that uses a global scalar value from
-a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+a compute as input. See the "Howto output"_Howto_output.html doc page
+for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive".
diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt
index b9f832dd03..6484076b37 100644
--- a/doc/src/compute_torque_chunk.txt
+++ b/doc/src/compute_torque_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the 3 components of the torque vector for eqch
chunk, due to the forces on the individual atoms in the chunk around
@@ -72,7 +71,7 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the torque for each chunk. These values
can be accessed by any command that uses global array values from a
-compute as input. See "Section 6.15"_Section_howto.html#howto_15
+compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt
index a0d9a3c5f7..70f1e99490 100644
--- a/doc/src/compute_vacf.txt
+++ b/doc/src/compute_vacf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -55,9 +55,8 @@ correctly with time=0 atom velocities from the restart file.
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
-from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options.
+from a compute as input. See the "Howto output"_Howto_output.html doc
+page for an overview of LAMMPS output options.
The vector values are "intensive". The vector values will be in
velocity^2 "units"_units.html.
diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt
index de02c586bf..7e8ad71208 100644
--- a/doc/src/compute_vcm_chunk.txt
+++ b/doc/src/compute_vcm_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
-defined and examples of how they can be used to measure properties of
-a system.
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
This compute calculates the x,y,z components of the center-of-mass
velocity for each chunk. This is done by summing mass*velocity for
@@ -63,8 +62,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the x,y,z center-of-mass velocity coordinates of each chunk.
These values can be accessed by any command that uses global array
-values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index a280b2b151..a8ce77882a 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -122,18 +122,16 @@ to locate vacancies (the coordinates are given by the atom coordinates
at the time step when the compute was first invoked), while column two
data can be used to identify interstitial atoms.
-If the {neighbors} value is set to yes, then
-this compute creates a local array with 3 columns. There
-is one row for each face of each Voronoi cell. The
-3 columns are the atom ID of the atom that owns the cell,
-the atom ID of the atom in the neighboring cell
-(or zero if the face is external), and the area of the face.
-The array can be accessed by any command that
-uses local values from a compute as input. See "this
-section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options. More specifically, the array can be accessed by a
-"dump local"_dump.html command to write a file containing
-all the Voronoi neighbors in a system:
+If the {neighbors} value is set to yes, then this compute creates a
+local array with 3 columns. There is one row for each face of each
+Voronoi cell. The 3 columns are the atom ID of the atom that owns the
+cell, the atom ID of the atom in the neighboring cell (or zero if the
+face is external), and the area of the face. The array can be
+accessed by any command that uses local values from a compute as
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options. More specifically, the array can be
+accessed by a "dump local"_dump.html command to write a file
+containing all the Voronoi neighbors in a system:
compute 6 all voronoi/atom neighbors yes
dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre
@@ -186,8 +184,8 @@ columns. In regular dynamic tessellation mode the first column is the
Voronoi volume, the second is the neighbor count, as described above
(read above for the output data in case the {occupation} keyword is
specified). These values can be accessed by any command that uses
-per-atom values from a compute as input. See "Section
-6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+per-atom values from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
options. If the {peratom} keyword is set to "no", the per-atom array
is still created, but it is not accessible.
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 1a151d63f9..609fde3582 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -162,7 +162,7 @@ or degrees) provided with the {2Theta} values. The second column contains
the computed diffraction intensities as described above.
The array can be accessed by any command that uses global values from
-a compute as input. See "this section"_Section_howto.html#howto_15
+a compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive".
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index 5d824ae1ef..d80e2d45f1 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt
index 6700ed29d3..8596cab51d 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/src/create_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt
index f4ef13654c..0993b4f927 100644
--- a/doc/src/create_box.txt
+++ b/doc/src/create_box.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,9 +73,9 @@ factors that exceed these limits, you can use the "box tilt"_box.html
command, with a setting of {large}; a setting of {small} is the
default.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
When a prism region is used, the simulation domain should normally be
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index 1aa71d341f..57faf97ad1 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt
index b1137a2288..b29fa82f2d 100644
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt
index e98badf87b..f93be8cc25 100644
--- a/doc/src/dielectric.txt
+++ b/doc/src/dielectric.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 06abe054e4..8adef6cf4b 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,10 +116,9 @@ computed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -131,8 +130,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index cb9fc72c22..1a2f37abbb 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -141,10 +141,9 @@ r3 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -156,8 +155,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt
index 5b43cbbe7f..1db69e40d5 100644
--- a/doc/src/dihedral_coeff.txt
+++ b/doc/src/dihedral_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 715682affc..7ef27e6bc9 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -52,10 +52,9 @@ A (real number) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -67,8 +66,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index 0accbb22bf..f51cbc9c8c 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,10 +44,9 @@ dm (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index d9a48ff384..1eda0c5d02 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ Some force fields let {n} be positive or negative which corresponds to
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 1e907557b2..3af4b410bc 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,10 +46,9 @@ C (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -61,8 +60,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index 8cb40eff44..c9ca86680c 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7d3c2ea083..7c22391923 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ A5 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 8392d83899..aa8f1e0d7f 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,9 @@ An (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt
index 3ce2aa1729..4c1ff2ea5d 100644
--- a/doc/src/dihedral_none.txt
+++ b/doc/src/dihedral_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index d1a6ba3ff2..f0cf91f30a 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,9 @@ K4 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index ca2f5aed40..e65cf2dee8 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -41,10 +41,9 @@ phi0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 7c17fbf5ef..10a757e898 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index ca592b29b5..6aff3f0994 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style zero"_dihedral_zero.html - topology but no interactions
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index 0b88f26a61..d722ef7c82 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -174,10 +174,9 @@ that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -189,8 +188,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index 1c83d4ffa0..cc7df8cdf9 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt
index 4d33126eeb..0c9995a563 100644
--- a/doc/src/dihedral_zero.txt
+++ b/doc/src/dihedral_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt
index 0531e92acf..b7dde76524 100644
--- a/doc/src/dimension.txt
+++ b/doc/src/dimension.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -26,7 +26,7 @@ prior to setting up a simulation box via the
"create_box"_create_box.html or "read_data"_read_data.html commands.
Restart files also store this setting.
-See the discussion in "Section 6"_Section_howto.html for
+See the discussion on the "Howto 2d"_Howto_2d.html doc page for
additional instructions on how to run 2d simulations.
NOTE: Some models in LAMMPS treat particles as finite-size spheres or
diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt
index 634add196b..b4afd5c3a9 100644
--- a/doc/src/displace_atoms.txt
+++ b/doc/src/displace_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index ff1bf6424d..5b478b7301 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -224,12 +224,12 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they represent a bounding box. See "this
-section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic boxes, as defined by LAMMPS, simple formulas
-for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
-calculated from the triclinic parameters, and how to transform those
-parameters to and from other commonly used triclinic representations.
+of xlo, etc, since they represent a bounding box. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a geometric description
+of triclinic boxes, as defined by LAMMPS, simple formulas for how the
+6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from
+the triclinic parameters, and how to transform those parameters to and
+from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
@@ -530,7 +530,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed
-in "Section 6.12"_Section_howto.html#howto_12.
+on the "Howto triclinic"_Howto_triclinic.html doc page.
Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index e257f9c4f1..665be14be1 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index 93c87d85b7..fbd682dad9 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index c1732be972..06332b5dcf 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -356,16 +356,16 @@ is used to define body particles with internal state
body style. If this keyword is not used, such particles will be drawn
as spheres, the same as if they were regular atoms.
-The "body"_body.html doc page describes the body styles LAMMPS
-currently supports, and provides more details as to the kind of body
-particles they represent and how they are drawn by this dump image
-command. For all the body styles, individual atoms can be either a
-body particle or a usual point (non-body) particle. Non-body
+The "Howto body"_Howto_body.html doc page describes the body styles
+LAMMPS currently supports, and provides more details as to the kind of
+body particles they represent and how they are drawn by this dump
+image command. For all the body styles, individual atoms can be
+either a body particle or a usual point (non-body) particle. Non-body
particles will be drawn the same way they would be as a regular atom.
The {bflag1} and {bflag2} settings are numerical values which are
passed to the body style to affect how the drawing of a body particle
-is done. See the "body"_body.html doc page for a description of what
-these parameters mean for each body style.
+is done. See the "Howto body"_Howto_body.html doc page for a
+description of what these parameters mean for each body style.
The only setting currently allowed for the {color} value is {type},
which will color the body particles according to the atom type of the
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 5365610d64..73107d07f7 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 7e68490a68..9fa04bd1ae 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index 70111a36a8..b1c6373651 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index d4d28c81fc..afc6099534 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index 3141c7a719..dc6918dc89 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index ba2088576f..fd966b5bd9 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,7 +133,7 @@ reduce"_compute_reduce.html command, or histogrammed by the "fix
ave/histo"_fix_ave_histo.html command. :l
:ule
-See this "howto section"_Section_howto.html#howto_15 for a summary of
+See the "Howto output"_Howto_output.html doc page for a summary of
various LAMMPS output options, many of which involve fixes.
The results of fixes that calculate global quantities can be either
@@ -151,16 +151,20 @@ for further info.
:line
-Each fix style has its own documentation page which describes its
-arguments and what it does, as listed below. Here is an alphabetic
-list of fix styles available in LAMMPS. They are also given in more
-compact form in the Fix section of "this
-page"_Section_commands.html#cmd_5.
+Each fix style has its own doc page which describes its arguments and
+what it does, as listed below. Here is an alphabetic list of fix
+styles available in LAMMPS. They are also listed in more compact form
+on the "Commands fix"_Commands_fix.html doc page.
There are also additional fix styles (not listed here) submitted by
-users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the fix section
-of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution. The full list of
+all fix styles is on the "Commands fix"_Commands_fix.html doc page.
+
+There are also additional accelerated fix styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands fix"_Commands_fix.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt
index 7a34f2ff44..0ca28fb869 100644
--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -270,10 +270,10 @@ fix 1 center adapt 10 atom diameter v_size :pre
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
For "rRESPA time integration"_run_style.html, this fix changes
parameters on the outermost rRESPA level.
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 5dd58bc39a..7e30a1d29d 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/doc/src/fix_adapt_fep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -243,10 +243,10 @@ parameters on the outermost rRESPA level.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index b2ac95eabb..51be39fdb2 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,12 +103,12 @@ converge properly.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -150,11 +150,11 @@ integrator the fix is adding its forces. Default is the outermost
level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the potential
-energy discussed above. The vector is the total force on the group of
-atoms before the forces on individual atoms are changed by the fix.
-The scalar and vector values calculated by this fix are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the potential energy discussed above. The vector is the
+total force on the group of atoms before the forces on individual
+atoms are changed by the fix. The scalar and vector values calculated
+by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index 793ec0e015..c80fad26da 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,11 +70,11 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its torque. Default is the outermost level.
This fix computes a global scalar and a global 3-vector, which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The scalar is the potential energy discussed above. The vector is the
-total torque on the group of atoms before the forces on individual
-atoms are changed by the fix. The scalar and vector values calculated
-by this fix are "extensive".
+accessed by various "output commands"_Howto_output.html. The scalar
+is the potential energy discussed above. The vector is the total
+torque on the group of atoms before the forces on individual atoms are
+changed by the fix. The scalar and vector values calculated by this
+fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index 27070c9be5..c6af361afc 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -87,10 +87,10 @@ define the lattice spacings.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt
index 49014f0591..6de917e571 100644
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,7 +102,13 @@ Note coupling and post-processing can be combined in the same simulations using
[Restart, fix_modify, output, run start/stop, minimize info:]
-No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html.
+No information about this fix is written to "binary restart
+files"_restart.html. The "fix_modify"_fix_modify.html options
+relevant to this fix are listed below. No global scalar or vector or
+per-atom quantities are stored by this fix for access by various
+"output commands"_Howto_output.html. No parameter of this fix can be
+used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index bf56277214..c1d84dade1 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,8 +150,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global vector of length 2, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The vector
-values are the following global cumulative quantities:
+by various "output commands"_Howto_output.html. The vector values are
+the following global cumulative quantities:
1 = swap attempts
2 = swap successes :ul
diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt
index 23e4ed235b..10deaf64cd 100644
--- a/doc/src/fix_ave_atom.txt
+++ b/doc/src/fix_ave_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,7 +38,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre
Use one or more per-atom vectors as inputs every few timesteps, and
average them atom by atom over longer timescales. The resulting
per-atom averages can be used by other "output
-commands"_Section_howto.html#howto_15 such as the "fix
+commands"_Howto_output.html such as the "fix
ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands.
The group specified with the command means only atoms within the group
@@ -155,14 +155,14 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+commands"_Howto_output.html.
This fix produces a per-atom vector or array which can be accessed by
-various "output commands"_Section_howto.html#howto_15. A vector is
-produced if only a single quantity is averaged by this fix. If two or
-more quantities are averaged, then an array of values is produced.
-The per-atom values can only be accessed on timesteps that are
-multiples of {Nfreq} since that is when averaging is performed.
+various "output commands"_Howto_output.html. A vector is produced if
+only a single quantity is averaged by this fix. If two or more
+quantities are averaged, then an array of values is produced. The
+per-atom values can only be accessed on timesteps that are multiples
+of {Nfreq} since that is when averaging is performed.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt
index 8e2a09e33f..d331e51295 100644
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,17 +85,17 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
Use one or more per-atom vectors as inputs every few timesteps, sum
the values over the atoms in each chunk at each timestep, then average
the per-chunk values over longer timescales. The resulting chunk
-averages can be used by other "output
-commands"_Section_howto.html#howto_15 such as "thermo_style
-custom"_thermo_style.html, and can also be written to a file.
+averages can be used by other "output commands"_Howto_output.html such
+as "thermo_style custom"_thermo_style.html, and can also be written to
+a file.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
-chunk/atom"_compute_chunk_atom.html doc page and "Section
-6.23"_Section_howto.html#howto_23 for details of how chunks can be
+chunk/atom"_compute_chunk_atom.html doc page and the "Howto
+chunk"_Howto_chunk.html doc page for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@@ -456,20 +456,19 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The values can
-only be accessed on timesteps that are multiples of {Nfreq} since that
-is when averaging is performed. The global array has # of rows =
-the number of chunks {Nchunk} as calculated by the specified "compute
+various "output commands"_Howto_output.html. The values can only be
+accessed on timesteps that are multiples of {Nfreq} since that is when
+averaging is performed. The global array has # of rows = the number
+of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The # of columns =
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
-columns for OrigID and CoordN are used, as explained above.
-Following the optional columns, the next column contains the count of
-atoms in the chunk, and the remaining columns are the Nvalue
-quantities. When the array is accessed with a row I that exceeds the
-current number of chunks, than a 0.0 is returned by the fix instead of
-an error, since the number of chunks can vary as a simulation runs
-depending on how that value is computed by the compute chunk/atom
-command.
+columns for OrigID and CoordN are used, as explained above. Following
+the optional columns, the next column contains the count of atoms in
+the chunk, and the remaining columns are the Nvalue quantities. When
+the array is accessed with a row I that exceeds the current number of
+chunks, than a 0.0 is returned by the fix instead of an error, since
+the number of chunks can vary as a simulation runs depending on how
+that value is computed by the compute chunk/atom command.
The array values calculated by this fix are treated as "intensive",
since they are typically already normalized by the count of atoms in
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index 98f352cb74..22e8768f1d 100644
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,7 +68,7 @@ calculate time correlations between them at varying time intervals,
and average the correlation data over longer timescales. The
resulting correlation values can be time integrated by
"variables"_variable.html or used by other "output
-commands"_Section_howto.html#howto_15 such as "thermo_style
+commands"_Howto_output.html such as "thermo_style
custom"_thermo_style.html, and can also be written to a file. See the
"fix ave/correlate/long"_fix_ave_correlate_long.html command for an
alternate method for computing correlation functions efficiently over
@@ -313,16 +313,15 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The values can
-only be accessed on timesteps that are multiples of {Nfreq} since that
-is when averaging is performed. The global array has # of rows =
-{Nrepeat} and # of columns = Npair+2. The first column has the time
-delta (in timesteps) between the pairs of input values used to
-calculate the correlation, as described above. The 2nd column has the
-number of samples contributing to the correlation average, as
-described above. The remaining Npair columns are for I,J pairs of the
-N input values, as determined by the {type} keyword, as described
-above.
+various "output commands"_Howto_output.html. The values can only be
+accessed on timesteps that are multiples of {Nfreq} since that is when
+averaging is performed. The global array has # of rows = {Nrepeat}
+and # of columns = Npair+2. The first column has the time delta (in
+timesteps) between the pairs of input values used to calculate the
+correlation, as described above. The 2nd column has the number of
+samples contributing to the correlation average, as described above.
+The remaining Npair columns are for I,J pairs of the N input values,
+as determined by the {type} keyword, as described above.
For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ...,
CNN. :ulb,l
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index 7b4bc53701..ac0ef873aa 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt
index 5155f42e7b..f1da130ff7 100644
--- a/doc/src/fix_ave_histo.txt
+++ b/doc/src/fix_ave_histo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,9 @@ fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre
Use one or more values as inputs every few timesteps to create a
single histogram. The histogram can then be averaged over longer
timescales. The resulting histogram can be used by other "output
-commands"_Section_howto.html#howto_15, and can also be written to a
-file. The fix ave/histo/weight command has identical syntax to fix
-ave/histo, except that exactly two values must be specified. See
-details below.
+commands"_Howto_output.html, and can also be written to a file. The
+fix ave/histo/weight command has identical syntax to fix ave/histo,
+except that exactly two values must be specified. See details below.
The group specified with this command is ignored for global and local
input values. For per-atom input values, only atoms in the group
@@ -320,10 +319,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector and global array which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The values can only be accessed on timesteps that are multiples of
-{Nfreq} since that is when a histogram is generated. The global
-vector has 4 values:
+accessed by various "output commands"_Howto_output.html. The values
+can only be accessed on timesteps that are multiples of {Nfreq} since
+that is when a histogram is generated. The global vector has 4
+values:
1 = total counts in the histogram
2 = values that were not histogrammed (see {beyond} keyword)
diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt
index b61f56cf02..a53e318d3f 100644
--- a/doc/src/fix_ave_time.txt
+++ b/doc/src/fix_ave_time.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -64,7 +64,7 @@ fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre
Use one or more global values as inputs every few timesteps, and
average them over longer timescales. The resulting averages can be
-used by other "output commands"_Section_howto.html#howto_15 such as
+used by other "output commands"_Howto_output.html such as
"thermo_style custom"_thermo_style.html, and can also be written to a
file. Note that if no time averaging is done, this command can be
used as a convenient way to simply output one or more global values to
@@ -305,10 +305,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global scalar or global vector or global array
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The values can only be
-accessed on timesteps that are multiples of {Nfreq} since that is when
-averaging is performed.
+which can be accessed by various "output commands"_Howto_output.html.
+The values can only be accessed on timesteps that are multiples of
+{Nfreq} since that is when averaging is performed.
A scalar is produced if only a single input value is averaged and
{mode} = scalar. A vector is produced if multiple input values are
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 5d7dec3e6a..1fc7e4a18d 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,12 +63,12 @@ to it.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -80,8 +80,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -95,10 +95,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt
index f148e6f996..2de17cdd2a 100644
--- a/doc/src/fix_balance.txt
+++ b/doc/src/fix_balance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -357,8 +357,8 @@ number of particles (or total weight) on any processor to the average
number of particles (or total weight) per processor.
These quantities can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar and vector values
-calculated by this fix are "intensive".
+commands"_Howto_output.html. The scalar and vector values calculated
+by this fix are "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f53b7c785c..f5bbc8a251 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index 83364b9efb..bdb2f2a862 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive".
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive".
These are the 2 quantities:
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index c0045ac0f0..ab34433cec 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -211,8 +211,8 @@ are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive".
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive".
These are the 2 quantities:
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index f85ef9bc1a..883968e012 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -298,9 +298,8 @@ relevant to this fix.
This fix computes one statistic for each {react} argument that it
stores in a global vector, of length 'number of react arguments', that
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated by
-this fix are "intensive".
+can be accessed by various "output commands"_Howto_output.html. The
+vector values calculated by this fix are "intensive".
These is 1 quantity for each react argument:
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index ca7069e247..a829171f33 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,13 +150,13 @@ the Boltzmann criterion.
This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The first component of the
-vector is the cumulative number of swaps performed by all processors.
-The second component of the vector is the cumulative number of swaps
-attempted (whether accepted or rejected). Note that a swap "attempt"
-only occurs when swap partners meeting the criteria described above
-are found on a particular timestep. The vector values calculated by
-this fix are "intensive".
+commands"_Howto_output.html. The first component of the vector is the
+cumulative number of swaps performed by all processors. The second
+component of the vector is the cumulative number of swaps attempted
+(whether accepted or rejected). Note that a swap "attempt" only
+occurs when swap partners meeting the criteria described above are
+found on a particular timestep. The vector values calculated by this
+fix are "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index e3d75ee858..8e21ec2c74 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -315,17 +315,15 @@ specified by the {press} keyword will be unaffected by the {temp}
setting.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-pressure-volume energy, plus the strain energy, if it exists,
-as described above.
-The energy values reported at the
-end of a minimization run under "Minimization stats" include this
-energy, and so differ from what LAMMPS normally reports as potential
-energy. This fix does not support the "fix_modify"_fix_modify.html
-{energy} option, because that would result in double-counting of the
-fix energy in the minimization energy. Instead, the fix energy can be
-explicitly added to the potential energy using one of these two
-variants:
+"output commands"_Howto_output.html. The scalar is the pressure-volume
+energy, plus the strain energy, if it exists, as described above. The
+energy values reported at the end of a minimization run under
+"Minimization stats" include this energy, and so differ from what
+LAMMPS normally reports as potential energy. This fix does not support
+the "fix_modify"_fix_modify.html {energy} option, because that would
+result in double-counting of the fix energy in the minimization
+energy. Instead, the fix energy can be explicitly added to the
+potential energy using one of these two variants:
variable emin equal pe+f_1 :pre
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index f8de2b4efe..6f3769fafe 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,9 +103,9 @@ the system's virial as part of "thermodynamic output"_thermo_style.html.
The default is {virial yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index e48dedacd9..4a1d84de64 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -99,9 +99,9 @@ to the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt
index b8d2cb43be..7458f1bcfa 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,9 +180,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector with 3 values which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The values
-can be accessed on any timestep, though they are only updated on
-timesteps that are a multiple of {Nevery}.
+by various "output commands"_Howto_output.html. The values can be
+accessed on any timestep, though they are only updated on timesteps
+that are a multiple of {Nevery}.
The three values are the most recent updates made to the control
variable by each of the 3 terms in the PID equation above. The first
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index c870c73bdc..e92d1e6b19 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the "USER-UEF
-package"_Section_packages.html#USER-UEF and its "fix
+package"_Packages_details.html#USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be
@@ -550,10 +550,9 @@ command if you want to include lattice spacings in a variable formula.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -565,18 +564,17 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix will restore the initial box settings from "binary restart
files"_restart.html, which allows the fix to be properly continue
deformation, when using the start/stop options of the "run"_run.html
-command. None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+command. None of the "fix_modify"_fix_modify.html options are
+relevant to this fix. No global or per-atom quantities are stored by
+this fix for access by various "output commands"_Howto_output.html.
This fix can perform deformation over multiple runs, using the {start}
and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 477c14ea89..277ca8777a 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ side = {in}.
NOTE: LAMMPS checks that the specified region is wholly inside the
simulation box. It can do this correctly for orthonormal simulation
-boxes. However for "triclinic boxes"_Section_howto.html#howto_12, it
-only tests against the larger orthonormal box that bounds the tilted
+boxes. However for "triclinic boxes"_Howto_triclinic.html, it only
+tests against the larger orthonormal box that bounds the tilted
simulation box. If the specified region includes volume outside the
tilted box, then an insertion will likely fail, leading to a "lost
atoms" error. Thus for triclinic boxes you should insure the
@@ -263,9 +263,9 @@ operation of the fix continues in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index 1c10d954d6..f539bc534e 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,10 +50,9 @@ examples/USER/dpd directory.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index b6decc657c..04af9a28a1 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,10 @@ cuboid domain to apply the source flux to.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt
index 235d3d38b5..92e68d13a4 100644
--- a/doc/src/fix_drag.txt
+++ b/doc/src/fix_drag.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -47,9 +47,9 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms by the drag force. The vector
-values calculated by this fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms by the drag force. The vector values
+calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt
index faa354b314..80eb79201b 100644
--- a/doc/src/fix_drude.txt
+++ b/doc/src/fix_drude.txt
@@ -3,7 +3,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,10 +25,10 @@ fix 1 all drude C C N C N D D D :pre
[Description:]
Assign each atom type in the system to be one of 3 kinds of atoms
-within the Drude polarization model. This fix is designed to be
-used with the "thermalized Drude oscillator
-model"_tutorial_drude.html. Polarizable models in LAMMPS
-are described in "this Section"_Section_howto.html#howto_25.
+within the Drude polarization model. This fix is designed to be used
+with the "thermalized Drude oscillator model"_Howto_drude.html.
+Polarizable models in LAMMPS are described on the "Howto
+polarizable"_Howto_polarizable.html doc page.
The three possible types can be designated with an integer (0,1,2)
or capital letter (N,C,D):
diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt
index 2e094d528c..8864cc4eb6 100644
--- a/doc/src/fix_drude_transform.txt
+++ b/doc/src/fix_drude_transform.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,8 +34,8 @@ Transform the coordinates of Drude oscillators from real to reduced
and back for thermalizing the Drude oscillators as described in
"(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is
designed to be used with the "thermalized Drude oscillator
-model"_tutorial_drude.html. Polarizable models in LAMMPS are
-described in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html. Polarizable models in LAMMPS are described
+on the "Howto polarizable"_Howto_polarizable.html doc page.
Drude oscillators are a pair of atoms representing a single
polarizable atom. Ideally, the mass of Drude particles would vanish
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index 7605395ca0..be4fbd255b 100644
--- a/doc/src/fix_dt_reset.txt
+++ b/doc/src/fix_dt_reset.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,8 +82,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar stores
-the last timestep on which the timestep was reset to a new value.
+"output commands"_Howto_output.html. The scalar stores the last
+timestep on which the timestep was reset to a new value.
The scalar value calculated by this fix is "intensive".
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index 5d2b86fe4b..b5a43f68aa 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -134,11 +134,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the potential
-energy discussed above. The vector is the total force added to the
-group of atoms. The scalar and vector values calculated by this fix
-are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the potential energy discussed above. The vector is the
+total force added to the group of atoms. The scalar and vector values
+calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index 40752a811f..cfcc917d01 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 4bbf41d25d..2925e44bda 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,10 +31,9 @@ not move from their initial z coordinate.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -46,8 +45,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -56,9 +55,9 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index 4c97304335..b94e2c64a9 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 42778d7978..743c51f415 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index 0c87874347..f9deab61c8 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,10 +156,9 @@ no 0.93 0.00 0.000 -1.76 :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index ed6c6d0377..6237a137fd 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,9 +73,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar, which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative number of deleted atoms. The scalar value calculated by
-this fix is "intensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+number of deleted atoms. The scalar value calculated by this fix is
+"intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt
index 30e34b4858..1dec226414 100644
--- a/doc/src/fix_external.txt
+++ b/doc/src/fix_external.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,10 +31,10 @@ fix 1 all external pf/array 10 :pre
[Description:]
This fix allows external programs that are running LAMMPS through its
-"library interface"_Section_howto.html#howto_19 to modify certain
-LAMMPS properties on specific timesteps, similar to the way other
-fixes do. The external driver can be a "C/C++ or Fortran
-program"_Section_howto.html#howto_19 or a "Python script"_Python.html.
+"library interface"_Howto_library.html to modify certain LAMMPS
+properties on specific timesteps, similar to the way other fixes do.
+The external driver can be a "C/C++ or Fortran
+program"_Howto_library.html or a "Python script"_Python.html.
:line
@@ -136,9 +136,8 @@ external program to the system's virial as part of "thermodynamic
output"_thermo_style.html. The default is {virial yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar stored by this fix
-is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar stored by this fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index b782d285c7..d1e5e12f3e 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,9 @@ No information about these fixes is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command. These fixes are not invoked during "energy
-minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command. These
+fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index efa58ea65f..843c2a66a5 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -128,11 +128,11 @@ integrator the fix computes and adds the external acceleration. Default is the
outermost level.
This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is the negative of the
-work done on the system, see above discussion. The vector is the total force
-that this fix applied to the group of atoms on the current timestep.
-The scalar and vector values calculated by this fix are "extensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the negative of the work done on the system, see above
+discussion. The vector is the total force that this fix applied to
+the group of atoms on the current timestep. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index a63ee4cb32..76a9fd3b1a 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -31,12 +31,12 @@ using "fix setforce"_fix_setforce.html.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -48,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -60,10 +60,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 191bc32b14..394690ea5d 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -382,8 +382,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global vector of length 8, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The vector
-values are the following global cumulative quantities:
+by various "output commands"_Howto_output.html. The vector values are
+the following global cumulative quantities:
1 = translation attempts
2 = translation successes
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 1425f62e13..1c5db6157d 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -126,7 +126,7 @@ sense, a restarted simulation should produce the same behavior.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15.
+access by various "output commands"_Howto_output.html.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 6568060f0c..9fdc72bf9f 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,9 +116,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index dae8ac5ed0..832c677f81 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,10 +90,9 @@ field.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -125,11 +124,11 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. This scalar is the
-gravitational potential energy of the particles in the defined field,
-namely mass * (g dot x) for each particles, where x and mass are the
-particles position and mass, and g is the gravitational field. The
-scalar value calculated by this fix is "extensive".
+"output commands"_Howto_output.html. This scalar is the gravitational
+potential energy of the particles in the defined field, namely mass *
+(g dot x) for each particles, where x and mass are the particles
+position and mass, and g is the gravitational field. The scalar value
+calculated by this fix is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 661f68ed99..506e266505 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt
index 08043eb5fb..ec117518d2 100644
--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,10 @@ files.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt
index 23db87dac2..6db7592609 100644
--- a/doc/src/fix_heat.txt
+++ b/doc/src/fix_heat.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,12 +108,11 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. This scalar is the
-most recent value by which velocites were scaled. The scalar value
-calculated by this fix is "intensive". If {eflux} is specified as
-an atom-style variable, this fix computes the average value by which
-the velocities were scaled for all of the atoms that had their
-velocities scaled.
+"output commands"_Howto_output.html. This scalar is the most recent
+value by which velocites were scaled. The scalar value calculated by
+this fix is "intensive". If {eflux} is specified as an atom-style
+variable, this fix computes the average value by which the velocities
+were scaled for all of the atoms that had their velocities scaled.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index b275612819..8e21a1619b 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -136,9 +136,9 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command. This
+fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt
index c9a791ae4e..9931793c0b 100644
--- a/doc/src/fix_indent.txt
+++ b/doc/src/fix_indent.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,8 +180,8 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global 3-vector of
forces (on the indenter), which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar and vector values
-calculated by this fix are "extensive".
+commands"_Howto_output.html. The scalar and vector values calculated
+by this fix are "extensive".
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. Note that if you
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index 07e8025d77..eba30ef088 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 93c73f5a5d..4d7728cdba 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,7 +101,7 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
+See the "Howto thermostat"_Howto_thermostat.html doc page for
a discussion of different ways to compute temperature and perform
thermostatting.
@@ -264,10 +264,9 @@ generates an average temperature of 220 K, instead of 300 K.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -279,8 +278,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -306,10 +305,10 @@ output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive". Note that calculation of this
-quantity requires setting the {tally} keyword to {yes}.
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive". Note that calculation of this quantity requires
+setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index c85ff24c96..19a3f87ffc 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -44,8 +44,9 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre
Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for
thermalizing the reduced degrees of freedom of Drude oscillators.
This link describes how to use the "thermalized Drude oscillator
-model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
-are discussed in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS
+are discussed on the "Howto polarizable"_Howto_polarizable.html doc
+page.
Drude oscillators are a way to simulate polarizables atoms, by
splitting them into a core and a Drude particle bound by a harmonic
@@ -99,8 +100,8 @@ Likewise, this fix should not normally be used on atoms that also have
their temperature controlled by another fix - e.g. by "fix
nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostating.
:line
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index 4a50bfae54..cf42f9c036 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -79,10 +79,10 @@ output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive". Note that calculation of this
-quantity requires setting the {tally} keyword to {yes}.
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive". Note that calculation of this quantity requires
+setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index b089cd7f58..1b1936376d 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 4edd610546..9bc589520b 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -118,9 +118,9 @@ of "thermodynamic output"_thermo_style.html. The default is {virial
yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index fc6203b0f2..5347f0147f 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -299,9 +299,9 @@ is written to the main LAMMPS "binary restart files"_restart.html.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index 97965e870d..a58c5d257e 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,10 @@ dimension.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can be
-used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index d2b6aafaab..bd121b7813 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,10 @@ algorithm if the force coupling constant has been set by default.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can be
-used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index 468ebe1ff5..bc8fa2ea25 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,12 +80,12 @@ assumes the constituent atoms are point particles); see
No information about the {rigid} and {rigid/nve} fixes are written to
"binary restart files"_restart.html.
-Similar to the "fix rigid"_fix_rigid.html command: The rigid
-fix computes a global scalar which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "intensive". The scalar is the current temperature of
-the collection of rigid bodies. This is averaged over all rigid
-bodies and their translational and rotational degrees of freedom. The
+Similar to the "fix rigid"_fix_rigid.html command: The rigid fix
+computes a global scalar which can be accessed by various "output
+commands"_Howto_output.html. The scalar value calculated by these
+fixes is "intensive". The scalar is the current temperature of the
+collection of rigid bodies. This is averaged over all rigid bodies
+and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v^2, where m = total
mass of the body and v = the velocity of its center of mass. The
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
@@ -94,17 +94,17 @@ of freedom constrained by the {force} and {torque} keywords are
removed from this calculation.
All of these fixes compute a global array of values which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The number of rows in the array is equal to the number of rigid
-bodies. The number of columns is 15. Thus for each rigid body, 15
-values are stored: the xyz coords of the center of mass (COM), the xyz
-components of the COM velocity, the xyz components of the force acting
-on the COM, the xyz components of the torque acting on the COM, and
-the xyz image flags of the COM, which have the same meaning as image
-flags for atom positions (see the "dump" command). The force and
-torque values in the array are not affected by the {force} and
-{torque} keywords in the fix rigid command; they reflect values before
-any changes are made by those keywords.
+accessed by various "output commands"_Howto_output.html. The number
+of rows in the array is equal to the number of rigid bodies. The
+number of columns is 15. Thus for each rigid body, 15 values are
+stored: the xyz coords of the center of mass (COM), the xyz components
+of the COM velocity, the xyz components of the force acting on the
+COM, the xyz components of the torque acting on the COM, and the xyz
+image flags of the COM, which have the same meaning as image flags for
+atom positions (see the "dump" command). The force and torque values
+in the array are not affected by the {force} and {torque} keywords in
+the fix rigid command; they reflect values before any changes are made
+by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the {single} keyword there is just one rigid body. For the
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index fcc69d2b43..7bbdd204e3 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,9 +57,9 @@ As described in the "fix viscous"_fix_viscous.html documentation:
"No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. This fix should only
diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt
index 65672fc5a5..3114ed6250 100644
--- a/doc/src/fix_lineforce.txt
+++ b/doc/src/fix_lineforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ it should continue to move along the line thereafter.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index 5fc25167a7..aa32a875bf 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -36,10 +36,10 @@ I have found that only {hftn} and {quickmin} with a very small time step perform
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 85f5838dd2..8f5ad29929 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,10 @@ LAMMPS.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 5b83573bc8..38d26b34d6 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,10 @@ LAMMPS.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index 308bba1ac3..ddb5f9a4cd 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index bcf4465fb8..f7fe35be2a 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -61,10 +61,9 @@ initial velocities with zero aggregate linear and/or angular momentum.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -76,18 +75,18 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt
index 7cb40ad132..08f38d0ed6 100644
--- a/doc/src/fix_move.txt
+++ b/doc/src/fix_move.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -203,10 +203,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The number of columns
-for each atom is 3, and the columns store the original unwrapped x,y,z
-coords of each atom. The per-atom values can be accessed on any
-timestep.
+"output commands"_Howto_output.html. The number of columns for each
+atom is 3, and the columns store the original unwrapped x,y,z coords
+of each atom. The per-atom values can be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index 7d16967955..aadc3caf5a 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 310692669a..91ffbbb0fa 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,8 +156,8 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_
These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar values calculated
-by this fix are "extensive"; the vector values are "intensive".
+commands"_Howto_output.html. The scalar values calculated by this fix
+are "extensive"; the vector values are "intensive".
[Restrictions:]
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index fb3c6fe888..1e9bf631fd 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,10 @@ addition to position and velocity, and must be used with the
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5d18c39d99..5341d6999c 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,9 +43,9 @@ Add nudging forces to atoms in the group for a multi-replica
simulation run via the "neb"_neb.html command to perform a nudged
elastic band (NEB) calculation for finding the transition state.
Hi-level explanations of NEB are given with the "neb"_neb.html command
-and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
-The fix neb command must be used with the "neb" command and defines
-how inter-replica nudging forces are computed. A NEB calculation is
+and on the "Howto replica"_Howto_replica.html doc page. The fix neb
+command must be used with the "neb" command and defines how
+inter-replica nudging forces are computed. A NEB calculation is
divided in two stages. In the first stage n replicas are relaxed
toward a MEP until convergence. In the second stage, the climbing
image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
@@ -192,9 +192,9 @@ target energy.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
as invoked by the "minimize"_minimize.html command via the
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index 41d0e6438f..f6b155e2db 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -386,9 +386,10 @@ have their temperature controlled by another fix - e.g. by "fix
langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
-thermostatting and barostatting.
+See the "Howto thermostat"_Howto_thermostat.html and "Howto
+barostat"_Howto_barostat.html doc pages for a discussion of different
+ways to compute temperature and perform thermostatting and
+barostatting.
:line
@@ -484,10 +485,9 @@ the various ways to do this.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -499,8 +499,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -538,9 +538,9 @@ and barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
These fixes compute a global scalar and a global vector of quantities,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "extensive"; the vector values are "intensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
The scalar is the cumulative energy change due to the fix.
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index 1731f1f331..afb319bfa5 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index bde1818371..0e73c57e08 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 8c35b6a1a7..6bfd9d3fe2 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -81,10 +81,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -96,8 +95,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 1e590f1cb3..377e1980eb 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,10 +80,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 62b45edfd7..8b7639c4c6 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,10 +90,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 292e46f94a..0bd5153152 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -140,10 +140,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -155,8 +154,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -193,9 +192,9 @@ included in the definition of internal energy E when calculating the value
of Delta in the above equation.
These fixes compute a global scalar and a global vector of quantities,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar value calculated by
-these fixes is "extensive"; the vector values are "intensive".
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
The scalar is the cumulative energy change due to the fix.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 5f3979e36e..9c95a80d33 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,10 +105,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index d89bf19db2..0d2b797299 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -104,10 +104,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -119,8 +118,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index c4cf2cb08d..dcb25d1c73 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -115,10 +115,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -130,8 +129,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index c04c17858e..e446b27397 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -34,10 +34,9 @@ ensemble.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -49,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -59,10 +58,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index 1f31fb9679..b7fb3e922c 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,20 +35,19 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index 5f1b271546..e57417bda5 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -38,10 +38,10 @@ Dynamics, since the velocity and angular momentum are updated by the
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index 604b5391cd..d072bfa161 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,9 +24,9 @@ fix 1 all nve/body :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for body particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
-consistent with the microcanonical ensemble. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html
-doc page for more details on using body particles.
+consistent with the microcanonical ensemble. See the "Howto
+body"_Howto_body.html doc page for more details on using body
+particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 0e0c8f8ecf..1041a248d8 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 93d875bca5..68c1b42328 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 156f184dac..7343ddc429 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,10 +35,10 @@ of electrons are also updated.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt
index 2ecec83e9c..8c8c66a0da 100644
--- a/doc/src/fix_nve_limit.txt
+++ b/doc/src/fix_nve_limit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,14 +63,14 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-count of how many updates of atom's velocity/position were limited by
-the maximum distance criterion. This should be roughly the number of
-atoms so affected, except that updates occur at both the beginning and
-end of a timestep in a velocity Verlet timestepping algorithm. This
-is a cumulative quantity for the current run, but is re-initialized to
-zero each time a run is performed. The scalar value calculated by
-this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the count of how
+many updates of atom's velocity/position were limited by the maximum
+distance criterion. This should be roughly the number of atoms so
+affected, except that updates occur at both the beginning and end of a
+timestep in a velocity Verlet timestepping algorithm. This is a
+cumulative quantity for the current run, but is re-initialized to zero
+each time a run is performed. The scalar value calculated by this fix
+is "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index ac5206aa5c..dd5101489b 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,9 +24,9 @@ fix 1 all nve/line :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for line segment particles in the
group each timestep. V is volume; E is energy. This creates a system
-trajectory consistent with the microcanonical ensemble. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual for an
-overview of using line segment particles.
+trajectory consistent with the microcanonical ensemble. See "Howto
+spherical"_Howto_spherical.html doc page for an overview of using line
+segment particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index e032a7e1cc..b333d093fb 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,7 +40,7 @@ the dynamics of particles constrained to curved surfaces can be
studied. If combined with "fix langevin"_fix_langevin.html, this
generates Brownian motion of particles constrained to a curved
surface. For a list of currently supported manifolds and their
-parameters, see "manifolds"_manifolds.html.
+parameters, see the "Howto manifold"_Howto_manifold.html doc page.
Note that the particles must initially be close to the manifold in
question. If not, RATTLE will not be able to iterate until the
@@ -68,10 +68,10 @@ conserved.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt
index a0dbcc80f1..da8d16bbb7 100644
--- a/doc/src/fix_nve_noforce.txt
+++ b/doc/src/fix_nve_noforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -40,10 +40,10 @@ fcm() group function to compute the total force on the group of atoms.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 21dc6cba8a..6e259bdb8e 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,10 +65,9 @@ moment of inertia, as used in the time integration.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -80,8 +79,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -90,10 +89,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index f4b38c270b..e31185bc88 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index cee27e2fa4..ebdda19e36 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -23,10 +23,10 @@ fix 1 all nve/tri :pre
Perform constant NVE integration to update position, velocity,
orientation, and angular momentum for triangular particles in the
-group each timestep. V is volume; E is energy. This creates a
-system trajectory consistent with the microcanonical ensemble. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual for an
-overview of using triangular particles.
+group each timestep. V is volume; E is energy. This creates a system
+trajectory consistent with the microcanonical ensemble. See the
+"Howto spherical"_Howto_spherical.html doc page for an overview of
+using triangular particles.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
@@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index 49fd8217ab..e3189f8e8a 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -42,10 +42,10 @@ energy prior to this fix.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 21b900f16a..7b97637175 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -86,10 +86,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -101,8 +100,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 6a5e09ba7f..4493a89277 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,10 +85,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index a620648a46..1b4ad79166 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,9 +37,13 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
[Description:]
-This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
-canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
-For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html
+This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time
+integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
+"(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
+canonical ensemble of particles constrained to a curved surface
+(manifold). This sampling does suffer from discretization bias of
+O(dt). For a list of currently supported manifolds and their
+parameters, see the "Howto manifold"_Howto_manifold.html doc page.
:line
@@ -48,10 +52,10 @@ For a list of currently supported manifolds and their parameters, see "manifolds
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 392dbc281c..9eb5065369 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,10 +109,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 408eb1da01..0200d5cb00 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index ecf0922b79..a87e4abe67 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -96,10 +96,9 @@ thermal degrees of freedom, and the bias is added back in.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -111,8 +110,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt
index 2d85c581eb..433ceb50f2 100644
--- a/doc/src/fix_oneway.txt
+++ b/doc/src/fix_oneway.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,10 +43,10 @@ membrane, or as an implementation of Maxwell's demon.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 20ff94866e..7552bea8c5 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -135,14 +135,14 @@ fixes. This allows to set at which level of the "r-RESPA"_run_style.html
integrator a fix is adding its forces. Default is the outermost level.
This fix calculates a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy change due to this fix. The scalar value calculated
-by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix also calculates a per-atom array which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The array
-stores the order parameter Xi and normalized order parameter (0 to 1)
-for each atom. The per-atom values can be accessed on any timestep.
+various "output commands"_Howto_output.html. The array stores the
+order parameter Xi and normalized order parameter (0 to 1) for each
+atom. The per-atom values can be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index aad6c2bfaa..30e5864e3d 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,7 +150,7 @@ fix. You can use it to change the temperature compute from thermo_temp
to the one that reflects the true temperature of atoms in the group.
No global scalar or vector or per-atom quantities are stored by this
-fix for access by various "output commands"_Section_howto.html#howto_15.
+fix for access by various "output commands"_Howto_output.html.
Instead, this fix outputs its initialization information (including
mapping information) and the calculated dynamical matrices to the file
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index 38022e4c7d..b61b3f3065 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -103,14 +103,13 @@ is appropriate for most situations.
The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
as described in "(Calhoun)"_#Calhoun. In LAMMPS this is done by using
-"multi-replica feature"_Section_howto.html#howto_5 in LAMMPS, where
-each quasi-particle system is stored and simulated on a separate
-partition of processors. The following diagram illustrates this
-approach. The original system with 2 ring polymers is shown in red.
-Since each ring has 4 quasi-beads (imaginary time slices), there are 4
-replicas of the system, each running on one of the 4 partitions of
-processors. Each replica (shown in green) owns one quasi-bead in each
-ring.
+"multi-replica feature"_Howto_replica.html in LAMMPS, where each
+quasi-particle system is stored and simulated on a separate partition
+of processors. The following diagram illustrates this approach. The
+original system with 2 ring polymers is shown in red. Since each ring
+has 4 quasi-beads (imaginary time slices), there are 4 replicas of the
+system, each running on one of the 4 partitions of processors. Each
+replica (shown in green) owns one quasi-bead in each ring.
:c,image(JPG/pimd.jpg)
diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt
index 67956c8b6d..ffe1952e31 100644
--- a/doc/src/fix_planeforce.txt
+++ b/doc/src/fix_planeforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -35,9 +35,9 @@ should continue to move in the plane thereafter.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 03abc058b8..1a79c2a048 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -114,9 +114,9 @@ early or late in a timestep, i.e. at the post-force stage or at the
final-integrate stage, respectively.
No global or per-atom quantities are stored by this fix for access by
-various "output commands"_Section_howto.html#howto_15. No parameter
-of this fix can be used with the {start/stop} keywords of the
-"run"_run.html command. This fix is not invoked during "energy
+various "output commands"_Howto_output.html. No parameter of this fix
+can be used with the {start/stop} keywords of the "run"_run.html
+command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index 54f78287e0..e58d8ebc3a 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -237,9 +237,9 @@ appropriately.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index 4133d7dd57..fafe78448b 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,8 +67,8 @@ to add this magnetic potential energy to the potential energy of the system,
fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix_modify 1 energy yes :pre
-This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15.
+This fix computes a global scalar which can be accessed by various
+"output commands"_Howto_output.html.
No information about this fix is written to "binary restart
files"_restart.html.
diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt
index 9c9da8ec7b..7f47a29ba3 100644
--- a/doc/src/fix_press_berendsen.txt
+++ b/doc/src/fix_press_berendsen.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,9 +58,8 @@ to control the temperature, such as "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html or "fix
temp/berendsen"_fix_temp_berendsen.html.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
-thermostatting and barostatting.
+See the "Howto baroostat"_Howto_barostat.html doc page for a
+discussion of different ways to perform barostatting.
:line
@@ -196,7 +195,7 @@ pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
No global or per-atom quantities are stored by this fix for access by
-various "output commands"_Section_howto.html#howto_15.
+various "output commands"_Howto_output.html.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt
index cf3b542833..d23c1103d3 100644
--- a/doc/src/fix_print.txt
+++ b/doc/src/fix_print.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -73,10 +73,10 @@ where ID is replaced with the fix-ID.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 95fc2c424d..136ed6c15e 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -200,18 +200,17 @@ added classes.
:line
-:link(isotopes)
-Example for using per-atom masses with TIP4P water to study isotope
-effects. When setting up simulations with the "TIP4P pair
-styles"_Section_howto.html#howto_8 for water, you have to provide
-exactly one atom type each to identify the water oxygen and hydrogen
+:link(isotopes) Example for using per-atom masses with TIP4P water to
+study isotope effects. When setting up simulations with the "TIP4P
+pair styles"_Howto_tip4p.html for water, you have to provide exactly
+one atom type each to identify the water oxygen and hydrogen
atoms. Since the atom mass is normally tied to the atom type, this
makes it impossible to study multiple isotopes in the same simulation.
With {fix property/atom rmass} however, the per-type masses are
replaced by per-atom masses. Asumming you have a working input deck
-for regular TIP4P water, where water oxygen is atom type 1 and
-water hydrogen is atom type 2, the following lines of input script
-convert this to using per-atom masses:
+for regular TIP4P water, where water oxygen is atom type 1 and water
+hydrogen is atom type 2, the following lines of input script convert
+this to using per-atom masses:
fix Isotopes all property/atom rmass ghost yes
set type 1 mass 15.9994
@@ -247,12 +246,12 @@ command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
-None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix. No global or per-atom quantities are stored by this fix for
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 787940d9eb..5e0c0369a5 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index f10f607a9b..a4e0eb3937 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -83,10 +83,10 @@ Examples for how to do this are in the {examples/python} folder.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index 2c116fb0f8..e96bd97f45 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,10 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_
The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of <i>etot</i>. This global scalar and the
vector of 5 quantities can be accessed by various "output
-commands"_Section_howto.html#howto_15. It is worth noting that the
-temp keyword under the "thermo_style"_thermo_style.html command print
-the instantaneous classical temperature <i>T</i><sup>cl</sup> as
-described in the command "fix qtb"_fix_qtb.html.
+commands"_Howto_output.html. It is worth noting that the temp keyword
+under the "thermo_style"_thermo_style.html command print the
+instantaneous classical temperature <i>T</i><sup>cl</sup> as described
+in the command "fix qtb"_fix_qtb.html.
:line
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index 194361e990..27fb613ef9 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,9 +179,8 @@ parameters. See the examples/qeq directory for some examples.
No information about these fixes is written to "binary restart
files"_restart.html. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command.
Thexe fixes are invoked during "energy minimization"_minimize.html.
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 7f82404127..99e86df030 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,10 +62,9 @@ equilibration calculation is written to the specified file.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -93,9 +92,9 @@ integrator the fix is performing charge equilibration. Default is
the outermost level.
This fix produces a per-atom vector which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The vector stores the
-gradient of the charge on each atom. The per-atom values be accessed
-on any timestep.
+"output commands"_Howto_output.html. The vector stores the gradient
+of the charge on each atom. The per-atom values be accessed on any
+timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index 18450c7cd5..cf16daf847 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -70,8 +70,8 @@ the {qeq/reax/omp} style. Otherwise they are processed separately.
No information about this fix is written to "binary restart
files"_restart.html. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command.
This fix is invoked during "energy minimization"_minimize.html.
@@ -80,10 +80,9 @@ This fix is invoked during "energy minimization"_minimize.html.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 1b4a850a42..657ee84181 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,9 +46,9 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of this fix can be used
+with the {start/stop} keywords of the "run"_run.html command. This
+fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 07a6af39ba..5b212934a9 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 3f8f237de1..49d61f4db8 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,17 +62,17 @@ version, but will also take longer to write.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+hardware, as discussed in "Speed"_Speed.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -87,7 +87,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section_accelerate"_Section_accelerate.html of the manual for
+See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 7c920791f7..5be1c46230 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -116,8 +116,8 @@ are relevant to this fix.
This fix computes both a global vector of length 2 and a per-atom
vector, either of which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The values in the global
-vector are "intensive".
+commands"_Howto_output.html. The values in the global vector are
+"intensive".
The 2 values in the global vector are as follows:
@@ -139,7 +139,7 @@ minimization"_minimize.html.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+hardware, as discussed in "Speed"_Speed.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@@ -154,7 +154,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section_accelerate"_Section_accelerate.html of the manual for
+See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt
index 342bed4251..cfac756cd1 100644
--- a/doc/src/fix_recenter.txt
+++ b/doc/src/fix_recenter.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -94,13 +94,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-distance the group is moved by fix recenter.
+"output commands"_Howto_output.html. The scalar is the distance the
+group is moved by fix recenter.
This fix also computes global 3-vector which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The 3
-quantities in the vector are xyz components of displacement applied to
-the group of atoms by the fix.
+various "output commands"_Howto_output.html. The 3 quantities in the
+vector are xyz components of displacement applied to the group of
+atoms by the fix.
The scalar and vector values calculated by this fix are "extensive".
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index 9de63defb7..2edc7e3296 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -187,8 +187,8 @@ added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
-This fix computes a global scalar and a global vector of length 3, which
-can be accessed by various "output commands"_Section_howto.html#howto_15.
+This fix computes a global scalar and a global vector of length 3,
+which can be accessed by various "output commands"_Howto_output.html.
The scalar is the total potential energy for {all} the restraints as
discussed above. The vector values are the sum of contributions to the
following individual categories:
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 2db920ac4b..68cce694e9 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 8d803ac6da..d5e3b01668 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -690,10 +690,9 @@ rigid/nvt.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -705,8 +704,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -746,29 +745,29 @@ computed early or late in a timestep, i.e. at the post-force stage or
at the final-integrate stage or the timestep, respectively.
The 2 NVE rigid fixes compute a global scalar which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The scalar
-value calculated by these fixes is "intensive". The scalar is the
-current temperature of the collection of rigid bodies. This is
-averaged over all rigid bodies and their translational and rotational
-degrees of freedom. The translational energy of a rigid body is 1/2 m
-v^2, where m = total mass of the body and v = the velocity of its
-center of mass. The rotational energy of a rigid body is 1/2 I w^2,
-where I = the moment of inertia tensor of the body and w = its angular
-velocity. Degrees of freedom constrained by the {force} and {torque}
-keywords are removed from this calculation, but only for the {rigid}
-and {rigid/nve} fixes.
+various "output commands"_Howto_output.html. The scalar value
+calculated by these fixes is "intensive". The scalar is the current
+temperature of the collection of rigid bodies. This is averaged over
+all rigid bodies and their translational and rotational degrees of
+freedom. The translational energy of a rigid body is 1/2 m v^2, where
+m = total mass of the body and v = the velocity of its center of mass.
+The rotational energy of a rigid body is 1/2 I w^2, where I = the
+moment of inertia tensor of the body and w = its angular velocity.
+Degrees of freedom constrained by the {force} and {torque} keywords
+are removed from this calculation, but only for the {rigid} and
+{rigid/nve} fixes.
The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The scalar value calculated by these fixes is "extensive". The scalar
-is the cumulative energy change due to the thermostatting and
-barostatting the fix performs.
+accessed by various "output commands"_Howto_output.html. The scalar
+value calculated by these fixes is "extensive". The scalar is the
+cumulative energy change due to the thermostatting and barostatting
+the fix performs.
All of the {rigid} styles (not the {rigid/small} styles) compute a
global array of values which can be accessed by various "output
-commands"_Section_howto.html#howto_15. Similar information about the
-bodies defined by the {rigid/small} styles can be accessed via the
-"compute rigid/local"_compute_rigid_local.html command.
+commands"_Howto_output.html. Similar information about the bodies
+defined by the {rigid/small} styles can be accessed via the "compute
+rigid/local"_compute_rigid_local.html command.
The number of rows in the array is equal to the number of rigid
bodies. The number of columns is 15. Thus for each rigid body, 15
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index 0810a34740..d39e41e922 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,10 +186,9 @@ read_data data.dpd fix foo_SPECIES NULL Species
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt
index 814e17b8e9..60708cd696 100644
--- a/doc/src/fix_saed_vtk.txt
+++ b/doc/src/fix_saed_vtk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index f5be0f93a5..14fceb7b49 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,12 +65,12 @@ to it.
:line
-Styles with a r {kk} suffix are functionally the same as the
-corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
The region keyword is also supported by Kokkos, but a Kokkos-enabled
region must be used. See the region "region"_region.html command for
@@ -85,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -103,10 +103,10 @@ so that setforce values are not counted multiple times. Default is to
to override forces at the outermost level.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms before the forces on individual
-atoms are changed by the fix. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms before the forces on individual atoms are
+changed by the fix. The vector values calculated by this fix are
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 46452a1f7e..ea38de41cd 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,12 +145,12 @@ info of atoms in the molecule.
:line
-Styles with a suffix are functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -162,8 +162,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -195,10 +195,9 @@ No information about these fixes is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of these fixes
-can be used with the {start/stop} keywords of the "run"_run.html
-command. These fixes are not invoked during "energy
-minimization"_minimize.html.
+commands"_Howto_output.html. No parameter of these fixes can be used
+with the {start/stop} keywords of the "run"_run.html command. These
+fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 24726d8610..33db2bf7cc 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -56,10 +56,9 @@ examples/USER/dpd directory.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -71,8 +70,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index cb4a40f0fd..2f083dafc3 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,12 +111,12 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a vector list of 7 quantities, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. The
-quantities in the vector are in this order: the x-, y-, and
-z-component of the pulling force, the total force in direction of the
-pull, the equilibrium distance of the spring, the distance between the
-two reference points, and finally the accumulated PMF (the sum of
-pulling forces times displacement).
+by various "output commands"_Howto_output.html. The quantities in the
+vector are in this order: the x-, y-, and z-component of the pulling
+force, the total force in direction of the pull, the equilibrium
+distance of the spring, the distance between the two reference points,
+and finally the accumulated PMF (the sum of pulling forces times
+displacement).
The force is the total force on the group of atoms by the spring. In
the case of the {couple} style, it is the force on the fix group
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 86b7363300..740b10559d 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index 17c9c0f400..cd676a51ce 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 28e38c7f97..7f16b4b7ce 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index 2cba001267..aeabf18768 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index f93a7d0965..6634751d6a 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -66,9 +66,9 @@ None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
-by various "output commands"_Section_howto.html#howto_15. This is the
-total force on the group of atoms. The vector values calculated by this
-fix are "extensive".
+by various "output commands"_Howto_output.html. This is the total
+force on the group of atoms. The vector values calculated by this fix
+are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index feb65b2312..a19b2c4cfb 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt
index 014a43aacc..690fc3e67c 100644
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -105,19 +105,19 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-spring energy = 0.5 * K * r^2.
+"output commands"_Howto_output.html. The scalar is the spring energy
+= 0.5 * K * r^2.
This fix also computes global 4-vector which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The first 3
-quantities in the vector are xyz components of the total force added
-to the group of atoms by the spring. In the case of the {couple}
-style, it is the force on the fix group (group-ID) or the negative of
-the force on the 2nd group (group-ID2). The 4th quantity in the
-vector is the magnitude of the force added by the spring, as a
-positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This
-sign convention can be useful when using the spring force to compute a
-potential of mean force (PMF).
+various "output commands"_Howto_output.html. The first 3 quantities
+in the vector are xyz components of the total force added to the group
+of atoms by the spring. In the case of the {couple} style, it is the
+force on the fix group (group-ID) or the negative of the force on the
+2nd group (group-ID2). The 4th quantity in the vector is the
+magnitude of the force added by the spring, as a positive value if
+(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention
+can be useful when using the spring force to compute a potential of
+mean force (PMF).
The scalar and vector values calculated by this fix are "extensive".
diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt
index 7630a009dd..9d4e8afd09 100644
--- a/doc/src/fix_spring_chunk.txt
+++ b/doc/src/fix_spring_chunk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,8 +60,8 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
+"output commands"_Howto_output.html. The scalar is the energy of all
+the springs, i.e. 0.5 * K * r^2 per-spring.
The scalar value calculated by this fix is "extensive".
diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt
index bff6b38e7e..b252163958 100644
--- a/doc/src/fix_spring_rg.txt
+++ b/doc/src/fix_spring_rg.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,10 @@ the time the fix is specified, and that value is used as the target.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
The "fix_modify"_fix_modify.html {respa} option is supported by this
fix. This allows to set at which level of the "r-RESPA"_run_style.html
diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt
index 68961a1512..0ac1d5eecb 100644
--- a/doc/src/fix_spring_self.txt
+++ b/doc/src/fix_spring_self.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,10 +57,10 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is an
-energy which is the sum of the spring energy for each atom, where the
-per-atom energy is 0.5 * K * r^2. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is an energy which is
+the sum of the spring energy for each atom, where the per-atom energy
+is 0.5 * K * r^2. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 4e190234fd..893557b9ac 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -341,11 +341,11 @@ are relevant to this fix.
This fix tabulates several SRD statistics which are stored in a vector
of length 12, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The vector values calculated
-by this fix are "intensive", meaning they do not scale with the size
-of the simulation. Technically, the first 8 do scale with the size of
-the simulation, but treating them as intensive means they are not
-scaled when printed as part of thermodynamic output.
+commands"_Howto_output.html. The vector values calculated by this fix
+are "intensive", meaning they do not scale with the size of the
+simulation. Technically, the first 8 do scale with the size of the
+simulation, but treating them as intensive means they are not scaled
+when printed as part of thermodynamic output.
These are the 12 quantities. All are values for the current timestep,
except for quantity 5 and the last three, each of which are
diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt
index c988431f9d..33ebc962d5 100644
--- a/doc/src/fix_store_force.txt
+++ b/doc/src/fix_store_force.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -26,7 +26,7 @@ timestep when the fix is invoked, as described below. This is useful
for storing forces before constraints or other boundary conditions are
computed which modify the forces, so that unmodified forces can be
"written to a dump file"_dump.html or accessed by other "output
-commands"_Section_howto.html#howto_15 that use per-atom quantities.
+commands"_Howto_output.html that use per-atom quantities.
This fix is invoked at the point in the velocity-Verlet timestepping
immediately after "pair"_pair_style.html, "bond"_bond_style.html,
@@ -54,9 +54,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a per-atom array which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The number of columns
-for each atom is 3, and the columns store the x,y,z forces on each
-atom. The per-atom values be accessed on any timestep.
+"output commands"_Howto_output.html. The number of columns for each
+atom is 3, and the columns store the x,y,z forces on each atom. The
+per-atom values be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt
index df694fb97b..df05adc5b9 100644
--- a/doc/src/fix_store_state.txt
+++ b/doc/src/fix_store_state.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,8 +68,7 @@ Define a fix that stores attributes for each atom in the group at the
time the fix is defined. If {N} is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
-"output commands"_Section_howto.html#howto_15 that take fixes as
-inputs.
+"output commands"_Howto_output.html that take fixes as inputs.
If {N} is not zero, then the attributes will be updated every {N}
steps.
@@ -108,9 +107,8 @@ fix.
If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The per-atom values be
-accessed on any timestep.
+can be accessed by various "output commands"_Howto_output.html. The
+per-atom values be accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
index b470babab7..ade64d2056 100644
--- a/doc/src/fix_surface_global.txt
+++ b/doc/src/fix_surface_global.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt
index 6944860e14..c1f1626782 100644
--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -68,8 +68,8 @@ be used on atoms that also have their temperature controlled by
another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
@@ -126,9 +126,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt
index 4129ad73c8..e50f821bfe 100644
--- a/doc/src/fix_temp_csvr.txt
+++ b/doc/src/fix_temp_csvr.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -76,8 +76,8 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
These fixes compute a temperature each timestep. To do this, the fix
@@ -135,9 +135,9 @@ the {start} and {stop} keywords of the "run"_run.html command. See the
These fixes are not invoked during "energy minimization"_minimize.html.
These fixes compute a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to the fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to the fix. The scalar value calculated by this fix
+is "extensive".
[Restrictions:]
diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt
index eff25297c1..5640317f1c 100644
--- a/doc/src/fix_temp_rescale.txt
+++ b/doc/src/fix_temp_rescale.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -75,8 +75,8 @@ be used on atoms that also have their temperature controlled by
another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
-See "this howto section"_Section_howto.html#howto_16 of the manual for
-a discussion of different ways to compute temperature and perform
+See the "Howto thermostat"_Howto_thermostat.html doc page for a
+discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
@@ -133,9 +133,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index f87c1a2192..0e08e4f1e8 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,9 +51,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index 3c81d62ee0..ddfa462619 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 0353c095b2..86fc6f2c72 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,9 +108,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative kinetic energy transferred between the bottom and middle
-of the simulation box (in the {edim} direction) is stored as a scalar
+"output commands"_Howto_output.html. The scalar is the cumulative
+kinetic energy transferred between the bottom and middle of the
+simulation box (in the {edim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined
and accumulates thereafter, once every N steps. The units of the
quantity are energy; see the "units"_units.html command for details.
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index 191f9e7c6b..afe5373220 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -121,13 +121,12 @@ fix to add the energy stored in the per-atom springs to the system's
potential energy as part of "thermodynamic output"_thermo_style.html.
This fix computes a global scalar and a global vector quantities which
-can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar is an energy which
-is the sum of the spring energy for each atom, where the per-atom
-energy is 0.5 * k * r^2. The vector has 2 positions, the first one is
-the coupling parameter lambda and the second one is the time
-derivative of lambda. The scalar and vector values calculated by this
-fix are "extensive".
+can be accessed by various "output commands"_Howto_output.html. The
+scalar is an energy which is the sum of the spring energy for each
+atom, where the per-atom energy is 0.5 * k * r^2. The vector has 2
+positions, the first one is the coupling parameter lambda and the
+second one is the time derivative of lambda. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index 71d8d2c767..c2541692f5 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,8 +90,7 @@ For more information about TMD, see "(Schlitter1)"_#Schlitter1 and
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15.
+by this fix for access by various "output commands"_Howto_output.html.
This fix can ramp its rho parameter over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 48dfd254a0..6001def581 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -272,18 +272,17 @@ None of the "fix_modify"_fix_modify.html options are relevant to these
fixes.
Both fixes compute 2 output quantities stored in a vector of length 2,
-which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The first quantity is the
-total energy of the electronic subsystem. The second quantity is the
-energy transferred from the electronic to the atomic subsystem on that
-timestep. Note that the velocity verlet integrator applies the fix ttm
-forces to the atomic subsystem as two half-step velocity updates: one
-on the current timestep and one on the subsequent timestep.
-Consequently, the change in the atomic subsystem energy is lagged by
-half a timestep relative to the change in the electronic subsystem
-energy. As a result of this, users may notice slight fluctuations in
-the sum of the atomic and electronic subsystem energies reported at
-the end of the timestep.
+which can be accessed by various "output commands"_Howto_output.html.
+The first quantity is the total energy of the electronic
+subsystem. The second quantity is the energy transferred from the
+electronic to the atomic subsystem on that timestep. Note that the
+velocity verlet integrator applies the fix ttm forces to the atomic
+subsystem as two half-step velocity updates: one on the current
+timestep and one on the subsequent timestep. Consequently, the change
+in the atomic subsystem energy is lagged by half a timestep relative
+to the change in the electronic subsystem energy. As a result of this,
+users may notice slight fluctuations in the sum of the atomic and
+electronic subsystem energies reported at the end of the timestep.
The vector values calculated are "extensive".
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index 60a34a26c9..b4e8472591 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt
index 385d24cff1..e1bfbe5738 100644
--- a/doc/src/fix_vector.txt
+++ b/doc/src/fix_vector.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -37,7 +37,7 @@ simply store them. For a single specified value, the values are
stored as a global vector of growing length. For multiple specified
values, they are stored as rows in a global array, whose number of
rows is growing. The resulting vector or array can be used by other
-"output commands"_Section_howto.html#howto_15.
+"output commands"_Howto_output.html.
One way to to use this command is to accumulate a vector that is
time-integrated using the "variable trap()"_variable.html function.
@@ -127,9 +127,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global vector or global array which can be
-accessed by various "output commands"_Section_howto.html#howto_15.
-The values can only be accessed on timesteps that are multiples of
-{Nevery}.
+accessed by various "output commands"_Howto_output.html. The values
+can only be accessed on timesteps that are multiples of {Nevery}.
A vector is produced if only a single input value is specified.
An array is produced if multiple input values are specified.
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index f6603be624..934da3efdd 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -100,13 +100,12 @@ accurately infer a viscosity and should try increasing the Nevery
parameter.
An alternative method for calculating a viscosity is to run a NEMD
-simulation, as described in "Section
-6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations
-deform the simulation box via the "fix deform"_fix_deform.html
-command. Thus they cannot be run on a charged system using a "PPPM
-solver"_kspace_style.html since PPPM does not currently support
-non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
-thus it does not suffer from this limitation.
+simulation, as described on the "Howto nemd"_Howto_nemd.html doc page.
+NEMD simulations deform the simulation box via the "fix
+deform"_fix_deform.html command. Thus they cannot be run on a charged
+system using a "PPPM solver"_kspace_style.html since PPPM does not
+currently support non-orthogonal boxes. Using fix viscosity keeps the
+box orthogonal; thus it does not suffer from this limitation.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -115,13 +114,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative momentum transferred between the bottom and middle of the
-simulation box (in the {pdim} direction) is stored as a scalar
-quantity by this fix. This quantity is zeroed when the fix is defined
-and accumulates thereafter, once every N steps. The units of the
-quantity are momentum = mass*velocity. The scalar value calculated by
-this fix is "intensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+momentum transferred between the bottom and middle of the simulation
+box (in the {pdim} direction) is stored as a scalar quantity by this
+fix. This quantity is zeroed when the fix is defined and accumulates
+thereafter, once every N steps. The units of the quantity are
+momentum = mass*velocity. The scalar value calculated by this fix is
+"intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt
index 9c30e40249..c5a3ede0b2 100644
--- a/doc/src/fix_viscous.txt
+++ b/doc/src/fix_viscous.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,9 +82,9 @@ easily be used as a thermostat.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
The "fix_modify"_fix_modify.html {respa} option is supported by this
fix. This allows to set at which level of the "r-RESPA"_run_style.html
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index e814c89a07..2ac59d9588 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -263,14 +263,14 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global vector of
forces, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. Note that the scalar energy is
-the sum of interactions with all defined walls. If you want the
-energy on a per-wall basis, you need to use multiple fix wall
-commands. The length of the vector is equal to the number of walls
-defined by the fix. Each vector value is the normal force on a
-specific wall. Note that an outward force on a wall will be a
-negative value for {lo} walls and a positive value for {hi} walls.
-The scalar and vector values calculated by this fix are "extensive".
+commands"_Howto_output.html. Note that the scalar energy is the sum
+of interactions with all defined walls. If you want the energy on a
+per-wall basis, you need to use multiple fix wall commands. The
+length of the vector is equal to the number of walls defined by the
+fix. Each vector value is the normal force on a specific wall. Note
+that an outward force on a wall will be a negative value for {lo}
+walls and a positive value for {hi} walls. The scalar and vector
+values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
@@ -288,10 +288,9 @@ option for this fix.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -303,8 +302,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index 4ba16b56c7..0946a85131 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,8 +43,8 @@ particles in the group interact with the wall when they are close
enough to touch it. The nature of the interaction between the wall
and the polygon particles is the same as that between the polygon
particles themselves, which is similar to a Hookean potential. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body particles.
+the "Howto body"_Howto_body.html doc page for more details on using
+body particles.
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
those specified with the "pair_style
@@ -83,9 +83,9 @@ to the derivative of this expression.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index c937cbdbbc..407cf9fb33 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -43,8 +43,8 @@ All particles in the group interact with the wall when they are close
enough to touch it. The nature of the interaction between the wall
and the polygon particles is the same as that between the polygon
particles themselves, which is similar to a Hookean potential. See
-"Section 6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body particles.
+the "Howto body"_Howto_body.html doc page for more details on using
+body particles.
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
those specified with the "pair_style
@@ -82,9 +82,9 @@ to the derivative of this expression.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index f141a19405..ae16ca40d2 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 5f1679604e..6c2769fc12 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -148,9 +148,9 @@ uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 92fb042194..187214c1a3 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -180,9 +180,9 @@ region with a different region ID.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
-access by various "output commands"_Section_howto.html#howto_15. No
-parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command. This fix is not invoked during "energy
+access by various "output commands"_Howto_output.html. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index 4d7756c237..eecf69ebf2 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -91,10 +91,10 @@ define the lattice spacings.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 954ec65bf6..78be84eb63 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -130,10 +130,9 @@ position = c0 + A (1 - cos(omega*delta)) :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
@@ -155,10 +154,10 @@ more instructions on how to use the accelerated styles effectively.
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt
index 9700545dc9..559a2f0d89 100644
--- a/doc/src/fix_wall_region.txt
+++ b/doc/src/fix_wall_region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -156,12 +156,11 @@ integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar energy and a global 3-length vector
of forces, which can be accessed by various "output
-commands"_Section_howto.html#howto_15. The scalar energy is the sum
-of energy interactions for all particles interacting with the wall
-represented by the region surface. The 3 vector quantities are the
-x,y,z components of the total force acting on the wall due to the
-particles. The scalar and vector values calculated by this fix are
-"extensive".
+commands"_Howto_output.html. The scalar energy is the sum of energy
+interactions for all particles interacting with the wall represented
+by the region surface. The 3 vector quantities are the x,y,z
+components of the total force acting on the wall due to the particles.
+The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt
index c465896d37..3a50c45ab7 100644
--- a/doc/src/fix_wall_srd.txt
+++ b/doc/src/fix_wall_srd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -166,9 +166,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
-various "output commands"_Section_howto.html#howto_15. The number of
-rows in the array is equal to the number of walls defined by the fix.
-The number of columns is 3, for the x,y,z components of force on each
+various "output commands"_Howto_output.html. The number of rows in
+the array is equal to the number of walls defined by the fix. The
+number of columns is 3, for the x,y,z components of force on each
wall.
Note that an outward normal force on a wall will be a negative value
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 9510217d02..7a45ed8086 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -168,6 +168,8 @@ Fixes :h1
fix_viscosity
fix_viscous
fix_wall
+ fix_wall_body_polygon
+ fix_wall_body_polyhedron
fix_wall_ees
fix_wall_gran
fix_wall_gran_region
diff --git a/doc/src/group.txt b/doc/src/group.txt
index dddb0459e3..8472677372 100644
--- a/doc/src/group.txt
+++ b/doc/src/group.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 94d188399b..242d6a69a4 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/if.txt b/doc/src/if.txt
index 52fad5aea7..513e451034 100644
--- a/doc/src/if.txt
+++ b/doc/src/if.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -65,9 +65,9 @@ above.
NOTE: If a command itself requires a quoted argument (e.g. a
"print"_print.html command), then double and single quotes can be used
and nested in the usual manner, as in the examples above and below.
-See "Section 3.2"_Section_commands.html#cmd_2 of the manual for
-more details on using quotes in arguments. Only one of level of
-nesting is allowed, but that should be sufficient for most use cases.
+The "Commands parse"_Commands_parse.html doc page has more details on
+using quotes in arguments. Only one of level of nesting is allowed,
+but that should be sufficient for most use cases.
Note that by using the line continuation character "&", the if command
can be spread across many lines, though it is still a single command:
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index 14ec6258de..c38f73c64d 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -87,10 +87,9 @@ radians internally; hence the units of M are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -102,8 +101,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt
index 5c01a23ae9..8ed65f9535 100644
--- a/doc/src/improper_coeff.txt
+++ b/doc/src/improper_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command.
Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 138a6a1650..04aa45255c 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ X0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index 5f69eccc60..d01faf2885 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -54,10 +54,9 @@ n (0,1,2,3,4,6) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -69,8 +68,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 7d49d17c97..93235fe601 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index f9062da207..78cc1b3f76 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -48,10 +48,9 @@ all (integer >= 0) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index bb17e5a641..f398dc425f 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,10 +58,9 @@ internally; hence the units of K are in energy/radian^2.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -73,8 +72,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 0c2beaef18..42afbe8577 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 34683ca2bb..2c0f2f0af8 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt
index af9964c743..f97af101fc 100644
--- a/doc/src/improper_none.txt
+++ b/doc/src/improper_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index c02d392474..60bbca170a 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -57,10 +57,9 @@ theta0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -72,8 +71,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 861701590f..3d29b28ec4 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html
command.
Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution. The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution. The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style zero"_improper_zero.html - topology but no interactions
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index d6df9ee6cc..b05cf4b181 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -22,7 +22,7 @@ improper_coeff 1 100.0 180.0 :pre
The {umbrella} improper style uses the following potential, which is
commonly referred to as a classic inversion and used in the
-"DREIDING"_Section_howto.html#howto_4 force field:
+"DREIDING"_Howto_bioFF.html force field:
:c,image(Eqs/improper_umbrella.jpg)
@@ -51,10 +51,9 @@ omega0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt
index 2a298573d5..f3f3485b57 100644
--- a/doc/src/improper_zero.txt
+++ b/doc/src/improper_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/include.txt b/doc/src/include.txt
index 95d08db352..c114056313 100644
--- a/doc/src/include.txt
+++ b/doc/src/include.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/info.txt b/doc/src/info.txt
index d5b5bd97b9..99211de4fb 100644
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index 4e3799f7b1..b5afeb6559 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 6d27bb7076..dd7b1e8dea 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -285,15 +285,15 @@ performance and accuracy in the results is obtained when these values
are different.
The {disp/auto} option controls whether the pppm/disp is allowed to
-generate PPPM parameters automatically. If set to {no}, parameters have
-to be specified using the {gewald/disp}, {mesh/disp},
-{force/disp/real} or {force/disp/kspace} keywords, or
-the code will stop with an error message. When this option is set to
-{yes}, the error message will not appear and the simulation will start.
-For a typical application, using the automatic parameter generation
-will provide simulations that are either inaccurate or slow. Using this
-option is thus not recommended. For guidelines on how to obtain good
-parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+generate PPPM parameters automatically. If set to {no}, parameters
+have to be specified using the {gewald/disp}, {mesh/disp},
+{force/disp/real} or {force/disp/kspace} keywords, or the code will
+stop with an error message. When this option is set to {yes}, the
+error message will not appear and the simulation will start. For a
+typical application, using the automatic parameter generation will
+provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the "Howto dispersion"_Howto_dispersion.html doc page.
[Restrictions:] none
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 4f27c9aa78..55ad4ab610 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,8 +145,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive).
However, for low relative accuracy, the staggered PPPM mesh size may
be essentially the same as for regular PPPM, which means the method
will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see
-"Section 5"_Section_accelerate.html.
+For more details and timings, see the "Speed tips"_Speed_tips.html doc
+page.
NOTE: Using {pppm/stagger} may not give the same increase in the
accuracy of energy and pressure as it does in forces, so some caution
@@ -161,15 +161,16 @@ similar to the {ewald/disp} style. The 1/r^6 capability means
that Lennard-Jones or Buckingham potentials can be used without a cutoff,
i.e. they become full long-range potentials.
-For these styles, you will possibly want to adjust the default choice of
-parameters by using the "kspace_modify"_kspace_modify.html command.
+For these styles, you will possibly want to adjust the default choice
+of parameters by using the "kspace_modify"_kspace_modify.html command.
This can be done by either choosing the Ewald and grid parameters, or
by specifying separate accuracies for the real and kspace
-calculations. When not making any settings, the simulation will stop with
-an error message. Further information on the influence of the parameters
-and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012,
-"(Isele-Holder2)"_#Isele-Holder2013 and the
-"How-To"_Section_howto.html#howto_24 discussion.
+calculations. When not making any settings, the simulation will stop
+with an error message. Further information on the influence of the
+parameters and how to choose them is described in
+"(Isele-Holder)"_#Isele-Holder2012,
+"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
+dispersion"_Howto_dispersion.html doc page.
:line
@@ -267,10 +268,9 @@ relative RMS error.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
More specifically, the {pppm/gpu} style performs charge assignment and
force interpolation calculations on the GPU. These processes are
@@ -291,8 +291,8 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/label.txt b/doc/src/label.txt
index c6a573141b..adab44188c 100644
--- a/doc/src/label.txt
+++ b/doc/src/label.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 4274ef48b3..c0ca357f21 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -1,19 +1,78 @@
#HTMLDOC 1.8.28
-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
Manual.html
-Section_intro.html
+Intro.html
+Intro_overview.html
+Intro_features.html
+Intro_nonfeatures.html
+Intro_opensource.html
+Intro_authors.html
+Intro_website.html
Section_start.html
-Section_commands.html
-Section_packages.html
-Section_accelerate.html
-accelerate_gpu.html
-accelerate_intel.html
-accelerate_kokkos.html
-accelerate_omp.html
-accelerate_opt.html
-Section_howto.html
+Commands.html
+Commands_input.html
+Commands_parse.html
+Commands_structure.html
+Commands_category.html
+Commands_all.html
+Commands_fix.html
+Commands_compute.html
+Commands_pair.html
+Commands_bond.html
+Commands_kspace.html
+Packages.html
+Packages_standard.html
+Packages_user.html
+Packages_details.html
+Speed.html
+Speed_bench.html
+Speed_measure.html
+Speed_tips.html
+Speed_packages.html
+Speed_gpu.html
+Speed_intel.html
+Speed_kokkos.html
+Speed_omp.html
+Speed_opt.html
+Speed_compare.html
+Howto.html
+Howto_github.html
+Howto_pylammps.html
+Howto_bash.html
+Howto_restart.html
+Howto_viz.html
+Howto_multiple.html
+Howto_replica.html
+Howto_library.html
+Howto_couple.html
+Howto_output.html
+Howto_chunk.html
+Howto_2d.html
+Howto_triclinic.html
+Howto_walls.html
+Howto_nemd.html
+Howto_granular.html
+Howto_spherical.html
+Howto_dispersion.html
+Howto_temperature.html
+Howto_thermostat.html
+Howto_barostat.html
+Howto_elastic.html
+Howto_kappa.html
+Howto_viscosity.html
+Howto_diffusion.html
+Howto_bioFF.html
+Howto_tip3p.html
+Howto_tip4p.html
+Howto_spc.html
+Howto_body.html
+Howto_polarizable.html
+Howto_coreshell.html
+Howto_drude.html
+Howto_drude2.html
+Howto_manifold.html
+Howto_spins.html
Examples.html
-Section_perf.html
Tools.html
Modify.html
Modify_overview.html
@@ -47,17 +106,6 @@ Errors_common.html
Errors_bugs.html
Errors_messages.html
Errors_warnings.html
-Section_history.html
-
-lammps_tutorials.html
-tutorial_bash_on_windows.html
-tutorial_drude.html
-tutorial_github.html
-tutorial_pylammps.html
-
-lammps_support.html
-body.html
-manifolds.html
lammps_commands.html
atom_modify.html
diff --git a/doc/src/lammps_support.txt b/doc/src/lammps_support.txt
deleted file mode 100644
index fa460ce6c2..0000000000
--- a/doc/src/lammps_support.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-
-Supporting Information :h1
-
-This section of the manual contains supporting information that
-is not documenting individual commands but general concepts and
-supporting information about entities like body particles or
-manifolds.
diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt
deleted file mode 100644
index 5ceda65b60..0000000000
--- a/doc/src/lammps_tutorials.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-
-Tutorials :h2
-
-The following pages contain some in-depth tutorials for
-selected topics, that did not fit into any other place
-in the manual.
diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt
index 7a90df1f5d..6f16dc5432 100644
--- a/doc/src/lattice.txt
+++ b/doc/src/lattice.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 92bb12e6db..7603768519 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/mass.txt b/doc/src/mass.txt
index 4b75132ccf..c693963044 100644
--- a/doc/src/mass.txt
+++ b/doc/src/mass.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt
index 73d142f5fa..9408eea167 100644
--- a/doc/src/min_modify.txt
+++ b/doc/src/min_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
index 245ac5864c..4948a34864 100644
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
min_style command :h3
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index a3f2c5d0bf..910fc7f821 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt
index cd9ecce42c..88c6292d8b 100644
--- a/doc/src/molecule.txt
+++ b/doc/src/molecule.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -176,9 +176,8 @@ LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
"special_bonds"_special_bonds.html command for more details. One
reason to list the special bond info explicitly is for the
-"thermalized Drude oscillator model"_tutorial_drude.html which treats
-the bonds between nuclear cores and Drude electrons in a different
-manner.
+"thermalized Drude oscillator model"_Howto_drude.html which treats the
+bonds between nuclear cores and Drude electrons in a different manner.
NOTE: Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 56f075c301..fbd77ee329 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -56,9 +56,8 @@ Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on just one or two
processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See
-"Section 6.5"_Section_howto.html#howto_5 of the manual for further
-discussion.
+would see with one or more physical processors per replica. See the
+"Howto replica"_Howto_replica.html doc page for further discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The minimizer uses whatever
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index c4544cb29b..6c4218cff5 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 062f79a5bb..7c7e7b05e5 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/newton.txt b/doc/src/newton.txt
index a3e7f4fa91..fd7b536920 100644
--- a/doc/src/newton.txt
+++ b/doc/src/newton.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 08f73b896c..5a0b30b2a7 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 5fd42f67d3..c2e7345bb7 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -149,9 +149,9 @@ the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist
across multiple invocations.
-See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
-manual for more details about using the various accelerator packages
-for speeding up LAMMPS simulations.
+See the "Speed packages"_Speed_packages.html doc page for more details
+about using the various accelerator packages for speeding up LAMMPS
+simulations.
:line
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 9d2a48dcbc..382a97ecea 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -125,10 +125,9 @@ array tabulated with a scaling by r.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -140,8 +139,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 402e537dad..34f9900139 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -58,11 +58,11 @@ and input files are provided in the examples/USER/misc/agni directory.
:line
Styles with {omp} suffix is functionally the same as the corresponding
-style without the suffix. They have been optimized to run faster, depending
-on your available hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated style takes the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+style without the suffix. They have been optimized to run faster,
+depending on your available hardware, as discussed on the "Speed
+packages"_Speed_packages.html doc page. The accelerated style takes
+the same arguments and should produce the same results, except for
+round-off and precision issues.
The accelerated style is part of the USER-OMP. They are only enabled if
LAMMPS was built with those packages. See the "Making
@@ -73,8 +73,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 1aa017f278..94a692226d 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -176,10 +176,9 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -191,8 +190,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index b798f7d128..2e961a1356 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -49,9 +49,8 @@ The {atm} potential is typically used in combination with a two-body
potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
-The potential is calculated if atoms J and K are in the
-"neighbor list"_neighbor.html of atom I
-and the distances between atoms satisfy rIJ rJK rKI > cutoff^3.
+The potential for a triplet of atom is calculated only if all 3
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt
index fe0e3c952a..ec87101d0d 100644
--- a/doc/src/pair_awpmd.txt
+++ b/doc/src/pair_awpmd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index e160f09b3d..ca4186e27b 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -51,10 +51,9 @@ Rc is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 8c5b6e155d..9fb88102eb 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -24,15 +24,14 @@ pair_coeff 1 1 1.0 1.5 2.5 :pre
Style {body/nparticle} is for use with body particles and calculates
pairwise body/body interactions as well as interactions between body
-and point-particles. See "Section 6.14"_Section_howto.html#howto_14
-of the manual and the "body"_body.html doc page for more details on
-using body particles.
+and point-particles. See the "Howto body"_Howto_body.html doc page
+for more details on using body particles.
This pair style is designed for use with the "nparticle" body style,
which is specified as an argument to the "atom-style body" command.
-See the "body"_body.html doc page for more details about the body
-styles LAMMPS supports. The "nparticle" style treats a body particle
-as a rigid body composed of N sub-particles.
+See the "Howto body"_Howto_body.html doc page for more details about
+the body styles LAMMPS supports. The "nparticle" style treats a body
+particle as a rigid body composed of N sub-particles.
The coordinates of a body particle are its center-of-mass (COM). If
the COMs of a pair of body particles are within the cutoff (global or
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index 9daeb08e9a..e724874032 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,9 +29,8 @@ pair_coeff 1 1 100.0 1.0 :pre
Style {body/rounded/polygon} is for use with 2d models of body
particles of style {rounded/polygon}. It calculates pairwise
body/body interactions which can include body particles modeled as
-1-vertex circular disks with a specified diameter. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body
+1-vertex circular disks with a specified diameter. See the "Howto
+body"_Howto_body.html doc page for more details on using body
rounded/polygon particles.
This pairwise interaction between rounded polygons is described in
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index dc559feaaf..0f8548d98e 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -29,9 +29,8 @@ pair_coeff 1 1 100.0 1.0 :pre
Style {body/rounded/polygon} is for use with 3d models of body
particles of style {rounded/polyhedron}. It calculates pairwise
body/body interactions which can include body particles modeled as
-1-vertex spheres with a specified diameter. See "Section
-6.14"_Section_howto.html#howto_14 of the manual and the
-"body"_body.html doc page for more details on using body
+1-vertex spheres with a specified diameter. See the "Howto
+body"_Howto_body.html doc page for more details on using body
rounded/polyhedron particles.
This pairwise interaction between the rounded polyhedra is described
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 2a611e4bd0..654a7eb0b3 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index f867107426..c408de6db6 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -3,7 +3,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -108,10 +108,10 @@ The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Section_howto.html#howto_25
-to allow charges on core and shell particles to be separated by r =
-0.0. The same correction is introduced for the {born/coul/dsf/cs}
-style which is identical to {born/coul/dsf}. And likewise for
+a term is added for the "core/shell model"_Howto_coreshell.html to
+allow charges on core and shell particles to be separated by r = 0.0.
+The same correction is introduced for the {born/coul/dsf/cs} style
+which is identical to {born/coul/dsf}. And likewise for
{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
Note that these potentials are related to the "Buckingham
@@ -145,10 +145,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index 79b71e91c7..eaff85cbbc 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -74,7 +74,7 @@ must be specified.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "this section"_Section_accelerate.html of
+hardware, as discussed in "this section"_Speed.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
@@ -88,7 +88,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "this section"_Section_accelerate.html of the manual for more
+See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index d18b39d5d9..cc782c11cf 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -93,9 +93,8 @@ used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Section_howto.html#howto_25
-to allow charges on core and shell particles to be separated by r =
-0.0.
+a term is added for the "core/shell model"_Howto_coreshell.html to
+allow charges on core and shell particles to be separated by r = 0.0.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@@ -140,10 +139,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -155,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 879972772b..485c35c6b2 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 05e760e1b2..551204f1a7 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,10 +102,9 @@ global Coulombic cutoff is allowed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 75a8e4bff9..39c6f29b04 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -184,10 +184,9 @@ the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -199,8 +198,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 36fae5068b..104c51474c 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -102,10 +102,9 @@ cutoff distance.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt
index fe9238f423..63f85f23d5 100644
--- a/doc/src/pair_coeff.txt
+++ b/doc/src/pair_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -111,9 +111,8 @@ Windows:
:line
The alphabetic list of pair styles defined in LAMMPS is given on the
-"pair_style"_pair_style.html doc page. They are also given in more
-compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+"pair_style"_pair_style.html doc page. They are also listed in more
+compact form on the "Commands pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
@@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command.
Note that there are also additional pair styles (not listed on the
"pair_style"_pair_style.html doc page) submitted by users which are
-included in the LAMMPS distribution. The list of these with links to
-the individual styles are given in the pair section of "this
-page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution. The full list of all pair styles
+is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed on the
"pair_style"_pair_style.html doc page) included in the LAMMPS
-distribution for faster performance on CPUs and GPUs. The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+distribution for faster performance on CPUs, GPUs, and KNLs. The
+individual style names on the "Commands pair"_Commands_pair.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
:line
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 83b15b358b..08540cfee0 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -127,10 +127,9 @@ commands for efficiency: "neighbor multi"_neighbor.html and
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -142,8 +141,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index f5461b1cbc..fc4cddbbae 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -112,10 +112,9 @@ nor file {ffield.comb3} with style {comb}.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -127,8 +126,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index aa3a008bd3..2fd9445785 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -205,9 +205,9 @@ pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {coul/long/cs} is identical to {coul/long} except that a term is
-added for the "core/shell model"_Section_howto.html#howto_25 to allow
-charges on core and shell particles to be separated by r = 0.0. The
-same correction is introduced for the {coul/wolf/cs} style which is
+added for the "core/shell model"_Howto_coreshell.html to allow charges
+on core and shell particles to be separated by r = 0.0. The same
+correction is introduced for the {coul/wolf/cs} style which is
identical to {coul/wolf}.
Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
@@ -226,16 +226,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
-information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighbor list cutoff for Coulomb
-interactions is effectively extended by a distance 2*qdist when using
-the TIP4P pair style, to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
-to slightly larger cost for the long-range calculation, so you can
-test the trade-off for your model.
+See the "Howto tip4p"_Howto_tip4p.html doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules. Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to
+shrink the size of the neighbor list. This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
:line
@@ -268,10 +268,9 @@ command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -283,8 +282,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index f651cb4b5e..14932c4835 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 19f69688d5..029e6e5b3b 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index c1084c6087..6540c4b8f0 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -54,8 +54,8 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
These pair styles are designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See
-"Section 6.25"_Section_howto.html#howto_25 of the manual for an
-overview of the model as implemented in LAMMPS.
+the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
+the model as implemented in LAMMPS.
The styles with a {coul/long} term are identical to the "pair_style
born/coul/long"_pair_born.html and "pair_style
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 2516e5eae4..1d8abc4521 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,10 +186,9 @@ type pair.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 9e29e93430..1b636795d9 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -110,10 +110,9 @@ random force.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -125,8 +124,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 867f3f2315..0d180ba068 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -129,10 +129,9 @@ significantly larger timesteps to be taken.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -144,8 +143,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 9e24100ab7..2478a96d5f 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 03e77f53ab..361dacb703 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -371,10 +371,9 @@ are listed.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -386,7 +385,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for more
+See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
@@ -414,15 +413,10 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
-All of these styles except the {eam/cd} style are part of the MANYBODY
-package. They are only enabled if LAMMPS was built with that package.
+All of these styles are part of the MANYBODY package. They are only
+enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The {eam/cd} style is part of the USER-MISC package and also requires
-the MANYBODY package. It is only enabled if LAMMPS was built with
-those packages. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
[Related commands:]
"pair_coeff"_pair_coeff.html
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index e5b1420b59..cce564856e 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -109,10 +109,9 @@ the EDIP package.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index ee7dc99932..a55860297e 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 75ad2d4683..6490a859c1 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -136,10 +136,9 @@ needs.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -151,8 +150,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 7eafa23543..08ab1cf3c9 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -153,10 +153,9 @@ pair interaction.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -168,8 +167,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt
index 9a784e2501..3acad1132d 100644
--- a/doc/src/pair_extep.txt
+++ b/doc/src/pair_extep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index f6f46a2de8..9662a4f29c 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -84,10 +84,9 @@ is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -99,8 +98,8 @@ by including their suffix, or you can use the "-suffix command-line
switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index c923578586..af41f6879e 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,9 @@ pair_coeff sigma to 1.0 as well.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index d7e87af013..55b00a172f 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,9 @@ potential.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index ec84a2d57a..9f34ac8c43 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -91,10 +91,9 @@ cutoff(s) specified in the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -106,8 +105,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 8f1251cf1f..809ff008bc 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index d3cf90ec14..60b0b02174 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -33,8 +33,8 @@ pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre
[Description:]
The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
-3-body hydrogen bond interaction for the
-"DREIDING"_Section_howto.html#howto_4 force field, given by:
+3-body hydrogen bond interaction for the "DREIDING"_Howto_bioFF.html
+force field, given by:
:c,image(Eqs/pair_hbond_dreiding.jpg)
@@ -65,8 +65,8 @@ potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.
-See this "howto section"_Section_howto.html#howto_4 of the manual for
-more information on the DREIDING forcefield.
+See the "Howto bioFF"_Howto_bioFF.html doc page for more information
+on the DREIDING forcefield.
NOTE: Because the Dreiding hydrogen bond potential is only one portion
of an overall force field which typically includes other pairwise
@@ -166,10 +166,9 @@ optional parameters.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -181,8 +180,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index d37dedc709..9b36109c27 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients to
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.
Since the {hybrid} and {hybrid/overlay} styles delegate computation to
the individual sub-styles, the suffix versions of the {hybrid} and
@@ -334,8 +334,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index dbc9c458e2..9c9304c4a7 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index c5d910e27c..889c1e892f 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM
API source package?" section.
To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org. The "KIM
-section of Section packages"_Section_packages.html#KIM has
+API library from the "OpenKIM website"_https://openkim.org. The KIM
+section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index a16d123b89..8fc6bbff49 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 97f132eacd..7dad2e3701 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index 148a1d47a0..ddf8551d56 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index 44cfeb48e9..c2c6beb97f 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 653e8b0c2d..023cc0be4f 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index e297d479bc..a55cb348d7 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -185,9 +185,9 @@ distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except
-that a term is added for the "core/shell
-model"_Section_howto.html#howto_25 to allow charges on core and shell
-particles to be separated by r = 0.0.
+that a term is added for the "core/shell model"_Howto_coreshell.html
+to allow charges on core and shell particles to be separated by r =
+0.0.
Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf
summation method, described in "Wolf"_#Wolf1, given by:
@@ -223,16 +223,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
-information on how to use the TIP4P pair styles and lists of
-parameters to set. Note that the neighbor list cutoff for Coulomb
-interactions is effectively extended by a distance 2*qdist when using
-the TIP4P pair style, to account for the offset distance of the
-fictitious charges on O atoms in water molecules. Thus it is
-typically best in an efficiency sense to use a LJ cutoff >= Coulomb
-cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
-to slightly larger cost for the long-range calculation, so you can
-test the trade-off for your model.
+See the "Howto tip4p"_Howto_tip4p.html doc page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules. Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to
+shrink the size of the neighbor list. This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
For all of the {lj/cut} pair styles, the following coefficients must
be defined for each pair of atoms types via the
@@ -269,10 +269,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -284,8 +283,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 83f6ec063d..7c68e26ace 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ cutoff specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index 4ca8c3c141..d04a3d8b9d 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -63,10 +63,9 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma =
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -78,8 +77,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index e0838426f6..3e9996da4d 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -53,10 +53,9 @@ optional. If not specified, the global LJ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 6be4562d18..1ba3610f86 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -90,7 +90,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-See the "howto section"_Section_howto.html#howto_8 for more
+See the the "Howto tip4p"_Howto_tip4p.html doc page for more
information on how to use the TIP4P pair style. Note that the
neighbor list cutoff for Coulomb interactions is effectively extended
by a distance 2*qdist when using the TIP4P pair style, to account for
@@ -156,10 +156,9 @@ specified in the pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index b1678cad58..575c023579 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -62,10 +62,9 @@ specified, the global values for Rin and Rc are used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 5f7c226cee..0fab768b8f 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ LJ cutoff specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index 2ef133da55..d10fcd0472 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -207,10 +207,9 @@ directory tree, under examples/USER/fep.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -222,8 +221,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index b39c7545c7..e9a0a0d291 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -143,7 +143,7 @@ must be specified.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "this section"_Section_accelerate.html of
+hardware, as discussed in "this section"_Speed.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
@@ -157,7 +157,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "this section"_Section_accelerate.html of the manual for more
+See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 720a8539b8..6b74c208bf 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index ca06f1bf8e..e5a8cac845 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index c7449428bd..45f88f0bbe 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 6653b397a0..9615512041 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -106,10 +106,9 @@ MEAM files.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -121,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index fa731799dd..ba0953a17c 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index bcdf717d68..ad3880e642 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index f8b0c9f071..09fe611686 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt
index ad602db9f1..818e37272b 100644
--- a/doc/src/pair_mie.txt
+++ b/doc/src/pair_mie.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt
index 34dbb5bc3d..c043fde5a7 100644
--- a/doc/src/pair_modify.txt
+++ b/doc/src/pair_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 77c4f184d9..545b650f75 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 3eb5ac5afe..85a42986ec 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -101,10 +101,9 @@ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -116,8 +115,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 38fd1ede4a..31d52a58c8 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index 57abcf4a4c..e09dde3f80 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -204,10 +204,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -219,8 +218,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 2395707fb4..720b9ea2a1 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -92,10 +92,9 @@ a particular simulation; LAMMPS ignores those entries.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -107,8 +106,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 81cea1a38d..355bfd5573 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -133,10 +133,9 @@ the "run_style respa"_run_style.html command. They do not support the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Restrictions:]
diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt
index f4e9525198..960dc05d97 100644
--- a/doc/src/pair_none.txt
+++ b/doc/src/pair_none.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index f272d15a86..5ec9915297 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 1b55031b2c..a1d2cfdb7c 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index deca093e3b..14abd4541e 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -139,10 +139,9 @@ details please see the description in "(Mtchell2011a)".
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -154,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index c088e8bb22..eb0c30f249 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 2f8ed7a27c..1433557e03 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 9436b0c4ed..3570a52801 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt
index 1d13f93706..a3b84955cd 100644
--- a/doc/src/pair_reax.txt
+++ b/doc/src/pair_reax.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index 39759b3111..ec57548640 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -50,11 +50,11 @@ as a package.
The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that
is derived from the {reax/c} style. The Kokkos version can run on GPUs
and can also use OpenMP multithreading. For more information about the
-Kokkos package, see "Section 4"_Section_packages.html#kokkos and
-"Section 5.3.3"_accelerate_kokkos.html. One important consideration
-when using the {reax/c/kk} style is the choice of either half or full
-neighbor lists. This setting can be changed using the Kokkos
-"package"_package.html command.
+Kokkos package, see "Packages details"_Packages_details.html and
+"Speed kokkos"_Speed_kokkos.html doc pages. One important
+consideration when using the {reax/c/kk} style is the choice of either
+half or full neighbor lists. This setting can be changed using the
+Kokkos "package"_package.html command.
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details. The {reax} style is a
@@ -303,10 +303,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -318,8 +317,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 9ad95eb5fc..6e72408ebc 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -145,10 +145,9 @@ specified in the pair_style command is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 360136a4ea..ccf704b6f7 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -85,10 +85,9 @@ pair_style command.
Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
@@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index eeaa3387a4..f2d633903a 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index f73acf74ee..3aeaa31553 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index c32bf3a22e..65526cfba8 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index 268fe78d02..a5bda54d5f 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c8d6b21b3f..c70202c2e1 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index 27dcf6082b..f9bd8910e4 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -175,10 +175,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -190,8 +189,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 08fa88c477..374711825b 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -82,10 +82,9 @@ variables.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -97,8 +96,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index 2387056a1b..d19c28a3cb 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index 957f901425..a670949a89 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index ef89c4ad3e..152e6cf8a2 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 352e717f76..3cd1c5abb2 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 9177ca80b8..7b9a8188f2 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index e6c5a6bb20..02f16d8982 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 24877906f3..375e59fe89 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,24 +25,46 @@ pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre
[Description:]
Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction
-between pairs of magnetic spins:
+between pairs of magnetic spins.
+According to the expression reported in "(Rohart)"_#Rohart, one has
+the following DM energy:
:c,image(Eqs/pair_spin_dmi_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
-eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
-two particles, and D is the DM vector defining the intensity and the
-sign of the interaction.
+eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j,
+and D is the DM vector defining the intensity (in eV) and the direction
+of the interaction.
-Examples and more explanations about this interaction and its parametrization are
-reported in "(Tranchida)"_#Tranchida5.
+In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented
+from the high spin-orbit layer to the magnetic ultrathin film.
-From this DM interaction, each spin i will be submitted to a magnetic torque
-omega and its associated atom to a force F (for spin-lattice calculations only).
+The application of a spin-lattice Poisson bracket to this energy (as described
+in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a
+mechanical force F (for spin-lattice calculations only) for each magnetic
+particle i:
+
+:c,image(Eqs/pair_spin_dmi_forces.jpg)
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida5.
+For the {spin/dmi} pair style, the following coefficients must be defined for
+each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
+the examples above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
+set in the following order:
+
+rc (distance units)
+|D| (energy units)
+Dx, Dy, Dz (direction of D) :ul
+
+Note that rc is the radius cutoff of the considered DM interaction, |D| is
+the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction.
+
+None of those coefficients is optional. If not specified, the {spin/dmi}
+pair style cannot be used.
+
:line
[Restrictions:]
@@ -61,6 +83,9 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
:line
+:link(Rohart)
+[(Rohart)] Rohart and Thiaville,
+Physical Review B, 88(18), 184422. (2013).
:link(Tranchida5)
[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, (2018).
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index ad3357cb5e..24eb635b81 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,18 +32,15 @@ pairs of magnetic spins:
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
and J(rij) is a function defining the intensity and the sign of the exchange
-interaction.
-
-This function is defined as:
+interaction for different neighboring shells. This function is defined as:
:c,image(Eqs/pair_spin_exchange_function.jpg)
where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command.
+"pair_coeff" command (see below for more explanations).
The coefficients a, b, and d need to be fitted so that the function above matches with
the value of the exchange interaction for the N neighbor shells taken into account.
-
Examples and more explanations about this function and its parametrization are reported
in "(Tranchida)"_#Tranchida3.
@@ -54,11 +51,30 @@ such as:
:c,image(Eqs/pair_spin_exchange_forces.jpg)
-with h the Planck constant (in metal units).
+with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit
+vector between sites i and j.
More details about the derivation of these torques/forces are reported in
"(Tranchida)"_#Tranchida3.
+For the {spin/exchange} pair style, the following coefficients must be defined
+for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
+the examples above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html commands, and
+set in the following order:
+
+rc (distance units)
+a (energy units)
+b (adim parameter)
+d (distance units) :ul
+
+Note that rc is the radius cutoff of the considered exchange interaction,
+and a, b and d are the three coefficients performing the parametrization
+of the function J(rij) defined above.
+
+None of those coefficients is optional. If not specified, the
+{spin/exchange} pair style cannot be used.
+
:line
[Restrictions:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index 8ba24c46af..b338fae5dc 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 8551f8d636..0967632ed2 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt
index e7f1e00d10..e784ac3d17 100644
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 7e29544a70..b0872e6447 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -78,22 +78,22 @@ previously specified pair_coeff values.
:line
Here is an alphabetic list of pair styles defined in LAMMPS. They are
-also given in more compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+also listed in more compact form on the "Commands
+pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated "pair_coeff"_pair_coeff.html command.
There are also additional pair styles (not listed here) submitted by
-users which are included in the LAMMPS distribution. The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution. The full list of
+all pair styles is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed here)
-included in the LAMMPS distribution for faster performance on CPUs and
-GPUs. The list of these with links to the individual styles are given
-in the pair section of "this page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution for faster performance on CPUs,
+GPUs, and KNLs. The individual style names on the "Commands
+pair"_Commands_pair.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
@@ -105,7 +105,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
"pair_style beck"_pair_beck.html - Beck potential
-"pair_style body"_pair_body.html - interactions between body particles
+"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index 4932fe55d3..e6741791df 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -144,10 +144,9 @@ taken from the ij and ik pairs (sigma, a, gamma)
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -164,8 +163,8 @@ additional 5 to 10 percent performance improvement when the
Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
These parameters are common for modeling silicon and water.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index b99491b477..5e3c1f5ff6 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -217,10 +217,9 @@ one that matches the specified keyword.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -232,8 +231,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index cd3a7ef31b..41be067bac 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -227,10 +227,9 @@ This pair style can only be used via the {pair} keyword of the
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -242,8 +241,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 918e889924..821c38f3e4 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -179,10 +179,9 @@ defined in various papers.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index e0c2b5a5cb..ac1f79a80b 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -131,10 +131,9 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -146,8 +145,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index 21d57e4e88..a89d4e3ea1 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -189,10 +189,9 @@ providing the base ZBL implementation.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -204,8 +203,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 41a4059cee..7ce8b7cf4b 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -9,7 +9,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -45,8 +45,8 @@ pair_style lj/cut/thole/long 2.6 12.0 :pre
The {thole} pair styles are meant to be used with force fields that
include explicit polarization through Drude dipoles. This link
describes how to use the "thermalized Drude oscillator
-model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
-are discussed in "this Section"_Section_howto.html#howto_25.
+model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS are
+discussed on the "Howto polarizable"_Howto_polarizable.html doc page.
The {thole} pair style should be used as a sub-style within in the
"pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a
@@ -130,10 +130,9 @@ the {pair_style} command line.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
[Mixing]:
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 42a5bbdfe2..3915ffc238 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index 88a22864cc..dbc6fd0664 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,10 +69,9 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -84,8 +83,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index d9c66d45c0..2e404e8bef 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -171,10 +171,9 @@ two-body parameters from the CCC and CSiSi entries.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -186,8 +185,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt
index 9f5970fcbc..48ad76e76e 100644
--- a/doc/src/pair_write.txt
+++ b/doc/src/pair_write.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index e7c063ded9..5a8363260a 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -49,10 +49,9 @@ cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 2037a9451f..515062d9eb 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -80,10 +80,9 @@ yukawa/colloid cutoff is used.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1984cd831f..1472c7b672 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -71,10 +71,9 @@ copper.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual. The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt
index e58b33c75f..b324003bd1 100644
--- a/doc/src/pair_zero.txt
+++ b/doc/src/pair_zero.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 1a5e98a109..4c3eef2cd1 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -10,8 +10,9 @@ Pair Styles :h1
pair_airebo
pair_awpmd
pair_beck
- pair_body
+ pair_body_nparticle
pair_body_rounded_polygon
+ pair_body_rounded_polyhedron
pair_bop
pair_born
pair_brownian
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index 610eee99b3..d4fe06c098 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index 3c0305e316..b2145ebad1 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -69,8 +69,8 @@ simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. However for PRD, this makes little sense, since running a
replica on virtual instead of physical processors,offers no effective
-parallel speed-up in searching for infrequent events. See "Section
-6.5"_Section_howto.html#howto_5 of the manual for further discussion.
+parallel speed-up in searching for infrequent events. See the "Howto
+replica"_Howto_replica.html doc page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
diff --git a/doc/src/print.txt b/doc/src/print.txt
index 77e0c7cfd3..476d4104fa 100644
--- a/doc/src/print.txt
+++ b/doc/src/print.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index e54b2cede3..df13ae1f61 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/python.txt b/doc/src/python.txt
index d670fcc77f..4f4faca8f4 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -199,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code
follows as a single argument to the {here} keyword. This can be done
using triple quotes as delimiters, as in the examples above. This
allows Python code to be listed verbatim in your input script, with
-proper indentation, blank lines, and comments, as desired. See
-"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how
-triple quotes can be used as part of input script syntax.
+proper indentation, blank lines, and comments, as desired. See the
+"Commands parse"_Commands_parse.html doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
The {exists} keyword takes no argument. It means that Python code
containing the required Python function defined by the {func} setting,
diff --git a/doc/src/quit.txt b/doc/src/quit.txt
index 843d3de7f3..802df97711 100644
--- a/doc/src/quit.txt
+++ b/doc/src/quit.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index fd297e36c1..ded51a4d99 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -322,9 +322,9 @@ with tilt factors that exceed these limits, you can use the "box
tilt"_box.html command, with a setting of {large}; a setting of
{small} is the default.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto triclinic"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
When a triclinic system is used, the simulation domain should normally
@@ -772,9 +772,9 @@ the "bodies" keyword.
Each body can have a variable number of integer and/or floating-point
values. The number and meaning of the values is defined by the body
-style, as described in the "body"_body.html doc page. The body style
-is given as an argument to the "atom_style body"_atom_style.html
-command.
+style, as described in the "Howto body"_Howto_body.html doc page. The
+body style is given as an argument to the "atom_style
+body"_atom_style.html command.
The Ninteger and Ndouble values determine how many integer and
floating-point values are specified for this particle. Ninteger and
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index 21c6df5017..a3c0733e07 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 6f6a828229..488c36f020 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 5039e4a516..21396ae1fd 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -186,9 +186,9 @@ functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius.
-See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
+See the "Howto tricilinc"_Howto_triclinic.html doc page for a
+geometric description of triclinic boxes, as defined by LAMMPS, and
+how to transform these parameters to and from other commonly used
triclinic representations.
The {union} style creates a region consisting of the volume of all the
@@ -358,12 +358,12 @@ sub-regions can be defined with the {open} keyword.
:line
-Styles with a {kk} suffix are functionally the same as the
-corresponding style without the suffix. They have been optimized to
-run faster, depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual. The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
The code using the region (such as a fix or compute) must also be supported
by Kokkos or no acceleration will occur. Currently, only {block} style
@@ -378,8 +378,8 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 08523ecdd8..0195dce911 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index edf94cc711..8eb3ebd5a1 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt
index 8655a9d54f..391b51fde9 100644
--- a/doc/src/reset_ids.txt
+++ b/doc/src/reset_ids.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt
index 79a5812ca1..0d518655fb 100644
--- a/doc/src/reset_timestep.txt
+++ b/doc/src/reset_timestep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 7c39ae1404..6f2dc5ca46 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/run.txt b/doc/src/run.txt
index 913d81bb4d..c7c73463d9 100644
--- a/doc/src/run.txt
+++ b/doc/src/run.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -127,9 +127,9 @@ be redefined, e.g. to reset a thermostat temperature. Or this could
be useful for invoking a command you have added to LAMMPS that wraps
some other code (e.g. as a library) to perform a computation
periodically during a long LAMMPS run. See the "Modify"_Modify.html
-doc page for info about how to add new commands to LAMMPS. See "this
-section"_Section_howto.html#howto_10 of the documentation for ideas
-about how to couple LAMMPS to other codes.
+doc page for info about how to add new commands to LAMMPS. See the
+"Howto couple"_Howto_couple.html doc page for ideas about how to
+couple LAMMPS to other codes.
With the {every} option, N total steps are simulated, in shorter runs
of M steps each. After each M-length run, the specified commands are
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 7717ede86f..deee51cfd3 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -119,13 +119,13 @@ switches"_Section_start.html#start_6 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyond the 1st timestep of the run.
-See "Section 5"_Section_accelerate.html of the manual for
-performance details of the speed-up offered by the {verlet/split}
-style. One important performance consideration is the assignment of
-logical processors in the 2 partitions to the physical cores of a
-parallel machine. The "processors"_processors.html command has
-options to support this, and strategies are discussed in
-"Section 5"_Section_accelerate.html of the manual.
+See the "Speed packages"_Speed_packages.html doc page for performance
+details of the speed-up offered by the {verlet/split} style. One
+important performance consideration is the assignment of logical
+processors in the 2 partitions to the physical cores of a parallel
+machine. The "processors"_processors.html command has options to
+support this, and strategies are discussed in "Section
+5"_Speed.html of the manual.
:line
@@ -274,21 +274,21 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
:line
-The {respa/omp} styles is a variant of {respa} adapted for use with
+The {respa/omp} style is a variant of {respa} adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an {omp}
-suffix. It is functionally equivalent to {respa} but performs additional
-operations required for managing {omp} styles. For more on {omp} styles
-see the "Section 5"_Section_accelerate.html of the manual.
-Accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+suffix. It is functionally equivalent to {respa} but performs
+additional operations required for managing {omp} styles. For more on
+{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
You can specify {respa/omp} explicitly in your input script, or
you can use the "-suffix command-line switch"_Section_start.html#start_6
when you invoke LAMMPS, or you can use the "suffix"_suffix.html
command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/set.txt b/doc/src/set.txt
index d2235d5c32..b83ad54f4e 100644
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/shell.txt b/doc/src/shell.txt
index 205164f874..d274f498e5 100644
--- a/doc/src/shell.txt
+++ b/doc/src/shell.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 1021c4856b..a57b61664d 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 74f69b6dfe..bb0619f1e0 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index f5e7c6d653..a26ff79318 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -92,9 +92,8 @@ restricts you to having exactly one processor per replica. For more
information, see the documentation for the "neb"_neb.html command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
-partitions remain idle. See "Section
-6.5"_Section_howto.html#howto_5 of the manual for further discussion of
-multi-replica simulations.
+partitions remain idle. See the "Howto replica"_Howto_replica.html doc
+page for further discussion of multi-replica simulations.
A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index b1c47c8076..c7b482acc6 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -32,14 +32,13 @@ replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the
-manual. Note that if you have MPI installed, you can run a
-multi-replica simulation with more replicas (partitions) than you have
-physical processors, e.g you can run a 10-replica simulation on one or
-two processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See "this
-section"_Section_howto.html#howto_5 of the manual for further
-discussion.
+switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
+Note that if you have MPI installed, you can run a multi-replica
+simulation with more replicas (partitions) than you have physical
+processors, e.g you can run a 10-replica simulation on one or two
+processors. You will simply not get the performance speed-up you
+would see with one or more physical processors per replica. See the
+"Howto replica"_Howto_replica.html doc page for further discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 6145c8704c..9cb1bab784 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4ad49f9e33..4eee225de7 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
temper/npt command :h3
diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt
index 1d5d34995c..5f12f98707 100644
--- a/doc/src/thermo.txt
+++ b/doc/src/thermo.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt
index e9aca0f20a..ca2957de77 100644
--- a/doc/src/thermo_modify.txt
+++ b/doc/src/thermo_modify.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 18c5ad5ba1..cbc2612f28 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -286,11 +286,11 @@ takes place.
The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta},
{cellgamma}, correspond to the usual crystallographic quantities that
-define the periodic unit cell of a crystal. See "this
-section"_Section_howto.html#howto_12 of the doc pages for a geometric
-description of triclinic periodic cells, including a precise definition
-of these quantities in terms of the internal LAMMPS cell dimensions
-{lx}, {ly}, {lz}, {yz}, {xz}, {xy}.
+define the periodic unit cell of a crystal. See the "Howto
+triclinic"_Howto_triclinic.html doc page for a geometric description
+of triclinic periodic cells, including a precise definition of these
+quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly},
+{lz}, {yz}, {xz}, {xy}.
:line
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 768c3e1353..10737dbda0 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt
index 639ad6f311..ee0ace05b9 100644
--- a/doc/src/timestep.txt
+++ b/doc/src/timestep.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt
deleted file mode 100644
index 338439ac8e..0000000000
--- a/doc/src/tutorials.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-Tutorials :h1
-
-<!-- RST
-
-.. toctree::
- :maxdepth: 1
-
- tutorial_drude
- tutorial_github
- tutorial_pylammps
- tutorial_bash_on_windows
- body
- manifolds
-
-END_RST -->
diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt
index 49b46781d7..4c788d4722 100644
--- a/doc/src/uncompute.txt
+++ b/doc/src/uncompute.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/undump.txt b/doc/src/undump.txt
index a2a371aca5..cc3d8b9103 100644
--- a/doc/src/undump.txt
+++ b/doc/src/undump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt
index dcc4499b20..9608b39c7e 100644
--- a/doc/src/unfix.txt
+++ b/doc/src/unfix.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/units.txt b/doc/src/units.txt
index 0b856dcc68..8df8fe6810 100644
--- a/doc/src/units.txt
+++ b/doc/src/units.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 717c77c079..c6598ccb51 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of
the Python code. Variables of style {internal} are used by a few
commands which set their value directly.
-NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the
-manual, an input script can use "immediate" variables, specified as
+NOTE: As discussed on the "Commands parse"_Commands_parse.html doc
+page, an input script can use "immediate" variables, specified as
$(formula) with parenthesis, where the formula has the same syntax as
equal-style variables described on this page. This is a convenient
way to evaluate a formula immediately without using the variable
@@ -198,7 +198,7 @@ the same thing.
:line
-"This section"_Section_commands.html#cmd_2 of the manual explains how
+The "Commands parse"_Commands_parse.html doc page explains how
occurrences of a variable name in an input script line are replaced by
the variable's string. The variable name can be referenced as $x if
the name "x" is a single character, or as $\{LoopVar\} if the name
@@ -312,8 +312,8 @@ If you simply wish to print a variable value with desired precision to
the screen or logfile via the "print"_print.html or "fix
print"_fix_print.html commands, you can also do this by specifying an
"immediate" variable with a trailing colon and format string, as part
-of the string argument of those commands. This is explained in
-"Section 3.2"_Section_commands.html#cmd_2.
+of the string argument of those commands. This is explained on the
+"Commands parse"_Commands_parse.html doc page.
For the {getenv} style, a single string is assigned to the variable
which should be the name of an environment variable. When the
@@ -1119,24 +1119,23 @@ Vectors" discussion above.
If you want an equal-style variable to be evaluated immediately, it
may be the case that you do not need to define a variable at all. See
-"Section 3.2"_Section_commands.html#cmd_2 of the manual, which
-describes the use of "immediate" variables in an input script,
-specified as $(formula) with parenthesis, where the formula has the
-same syntax as equal-style variables described on this page. This
-effectively evaluates a formula immediately without using the variable
-command to define a named variable.
+the "Commands parse"_Commands_parse.html doc page for info on how to
+use "immediate" variables in an input script, specified as $(formula)
+with parenthesis, where the formula has the same syntax as equal-style
+variables described on this page. This effectively evaluates a
+formula immediately without using the variable command to define a
+named variable.
More generally, there is a difference between referencing a variable
with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
(e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
-into the command. As explained in "Section
-3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
-un-named "immediate" variables for this purpose. For example, a
-string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
-command evaluates the string between the parenthesis as an equal-style
-variable formula.
+into the command. As explained on the "Commands
+parse"_Commands_parse.html doc page, you can also use un-named
+"immediate" variables for this purpose. For example, a string like
+this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates
+the string between the parenthesis as an equal-style variable formula.
Referencing a variable with a leading "v_" is an optional or required
kind of argument for some commands (e.g. the "fix
@@ -1180,10 +1179,9 @@ quotes if it contains variables preceded by $ signs. For example,
variable vratio equal "$\{vfinal\}/$\{v0\}" :pre
-This is because the quotes prevent variable substitution (see "this
-section"_Section_commands.html#cmd_2 on parsing input script
-commands), and thus an error will occur when the formula for "vratio"
-is evaluated later.
+This is because the quotes prevent variable substitution (explained on
+the "Commands parse"_Commands_parse.html doc page), and thus an error
+will occur when the formula for "vratio" is evaluated later.
:line
diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt
index b8299a5acf..96d3fa6dc4 100644
--- a/doc/src/velocity.txt
+++ b/doc/src/velocity.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -139,10 +139,9 @@ if rot = yes, the angular momentum is zeroed.
If specified, the {temp} keyword is used by {create} and {scale} to
specify a "compute"_compute.html that calculates temperature in a
desired way, e.g. by first subtracting out a velocity bias, as
-discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc
-pages. If this keyword is not specified, {create} and {scale}
-calculate temperature using a compute that is defined internally as
-follows:
+discussed on the "Howto thermostat"_Howto_thermostat.html doc page.
+If this keyword is not specified, {create} and {scale} calculate
+temperature using a compute that is defined internally as follows:
compute velocity_temp group-ID temp :pre
@@ -161,11 +160,11 @@ The {bias} keyword with a {yes} setting is used by {create} and
If the temperature compute also calculates a velocity bias, the the
bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is
-added back to the atom velocities. See "Section
-6.16"_Section_howto.html#howto_16 of the doc pages for more discussion
-of temperature computes with biases. Note that the velocity bias is
-only applied to atoms in the temperature compute specified with the
-{temp} keyword.
+added back to the atom velocities. See the "Howto
+thermostat"_Howto_thermostat.html doc page for more discussion of
+temperature computes with biases. Note that the velocity bias is only
+applied to atoms in the temperature compute specified with the {temp}
+keyword.
As an example, assume atoms are currently streaming in a flow
direction (which could be separately initialized with the {ramp}
diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt
index 764e119a9d..5dc4b331de 100644
--- a/doc/src/write_coeff.txt
+++ b/doc/src/write_coeff.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index c76f20319c..d8a33f457f 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt
index 840716085f..e676979001 100644
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index ff3b652dba..3935a5d538 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py
index 79a75d72f6..ed9f47a4e4 100755
--- a/doc/utils/converters/lammpsdoc/txt2html.py
+++ b/doc/utils/converters/lammpsdoc/txt2html.py
@@ -662,14 +662,15 @@ class TxtConverter:
parser = self.get_argument_parser()
parsed_args = parser.parse_args(args)
- write_to_files = len(parsed_args.files) > 1
+ write_to_files = parsed_args.output_dir or (len(parsed_args.files) > 1)
for filename in parsed_args.files:
if parsed_args.skip_files and filename in parsed_args.skip_files:
continue
with open(filename, 'r') as f:
- print("Converting", filename, "...", file=err)
+ if parsed_args.verbose:
+ print("Converting", filename, "...", file=err)
content = f.read()
converter = self.create_converter(parsed_args)
@@ -683,7 +684,10 @@ class TxtConverter:
result = msg
if write_to_files:
- output_filename = self.get_output_filename(filename)
+ if parsed_args.output_dir:
+ output_filename = os.path.join(parsed_args.output_dir, os.path.basename(self.get_output_filename(filename)))
+ else:
+ output_filename = self.get_output_filename(filename)
with open(output_filename, "w+t") as outfile:
outfile.write(result)
else:
@@ -698,6 +702,8 @@ class Txt2HtmlConverter(TxtConverter):
'HTML file. useful when set of HTML files'
' will be converted to PDF')
parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append')
+ parser.add_argument('--verbose', '-v', dest='verbose', action='store_true')
+ parser.add_argument('--output-directory', '-o', dest='output_dir')
parser.add_argument('--generate-title', dest='create_title', action='store_true', help='add HTML head page'
'title based on first '
'h1,h2,h3,h4... element')
diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index 17d0916157..8119ad3a78 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -395,6 +395,8 @@ class Txt2RstConverter(TxtConverter):
parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into '
'Restructured Text for Sphinx.')
parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append')
+ parser.add_argument('--verbose', '-v', dest='verbose', action='store_true')
+ parser.add_argument('--output-directory', '-o', dest='output_dir')
parser.add_argument('files', metavar='file', nargs='+', help='one or more files to convert')
return parser
diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt
new file mode 100644
index 0000000000..2806c16498
--- /dev/null
+++ b/doc/utils/requirements.txt
@@ -0,0 +1 @@
+Sphinx
diff --git a/examples/DIFFUSE/README b/examples/DIFFUSE/README
index df2a675f73..e78ca2eacf 100644
--- a/examples/DIFFUSE/README
+++ b/examples/DIFFUSE/README
@@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures
give roughly the same answer and rapidly become roughly constant for
the 100K step simulation.
-Dcoeff = 0.36
+Dcoeff = 0.33
(2) in.vacf.2d
@@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can
see the VACF approach gives a more noise, fluctuating value for the
diffusion coefficient, compared to the MSD approach.
-Dcoeff = 0.25 to 0.45
+Dcoeff = ~0.25
diff --git a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 b/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
deleted file mode 100644
index 473aa56527..0000000000
--- a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8
+++ /dev/null
@@ -1,245 +0,0 @@
-LAMMPS (13 Oct 2016)
-# sample LAMMPS input script for diffusion of 2d LJ liquid
-# mean-squared displacement via compute msd
-
-# settings
-
-variable x equal 40
-variable y equal 40
-
-variable rho equal 0.6
-variable t equal 1.0
-variable rc equal 2.5
-
-# problem setup
-
-units lj
-dimension 2
-atom_style atomic
-neigh_modify delay 0 every 1
-
-lattice sq2 ${rho}
-lattice sq2 0.6
-Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
-region simbox block 0 $x 0 $y -0.1 0.1
-region simbox block 0 40 0 $y -0.1 0.1
-region simbox block 0 40 0 40 -0.1 0.1
-create_box 1 simbox
-Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
- 4 by 2 by 1 MPI processor grid
-create_atoms 1 box
-Created 3200 atoms
-
-pair_style lj/cut ${rc}
-pair_style lj/cut 2.5
-pair_coeff * * 1 1
-
-mass * 1.0
-velocity all create $t 97287
-velocity all create 1 97287
-
-fix 1 all nve
-fix 2 all langevin $t $t 0.1 498094
-fix 2 all langevin 1 $t 0.1 498094
-fix 2 all langevin 1 1 0.1 498094
-fix 3 all enforce2d
-
-# equilibration run
-
-thermo 1000
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 53 53 1
-Memory usage per processor = 2.478 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1 -1.56492 0 -0.5652325 -1.5346995
- 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
- 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
- 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
- 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
- 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms
-
-Performance: 3896017.421 tau/day, 9018.559 timesteps/s
-98.9% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39
-Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62
-Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34
-Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02
-Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96
-Other | | 0.04251 | | | 7.67
-
-Nlocal: 400 ave 406 max 394 min
-Histogram: 1 1 0 1 0 2 1 0 1 1
-Nghost: 202.5 ave 212 max 191 min
-Histogram: 1 0 0 0 3 1 0 2 0 1
-Neighs: 2800.88 ave 2903 max 2690 min
-Histogram: 1 1 0 0 1 2 1 0 1 1
-
-Total # of neighbors = 22407
-Ave neighs/atom = 7.00219
-Neighbor list builds = 599
-Dangerous builds = 0
-
-unfix 2
-
-# data gathering run
-
-reset_timestep 0
-
-# factor of 4 in 2 variables is for 2d
-
-compute msd all msd com yes
-variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
-fix 9 all vector 10 c_msd[4]
-variable fitslope equal slope(f_9)/4/(10*dt)
-
-thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
-
-# only need to run for 10K steps to make a good 100-frame movie
-
-#dump 1 all custom 1 tmp.dump id type vx vy vz
-
-#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
-
-thermo 1000
-run 100000
-Memory usage per processor = 2.853 Mbytes
-Step Temp c_msd[4] v_twopoint v_fitslope
- 0 0.97069905 0 0 5e+20
- 1000 0.98138076 4.0484996 0.20242494 0.18046446
- 2000 0.97606079 9.2121392 0.23030346 0.2091528
- 3000 0.97924866 14.815034 0.24691721 0.22619184
- 4000 0.98568451 20.516817 0.25646019 0.23715506
- 5000 0.97551815 27.33922 0.27339219 0.24709999
- 6000 0.98482252 34.37734 0.28647782 0.25735178
- 7000 0.9672559 41.696689 0.29783348 0.26654059
- 8000 0.9836541 48.340277 0.30212673 0.27440308
- 9000 0.99087147 56.042692 0.31134828 0.28113047
- 10000 0.99663166 63.69663 0.31848314 0.28767921
- 11000 0.97776688 71.144109 0.32338231 0.29344527
- 12000 0.98246011 78.301774 0.32625739 0.29849471
- 13000 0.98788732 85.061923 0.32716124 0.3026655
- 14000 0.96872483 91.1658 0.32559214 0.30601023
- 15000 0.98955796 97.278388 0.32426129 0.3084275
- 16000 0.99855196 104.23997 0.3257499 0.31049883
- 17000 0.98600861 110.66055 0.3254722 0.31220348
- 18000 0.98696963 116.90111 0.32472531 0.31352676
- 19000 0.9881192 124.21305 0.32687644 0.31480062
- 20000 0.98527319 131.09874 0.32774685 0.31596198
- 21000 0.99015191 137.89263 0.32831579 0.31705324
- 22000 0.97972418 146.68982 0.33338595 0.31833889
- 23000 0.98911012 155.1264 0.33723129 0.31979515
- 24000 0.98810498 162.88634 0.33934653 0.32131187
- 25000 0.96961962 170.37907 0.34075814 0.32276215
- 26000 0.99118408 179.26511 0.34474059 0.32427111
- 27000 0.98515159 185.90764 0.3442734 0.32574529
- 28000 0.98951677 192.12183 0.34307469 0.32700292
- 29000 0.9832026 196.99457 0.33964581 0.32799023
- 30000 0.98449493 203.48475 0.33914124 0.3287171
- 31000 0.96585993 210.06193 0.33880956 0.32935775
- 32000 0.98758117 218.94174 0.34209646 0.33001591
- 33000 0.98875584 225.96489 0.34237104 0.33072947
- 34000 0.98007229 233.5792 0.34349882 0.3314385
- 35000 0.98415295 241.98148 0.34568783 0.33216634
- 36000 0.98101154 250.30876 0.34765106 0.33295272
- 37000 0.97606878 258.2127 0.34893608 0.33377673
- 38000 0.97220293 266.40464 0.35053242 0.33459273
- 39000 0.979783 272.8578 0.34981769 0.33539728
- 40000 0.98375673 279.87598 0.34984497 0.33609699
- 41000 0.97506523 288.07676 0.35131312 0.33677708
- 42000 0.97106749 296.11647 0.3525196 0.33751312
- 43000 0.97717259 304.46747 0.35403194 0.33823441
- 44000 0.98541435 312.57228 0.35519578 0.3389771
- 45000 0.97678287 321.82674 0.35758527 0.33973306
- 46000 0.98169719 329.78197 0.35845866 0.34051748
- 47000 0.99471466 337.11283 0.35863066 0.34127239
- 48000 0.98332437 346.0754 0.3604952 0.34202442
- 49000 0.98126947 356.11859 0.36338631 0.34282132
- 50000 0.98809751 365.65248 0.36565248 0.34368171
- 51000 0.95919516 373.91833 0.36658659 0.34454516
- 52000 0.98097913 381.26492 0.36660089 0.34538506
- 53000 0.97774072 388.81031 0.36680218 0.34618232
- 54000 0.99096915 395.56767 0.36626636 0.3469296
- 55000 0.97652739 401.72735 0.36520668 0.34760374
- 56000 0.99185306 407.28834 0.3636503 0.34819906
- 57000 0.96289342 414.75298 0.3638184 0.34871992
- 58000 0.97871716 424.69443 0.36611588 0.34927986
- 59000 0.98637393 433.14205 0.36706953 0.34986296
- 60000 0.98009845 438.14533 0.36512111 0.35040349
- 61000 0.99416712 446.08007 0.3656394 0.35088379
- 62000 0.97612483 450.90846 0.36363585 0.35132647
- 63000 0.97786531 455.36749 0.36140277 0.35167458
- 64000 0.99080668 458.04873 0.35785057 0.3519105
- 65000 0.97952497 461.31241 0.3548557 0.3520506
- 66000 0.98095955 463.91727 0.35145248 0.35207764
- 67000 0.98370788 468.93 0.34994776 0.35204043
- 68000 0.96931818 471.07765 0.34638063 0.35192685
- 69000 0.98512552 474.59146 0.34390685 0.35174053
- 70000 0.98065743 478.66071 0.3419005 0.35149002
- 71000 0.98971283 482.57357 0.33984054 0.35119434
- 72000 0.99890324 485.32018 0.3370279 0.35084345
- 73000 0.98649924 490.19497 0.33574998 0.35043722
- 74000 0.98723422 496.04991 0.33516886 0.35003351
- 75000 1.0025633 501.6313 0.33442087 0.34962094
- 76000 0.97859959 505.97813 0.33288035 0.34921013
- 77000 0.97973006 510.55334 0.33152814 0.3487692
- 78000 0.9903944 515.06966 0.33017286 0.34830833
- 79000 0.96847518 518.76483 0.32833217 0.3478214
- 80000 0.99171112 524.18127 0.32761329 0.34733349
- 81000 0.97202573 529.09959 0.32660468 0.3468315
- 82000 0.99368438 535.80271 0.32670897 0.34633058
- 83000 0.97932483 543.08233 0.32715803 0.34586259
- 84000 0.99078651 547.57861 0.32593965 0.34540839
- 85000 0.98973457 552.24581 0.32485048 0.34493584
- 86000 0.9835873 557.3493 0.32404029 0.34446152
- 87000 0.97180564 564.93434 0.32467491 0.34400358
- 88000 0.99743353 571.39837 0.32465817 0.3435667
- 89000 0.98993437 577.81703 0.32461631 0.3431411
- 90000 0.9926071 583.39378 0.32410765 0.342724
- 91000 0.98800458 591.08741 0.3247733 0.34232767
- 92000 0.98501879 596.10133 0.32396811 0.34193949
- 93000 0.98810082 604.02652 0.32474544 0.3415681
- 94000 0.97563748 609.43676 0.32416849 0.341209
- 95000 0.97283448 615.15754 0.32376713 0.34084828
- 96000 0.9883071 622.30912 0.32411933 0.34049871
- 97000 0.97717678 628.84457 0.32414669 0.34016355
- 98000 0.97190208 634.37377 0.32366009 0.3398341
- 99000 0.98687379 640.66666 0.32356902 0.33950845
- 100000 0.97559757 646.96406 0.32348203 0.33919036
-Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms
-
-Performance: 4505729.040 tau/day, 10429.928 timesteps/s
-99.4% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49
-Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35
-Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81
-Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09
-Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24
-Other | | 0.7686 | | | 8.02
-
-Nlocal: 400 ave 413 max 391 min
-Histogram: 2 1 0 2 0 0 1 1 0 1
-Nghost: 204.75 ave 213 max 197 min
-Histogram: 1 1 0 1 0 3 0 1 0 1
-Neighs: 2800.62 ave 2959 max 2661 min
-Histogram: 1 1 1 2 0 0 0 1 1 1
-
-Total # of neighbors = 22405
-Ave neighs/atom = 7.00156
-Neighbor list builds = 12728
-Dangerous builds = 0
-Total wall time: 0:00:10
diff --git a/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
new file mode 100644
index 0000000000..113da9040d
--- /dev/null
+++ b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8
@@ -0,0 +1,251 @@
+LAMMPS (2 Aug 2018)
+# sample LAMMPS input script for diffusion of 2d LJ liquid
+# mean-squared displacement via compute msd
+
+# settings
+
+variable x equal 40
+variable y equal 40
+
+variable rho equal 0.6
+variable t equal 1.0
+variable rc equal 2.5
+
+# problem setup
+
+units lj
+dimension 2
+atom_style atomic
+neigh_modify delay 0 every 1
+
+lattice sq2 ${rho}
+lattice sq2 0.6
+Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
+region simbox block 0 $x 0 $y -0.1 0.1
+region simbox block 0 40 0 $y -0.1 0.1
+region simbox block 0 40 0 40 -0.1 0.1
+create_box 1 simbox
+Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
+ 4 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 3200 atoms
+ Time spent = 0.000706911 secs
+
+pair_style lj/cut ${rc}
+pair_style lj/cut 2.5
+pair_coeff * * 1 1
+
+mass * 1.0
+velocity all create $t 97287
+velocity all create 1 97287
+
+fix 1 all nve
+fix 2 all langevin $t $t 0.1 498094
+fix 2 all langevin 1 $t 0.1 498094
+fix 2 all langevin 1 1 0.1 498094
+fix 3 all enforce2d
+
+# equilibration run
+
+thermo 1000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1 -1.56492 0 -0.5652325 -1.5346995
+ 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
+ 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416
+ 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
+ 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
+ 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
+Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms
+
+Performance: 3236214.756 tau/day, 7491.238 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27
+Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68
+Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06
+Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02
+Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43
+Other | | 0.05701 | | | 8.54
+
+Nlocal: 400 ave 406 max 394 min
+Histogram: 1 1 0 1 0 2 1 0 1 1
+Nghost: 202.5 ave 212 max 191 min
+Histogram: 1 0 0 0 3 1 0 2 0 1
+Neighs: 2800.88 ave 2903 max 2690 min
+Histogram: 1 1 0 0 1 2 1 0 1 1
+
+Total # of neighbors = 22407
+Ave neighs/atom = 7.00219
+Neighbor list builds = 599
+Dangerous builds = 0
+
+unfix 2
+
+# data gathering run
+
+reset_timestep 0
+
+# factor of 4 in 2 variables is for 2d
+
+compute msd all msd com yes
+variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6)
+fix 9 all vector 10 c_msd[4]
+variable fitslope equal slope(f_9)/4/(10*dt)
+
+thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
+
+# only need to run for 10K steps to make a good 100-frame movie
+
+#dump 1 all custom 1 tmp.dump id type vx vy vz
+
+#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2
+
+thermo 1000
+run 100000
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
+Step Temp c_msd[4] v_twopoint v_fitslope
+ 0 0.97069905 0 0 5e+20
+ 1000 0.98138076 4.0484996 0.20242494 0.20685564
+ 2000 0.97606079 9.2121392 0.23030346 0.23687918
+ 3000 0.97924866 14.815034 0.24691721 0.25405247
+ 4000 0.98568451 20.516817 0.25646019 0.26353644
+ 5000 0.97551815 27.33922 0.27339219 0.27544492
+ 6000 0.98482252 34.37734 0.28647782 0.28966619
+ 7000 0.9672559 41.696689 0.29783348 0.30165524
+ 8000 0.9836541 48.340277 0.30212673 0.31085371
+ 9000 0.99087147 56.042692 0.31134828 0.31811489
+ 10000 0.99663166 63.69663 0.31848314 0.32589374
+ 11000 0.97776688 71.144109 0.32338231 0.33219745
+ 12000 0.98246011 78.301774 0.32625739 0.33723
+ 13000 0.98788732 85.061923 0.32716124 0.34053027
+ 14000 0.96872483 91.1658 0.32559214 0.34231162
+ 15000 0.98955796 97.278388 0.32426129 0.34229511
+ 16000 0.99855196 104.23997 0.3257499 0.34217252
+ 17000 0.98600861 110.66055 0.3254722 0.34172446
+ 18000 0.98696963 116.90111 0.32472531 0.3408227
+ 19000 0.9881192 124.21305 0.32687644 0.34036538
+ 20000 0.98527319 131.09874 0.32774685 0.34003478
+ 21000 0.99015191 137.89263 0.32831579 0.33987868
+ 22000 0.97972418 146.68982 0.33338595 0.34060035
+ 23000 0.98911012 155.1264 0.33723129 0.34201036
+ 24000 0.98810498 162.88634 0.33934653 0.34371488
+ 25000 0.96961962 170.37907 0.34075814 0.34531409
+ 26000 0.99118408 179.26511 0.34474059 0.34717195
+ 27000 0.98515159 185.90764 0.3442734 0.34898035
+ 28000 0.98951677 192.12183 0.34307469 0.35021808
+ 29000 0.9832026 196.99457 0.33964581 0.35075459
+ 30000 0.98449493 203.48475 0.33914124 0.35066186
+ 31000 0.96585993 210.06193 0.33880956 0.35046715
+ 32000 0.98758117 218.94174 0.34209646 0.35046623
+ 33000 0.98875584 225.96489 0.34237104 0.35073944
+ 34000 0.98007229 233.5792 0.34349882 0.35109188
+ 35000 0.98415295 241.98148 0.34568783 0.35157879
+ 36000 0.98101154 250.30876 0.34765106 0.3523013
+ 37000 0.97606878 258.2127 0.34893608 0.35318097
+ 38000 0.97220293 266.40464 0.35053242 0.3540743
+ 39000 0.979783 272.8578 0.34981769 0.35496561
+ 40000 0.98375673 279.87598 0.34984497 0.35558182
+ 41000 0.97506523 288.07676 0.35131312 0.35618259
+ 42000 0.97106749 296.11647 0.3525196 0.35698571
+ 43000 0.97717259 304.46747 0.35403194 0.3577736
+ 44000 0.98541435 312.57228 0.35519578 0.35865003
+ 45000 0.97678287 321.82674 0.35758527 0.35958623
+ 46000 0.98169719 329.78197 0.35845866 0.36062236
+ 47000 0.99471466 337.11283 0.35863066 0.36158322
+ 48000 0.98332437 346.0754 0.3604952 0.36255042
+ 49000 0.98126947 356.11859 0.36338631 0.3636628
+ 50000 0.98809751 365.65248 0.36565248 0.36496809
+ 51000 0.95919516 373.91833 0.36658659 0.36628073
+ 52000 0.98097913 381.26492 0.36660089 0.36752237
+ 53000 0.97774072 388.81031 0.36680218 0.36863962
+ 54000 0.99096915 395.56767 0.36626636 0.36961521
+ 55000 0.97652739 401.72735 0.36520668 0.37038579
+ 56000 0.99185306 407.28834 0.3636503 0.37094092
+ 57000 0.96289342 414.75298 0.3638184 0.37130039
+ 58000 0.97871716 424.69443 0.36611588 0.37180428
+ 59000 0.98637393 433.14205 0.36706953 0.37239862
+ 60000 0.98009845 438.14533 0.36512111 0.37288487
+ 61000 0.99416712 446.08007 0.3656394 0.37321496
+ 62000 0.97612483 450.90846 0.36363585 0.37345792
+ 63000 0.97786531 455.36749 0.36140277 0.37344803
+ 64000 0.99080668 458.04873 0.35785057 0.37313914
+ 65000 0.97952497 461.31241 0.3548557 0.3725875
+ 66000 0.98095955 463.91727 0.35145248 0.37174735
+ 67000 0.98370788 468.93 0.34994776 0.37076942
+ 68000 0.96931818 471.07765 0.34638063 0.36961868
+ 69000 0.98512552 474.59146 0.34390685 0.36830908
+ 70000 0.98065743 478.66071 0.3419005 0.36686789
+ 71000 0.98971283 482.57357 0.33984054 0.36535224
+ 72000 0.99890324 485.32018 0.3370279 0.36373174
+ 73000 0.98649924 490.19497 0.33574998 0.36200692
+ 74000 0.98723422 496.04991 0.33516886 0.36034919
+ 75000 1.0025633 501.6313 0.33442087 0.35872052
+ 76000 0.97859959 505.97813 0.33288035 0.35714939
+ 77000 0.97973006 510.55334 0.33152814 0.35553808
+ 78000 0.9903944 515.06966 0.33017286 0.35391584
+ 79000 0.96847518 518.76483 0.32833217 0.35226287
+ 80000 0.99171112 524.18127 0.32761329 0.35065267
+ 81000 0.97202573 529.09959 0.32660468 0.34904364
+ 82000 0.99368438 535.80271 0.32670897 0.34747913
+ 83000 0.97932483 543.08233 0.32715803 0.34605097
+ 84000 0.99078651 547.57861 0.32593965 0.34469765
+ 85000 0.98973457 552.24581 0.32485048 0.34332115
+ 86000 0.9835873 557.3493 0.32404029 0.34197018
+ 87000 0.97180564 564.93434 0.32467491 0.34069702
+ 88000 0.99743353 571.39837 0.32465817 0.33951258
+ 89000 0.98993437 577.81703 0.32461631 0.33838511
+ 90000 0.9926071 583.39378 0.32410765 0.33730429
+ 91000 0.98800458 591.08741 0.3247733 0.33630505
+ 92000 0.98501879 596.10133 0.32396811 0.33534725
+ 93000 0.98810082 604.02652 0.32474544 0.33445545
+ 94000 0.97563748 609.43676 0.32416849 0.33361404
+ 95000 0.97283448 615.15754 0.32376713 0.33278044
+ 96000 0.9883071 622.30912 0.32411933 0.33199212
+ 97000 0.97717678 628.84457 0.32414669 0.33125729
+ 98000 0.97190208 634.37377 0.32366009 0.33054877
+ 99000 0.98687379 640.66666 0.32356902 0.32986014
+ 100000 0.97559757 646.96406 0.32348203 0.32920186
+Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms
+
+Performance: 5670494.518 tau/day, 13126.145 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19
+Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11
+Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34
+Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06
+Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60
+Other | | 0.4348 | | | 5.71
+
+Nlocal: 400 ave 413 max 391 min
+Histogram: 2 1 0 2 0 0 1 1 0 1
+Nghost: 204.75 ave 213 max 197 min
+Histogram: 1 1 0 1 0 3 0 1 0 1
+Neighs: 2800.62 ave 2959 max 2661 min
+Histogram: 1 1 1 2 0 0 0 1 1 1
+
+Total # of neighbors = 22405
+Ave neighs/atom = 7.00156
+Neighbor list builds = 12728
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
similarity index 84%
rename from examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
rename to examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
index 458315bc29..80c57ada9c 100644
--- a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8
+++ b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8
@@ -1,4 +1,4 @@
-LAMMPS (13 Oct 2016)
+LAMMPS (2 Aug 2018)
# sample LAMMPS input script for diffusion of 2d LJ liquid
# mean-squared displacement via compute msd
@@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574)
4 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3200 atoms
+ Time spent = 0.000712872 secs
pair_style lj/cut ${rc}
pair_style lj/cut 2.5
@@ -49,13 +50,18 @@ fix 3 all enforce2d
thermo 1000
run 5000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 53 53 1
-Memory usage per processor = 2.478 Mbytes
+ binsize = 1.4, bins = 53 53 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -1.56492 0 -0.5652325 -1.5346995
1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783
@@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press
3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297
4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691
5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287
-Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms
+Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms
-Performance: 3873826.669 tau/day, 8967.191 timesteps/s
-99.1% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 3332829.949 tau/day, 7714.884 timesteps/s
+99.9% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27
-Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55
-Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60
-Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02
-Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89
-Other | | 0.0372 | | | 6.67
+Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96
+Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01
+Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66
+Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02
+Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02
+Other | | 0.05398 | | | 8.33
Nlocal: 400 ave 406 max 394 min
Histogram: 1 1 0 1 0 2 1 0 1 1
@@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf
thermo 1000
run 100000
-Memory usage per processor = 2.853 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes
Step Temp c_vacf[4] v_vacf
0 0.97069905 1.9407914 0
1000 0.98138076 0.029239763 0.22157396
@@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf
98000 0.97190208 0.015065013 0.20906937
99000 0.98687379 -0.036869401 0.22993959
100000 0.97559757 0.045464091 0.23369283
-Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms
+Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms
-Performance: 3987213.825 tau/day, 9229.662 timesteps/s
-99.5% CPU use with 8 MPI tasks x no OpenMP threads
+Performance: 5289636.190 tau/day, 12244.528 timesteps/s
+100.0% CPU use with 8 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66
-Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68
-Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03
-Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15
-Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59
-Other | | 0.6383 | | | 5.89
+Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83
+Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15
+Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95
+Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21
+Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42
+Other | | 0.363 | | | 4.45
Nlocal: 400 ave 413 max 391 min
Histogram: 2 1 0 2 0 0 1 1 0 1
@@ -243,4 +249,4 @@ Total # of neighbors = 22405
Ave neighs/atom = 7.00156
Neighbor list builds = 12728
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:08
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index 2442b12b72..de23ba87ba 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -21,9 +21,11 @@ mass 1 1.0
set group all spin/random 11 2.50
-pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965
pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
@@ -44,10 +46,11 @@ variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
-thermo_style custom step time v_magnorm v_emag temp etotal
-thermo 50
+#thermo_style custom step time v_magnorm v_emag temp etotal
+thermo_style custom step time v_magnorm pe ke v_emag temp etotal
+thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-run 5000
+run 2000
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 4a42ec419a..35aa1df86c 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -19,8 +19,8 @@ create_atoms 1 box
mass 1 58.93
-#set group all spin/random 31 1.72
-set group all spin 1.72 0.0 0.0 1.0
+set group all spin/random 31 1.72
+#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
@@ -29,11 +29,11 @@ pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
-
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
-fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
@@ -56,4 +56,4 @@ thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
-run 2000
+run 20000
diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in
index a18163175c..0fa9c1b74c 100644
--- a/examples/USER/diffraction/BulkNi.in
+++ b/examples/USER/diffraction/BulkNi.in
@@ -20,7 +20,7 @@ compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
dR_Ewald 0.05 echo manual
-fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
+fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 5ec5a7cca8..0e7aaea1e1 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -641,18 +641,15 @@ int FixWallBodyPolygon::compute_distance_to_wall(double* x0, double rradi,
mode = VERTEX;
contact = 1;
} else {
+ mode = NONE;
if (side == XLO) {
if (x0[0] < wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == XHI) {
if (x0[0] > wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == YLO) {
if (x0[1] < wall_pos) mode = VERTEX;
- else mode = NONE;
} else if (side == YHI) {
if (x0[1] > wall_pos) mode = VERTEX;
- else mode = NONE;
}
}
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 2ff209d609..051be762e5 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -685,7 +685,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
{
int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
- double delx,dely,delz,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -749,7 +749,9 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
delx = h[0] - x[jbody][0];
dely = h[1] - x[jbody][1];
delz = h[2] - x[jbody][2];
- rij = sqrt(delx*delx + dely*dely + delz*delz);
+ rsq = delx*delx + dely*dely + delz*delz;
+ rsqinv = (rsq == 0.0) ? 0.0 : 1.0/rsq;
+ rij = sqrt(rsq);
R = rij - contact_dist;
energy = 0;
@@ -2077,6 +2079,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
double s1,s2,x13[3],x23[3],x13h[3];
double t13,t23,t31,t41,x31[3],x41[3];
+ t13=t23=t31=t41=0.0;
MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3
MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index 679690ea82..347177b7f4 100644
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -148,7 +148,7 @@ void FixNHKokkos<DeviceType>::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 92d9338dc8..9afa36b3c0 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -78,7 +78,7 @@ void PairATM::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
double xi,yi,zi,evdwl;
- double rij2,rik2,rjk2,r6;
+ double rij2,rik2,rjk2;
double rij[3],rik[3],rjk[3],fj[3],fk[3];
double nu_local;
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -91,8 +91,7 @@ void PairATM::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
- double cutoff_sixth = cut_global*cut_global;
- cutoff_sixth = cutoff_sixth*cutoff_sixth*cutoff_sixth;
+ double cutoff_squared = cut_global*cut_global;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -118,6 +117,7 @@ void PairATM::compute(int eflag, int vflag)
rij[2] = x[j][2] - zi;
if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ if (rij2 > cutoff_squared) continue;
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
@@ -130,20 +130,19 @@ void PairATM::compute(int eflag, int vflag)
rjk[2] = x[k][2] - x[j][2];
if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ if (rjk2 > cutoff_squared) continue;
rik[0] = x[k][0] - xi;
rik[1] = x[k][1] - yi;
rik[2] = x[k][2] - zi;
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
-
- r6 = rij2*rik2*rjk2;
- if (r6 > cutoff_sixth) continue;
+ if (rik2 > cutoff_squared) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
interaction_ddd(nu_local,
- r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+ rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
@@ -330,11 +329,12 @@ void PairATM::read_restart_settings(FILE *fp)
------------------------------------------------------------------------- */
void PairATM::interaction_ddd(double nu,
- double r6, double rij2, double rik2, double rjk2,
+ double rij2, double rik2, double rjk2,
double *rij, double *rik, double *rjk,
double *fj, double *fk, int eflag, double &eng)
{
- double r5inv,rri,rrj,rrk,rrr;
+ double r6,r5inv,rri,rrj,rrk,rrr;
+ r6 = rij2*rik2*rjk2;
r5inv = nu / (r6*r6*sqrt(r6));
rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 210351cfad..60d22348c3 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -39,11 +39,11 @@ class PairATM : public Pair {
void read_restart_settings(FILE *);
protected:
- double cut_global, cut_sixth;
+ double cut_global, cutoff_squared;
double ***nu;
void allocate();
- void interaction_ddd(double, double, double, double, double, double *,
+ void interaction_ddd(double, double, double, double, double *,
double *, double *, double *, double *, int, double &);
};
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
new file mode 100644
index 0000000000..66ebad6244
--- /dev/null
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -0,0 +1,677 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Alexander Stukowski
+ Technical University of Darmstadt,
+ Germany Department of Materials Science
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "pair_eam_cd.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define ASSERT(cond)
+#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
+
+PairEAMCD::PairEAMCD(LAMMPS *lmp, int _cdeamVersion)
+ : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion)
+{
+ single_enable = 0;
+ restartinfo = 0;
+
+ rhoB = NULL;
+ D_values = NULL;
+ hcoeff = NULL;
+
+ // Set communication buffer sizes needed by this pair style.
+
+ if (cdeamVersion == 1) {
+ comm_forward = 4;
+ comm_reverse = 3;
+ } else if (cdeamVersion == 2) {
+ comm_forward = 3;
+ comm_reverse = 2;
+ } else {
+ error->all(FLERR,"Invalid eam/cd potential version.");
+ }
+}
+
+PairEAMCD::~PairEAMCD()
+{
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ if (hcoeff) delete[] hcoeff;
+}
+
+void PairEAMCD::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,rhoip,rhojp,recip,phi;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+ // Grow per-atom arrays if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(rho);
+ memory->destroy(fp);
+ memory->destroy(rhoB);
+ memory->destroy(D_values);
+ nmax = atom->nmax;
+ memory->create(rho,nmax,"pair:rho");
+ memory->create(rhoB,nmax,"pair:rhoB");
+ memory->create(fp,nmax,"pair:fp");
+ memory->create(D_values,nmax,"pair:D_values");
+ }
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // Zero out per-atom arrays.
+
+ int m = nlocal + atom->nghost;
+ for (i = 0; i < m; i++) {
+ rho[i] = 0.0;
+ rhoB[i] = 0.0;
+ D_values[i] = 0.0;
+ }
+
+ // Stage I
+
+ // Compute rho and rhoB at each local atom site.
+
+ // Additionally calculate the D_i values here if we are using the
+ // one-site formulation. For the two-site formulation we have to
+ // calculate the D values in an extra loop (Stage II).
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+ double localrho = RhoOfR(index, jtype, itype);
+ rho[i] += localrho;
+ if (jtype == speciesB) rhoB[i] += localrho;
+ if (newton_pair || j < nlocal) {
+ localrho = RhoOfR(index, itype, jtype);
+ rho[j] += localrho;
+ if (itype == speciesB) rhoB[j] += localrho;
+ }
+
+ if (cdeamVersion == 1 && itype != jtype) {
+
+ // Note: if the i-j interaction is not concentration dependent (because either
+ // i or j are not species A or B) then its contribution to D_i and D_j should
+ // be ignored.
+ // This if-clause is only required for a ternary.
+
+ if ((itype == speciesA && jtype == speciesB)
+ || (jtype == speciesA && itype == speciesB)) {
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+ D_values[i] += Phi_AB;
+ if (newton_pair || j < nlocal)
+ D_values[j] += Phi_AB;
+ }
+ }
+ }
+ }
+ }
+
+ // Communicate and sum densities.
+
+ if (newton_pair) {
+ communicationStage = 1;
+ comm->reverse_comm_pair(this);
+ }
+
+ // fp = derivative of embedding energy at each atom
+ // phi = embedding energy at each atom
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ EAMTableIndex index = rhoToTableIndex(rho[i]);
+ fp[i] = FPrimeOfRho(index, type[i]);
+ if (eflag) {
+ phi = FofRho(index, type[i]);
+ if (eflag_global) eng_vdwl += phi;
+ if (eflag_atom) eatom[i] += phi;
+ }
+ }
+
+ // Communicate derivative of embedding function and densities
+ // and D_values (this for one-site formulation only).
+
+ communicationStage = 2;
+ comm->forward_comm_pair(this);
+
+ // The electron densities may not drop to zero because then the
+ // concentration would no longer be defined. But the concentration
+ // is not needed anyway if there is no interaction with another atom,
+ // which is the case if the electron density is exactly zero.
+ // That's why the following lines have been commented out.
+ //
+ //for (i = 0; i < nlocal + atom->nghost; i++) {
+ // if (rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
+ // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
+ //}
+
+ // Stage II
+ // This is only required for the original two-site formulation of the CD-EAM potential.
+
+ if (cdeamVersion == 2) {
+
+ // Compute intermediate value D_i for each atom.
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // This code line is required for ternary alloys.
+
+ if (itype != speciesA && itype != speciesB) continue;
+
+ double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+ jtype = type[j];
+ if (itype == jtype) continue;
+
+ // This code line is required for ternary alloys.
+
+ if (jtype != speciesA && jtype != speciesB) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // The concentration independent part of the cross pair potential.
+
+ double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
+
+ // Average concentration of two sites
+
+ double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
+
+ // Calculate derivative of h(x_ij) polynomial function.
+
+ double h_prime = evalHprime(x_ij);
+
+ D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
+ if (newton_pair || j < nlocal)
+ D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
+ }
+ }
+ }
+
+ // Communicate and sum D values.
+
+ if (newton_pair) {
+ communicationStage = 3;
+ comm->reverse_comm_pair(this);
+ }
+ communicationStage = 4;
+ comm->forward_comm_pair(this);
+ }
+
+ // Stage III
+
+ // Compute force acting on each atom.
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ // Concentration at site i
+ // The value -1 indicates: no concentration dependence for all interactions of atom i.
+ // It will be replaced by the concentration at site i if atom i is either A or B.
+
+ double x_i = -1.0;
+ double D_i, h_prime_i;
+
+ // This if-clause is only required for ternary alloys.
+
+ if ((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
+
+ // Compute local concentration at site i.
+
+ x_i = rhoB[i]/rho[i];
+ ASSERT(x_i >= 0 && x_i<=1.0);
+
+ if (cdeamVersion == 1) {
+
+ // Calculate derivative of h(x_i) polynomial function.
+
+ h_prime_i = evalHprime(x_i);
+ D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
+ } else if (cdeamVersion == 2) {
+ D_i = D_values[i];
+ } else {
+ ASSERT(false);
+ }
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq < cutforcesq) {
+ jtype = type[j];
+ double r = sqrt(rsq);
+ const EAMTableIndex index = radiusToTableIndex(r);
+
+ // rhoip = derivative of (density at atom j due to atom i)
+ // rhojp = derivative of (density at atom i due to atom j)
+ // psip needs both fp[i] and fp[j] terms since r_ij appears in two
+ // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
+ // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+
+ rhoip = RhoPrimeOfR(index, itype, jtype);
+ rhojp = RhoPrimeOfR(index, jtype, itype);
+ fpair = fp[i]*rhojp + fp[j]*rhoip;
+ recip = 1.0/r;
+
+ // The value -1 indicates: no concentration dependence for this
+ // i-j pair because atom j is not of species A nor B.
+
+ double x_j = -1;
+
+ // This code line is required for ternary alloy.
+
+ if (jtype == speciesA || jtype == speciesB) {
+ ASSERT(rho[i] != 0.0);
+ ASSERT(rho[j] != 0.0);
+
+ // Compute local concentration at site j.
+
+ x_j = rhoB[j]/rho[j];
+ ASSERT(x_j >= 0 && x_j<=1.0);
+
+ double D_j=0.0;
+ if (cdeamVersion == 1) {
+
+ // Calculate derivative of h(x_j) polynomial function.
+
+ double h_prime_j = evalHprime(x_j);
+ D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
+ } else if (cdeamVersion == 2) {
+ D_j = D_values[j];
+ } else {
+ ASSERT(false);
+ }
+ double t2 = -rhoB[j];
+ if (itype == speciesB) t2 += rho[j];
+ fpair += D_j * rhoip * t2;
+ }
+
+ // This if-clause is only required for a ternary alloy.
+ // Actually we don't need it at all because D_i should be zero
+ // anyway if atom i has no concentration dependent interactions
+ // (because it is not species A or B).
+
+ if (x_i != -1.0) {
+ double t1 = -rhoB[i];
+ if (jtype == speciesB) t1 += rho[i];
+ fpair += D_i * rhojp * t1;
+ }
+
+ double phip;
+ double phi = PhiOfR(index, itype, jtype, recip, phip);
+ if (itype == jtype || x_i == -1.0 || x_j == -1.0) {
+
+ // Case of no concentration dependence.
+
+ fpair += phip;
+ } else {
+
+ // We have a concentration dependence for the i-j interaction.
+
+ double h=0.0;
+ if (cdeamVersion == 1) {
+
+ // Calculate h(x_i) polynomial function.
+
+ double h_i = evalH(x_i);
+
+ // Calculate h(x_j) polynomial function.
+
+ double h_j = evalH(x_j);
+ h = 0.5 * (h_i + h_j);
+ } else if (cdeamVersion == 2) {
+
+ // Average concentration.
+
+ double x_ij = 0.5 * (x_i + x_j);
+
+ // Calculate h(x_ij) polynomial function.
+
+ h = evalH(x_ij);
+ } else {
+ ASSERT(false);
+ }
+ fpair += h * phip;
+ phi *= h;
+ }
+
+ // Divide by r_ij and negate to get forces from gradient.
+
+ fpair /= -r;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) evdwl = phi;
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::coeff(int narg, char **arg)
+{
+ PairEAMAlloy::coeff(narg, arg);
+
+ // Make sure the EAM file is a CD-EAM binary alloy.
+
+ if (setfl->nelements < 2)
+ error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
+
+ // Read in the coefficients of the h polynomial from the end of the EAM file.
+
+ read_h_coeff(arg[2]);
+
+ // Determine which atom type is the A species and which is the B
+ // species in the alloy. By default take the first element (index 0)
+ // in the EAM file as the A species and the second element (index 1)
+ // in the EAM file as the B species.
+
+ speciesA = -1;
+ speciesB = -1;
+ for (int i = 1; i <= atom->ntypes; i++) {
+ if (map[i] == 0) {
+ if (speciesA >= 0)
+ error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
+ speciesA = i;
+ }
+ if (map[i] == 1) {
+ if (speciesB >= 0)
+ error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
+ speciesB = i;
+ }
+ }
+ if (speciesA < 0)
+ error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
+ if (speciesB < 0)
+ error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
+}
+
+/* ----------------------------------------------------------------------
+ Reads in the h(x) polynomial coefficients
+------------------------------------------------------------------------- */
+
+void PairEAMCD::read_h_coeff(char *filename)
+{
+ if (comm->me == 0) {
+
+ // Open potential file
+
+ FILE *fptr;
+ char line[MAXLINE];
+ char nextline[MAXLINE];
+ fptr = force->open_potential(filename);
+ if (fptr == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open EAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
+
+ // h coefficients are stored at the end of the file.
+ // Skip to last line of file.
+
+ while(fgets(nextline, MAXLINE, fptr) != NULL) {
+ strcpy(line, nextline);
+ }
+ char* ptr = strtok(line, " \t\n\r\f");
+ int degree = atoi(ptr);
+ nhcoeff = degree+1;
+ hcoeff = new double[nhcoeff];
+ int i = 0;
+ while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
+ hcoeff[i++] = atof(ptr);
+ }
+ if (i != nhcoeff || nhcoeff < 1)
+ error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
+
+ // Close the potential file.
+
+ fclose(fptr);
+ }
+
+ MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
+ if (comm->me != 0) hcoeff = new double[nhcoeff];
+ MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+
+ m = 0;
+ if (communicationStage == 2) {
+ if (cdeamVersion == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ buf[m++] = D_values[j];
+ }
+ return m;
+ } else if (cdeamVersion == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = fp[j];
+ buf[m++] = rho[j];
+ buf[m++] = rhoB[j];
+ }
+ return m;
+ } else { ASSERT(false); return 0; }
+ } else if (communicationStage == 4) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = D_values[j];
+ }
+ return m;
+ } else return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ if (communicationStage == 2) {
+ if (cdeamVersion == 1) {
+ for (i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ D_values[i] = buf[m++];
+ }
+ } else if (cdeamVersion == 2) {
+ for (i = first; i < last; i++) {
+ fp[i] = buf[m++];
+ rho[i] = buf[m++];
+ rhoB[i] = buf[m++];
+ }
+ } else {
+ ASSERT(false);
+ }
+ } else if (communicationStage == 4) {
+ for (i = first; i < last; i++) {
+ D_values[i] = buf[m++];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+int PairEAMCD::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+
+ if (communicationStage == 1) {
+ if (cdeamVersion == 1) {
+ for (i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ buf[m++] = D_values[i];
+ }
+ return m;
+ } else if (cdeamVersion == 2) {
+ for (i = first; i < last; i++) {
+ buf[m++] = rho[i];
+ buf[m++] = rhoB[i];
+ }
+ return m;
+ } else { ASSERT(false); return 0; }
+ } else if (communicationStage == 3) {
+ for (i = first; i < last; i++) {
+ buf[m++] = D_values[i];
+ }
+ return m;
+ } else return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairEAMCD::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ if (communicationStage == 1) {
+ if (cdeamVersion == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ D_values[j] += buf[m++];
+ }
+ } else if (cdeamVersion == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ rho[j] += buf[m++];
+ rhoB[j] += buf[m++];
+ }
+ } else {
+ ASSERT(false);
+ }
+ } else if (communicationStage == 3) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ D_values[j] += buf[m++];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+double PairEAMCD::memory_usage()
+{
+ double bytes = 2 * nmax * sizeof(double);
+ return PairEAMAlloy::memory_usage() + bytes;
+}
diff --git a/src/USER-MISC/pair_cdeam.h b/src/MANYBODY/pair_eam_cd.h
similarity index 93%
rename from src/USER-MISC/pair_cdeam.h
rename to src/MANYBODY/pair_eam_cd.h
index 934b7601a4..ee84fb09c5 100644
--- a/src/USER-MISC/pair_cdeam.h
+++ b/src/MANYBODY/pair_eam_cd.h
@@ -13,26 +13,26 @@
#ifdef PAIR_CLASS
-PairStyle(eam/cd,PairCDEAM_OneSite)
-PairStyle(eam/cd/old,PairCDEAM_TwoSite)
+PairStyle(eam/cd,PairEAMCD_OneSite)
+PairStyle(eam/cd/old,PairEAMCD_TwoSite)
#else
-#ifndef LMP_PAIR_CDEAM_H
-#define LMP_PAIR_CDEAM_H
+#ifndef LMP_PAIR_EAM_CD_H
+#define LMP_PAIR_EAM_CD_H
#include "pair_eam_alloy.h"
namespace LAMMPS_NS {
-class PairCDEAM : public PairEAMAlloy
+class PairEAMCD : public PairEAMAlloy
{
public:
/// Constructor.
- PairCDEAM(class LAMMPS*, int cdeamVersion);
+ PairEAMCD(class LAMMPS*, int cdeamVersion);
/// Destructor.
- virtual ~PairCDEAM();
+ virtual ~PairEAMCD();
/// Calculates the energies and forces for all atoms in the system.
virtual void compute(int, int);
@@ -211,19 +211,19 @@ public:
};
/// The one-site concentration formulation of CD-EAM.
- class PairCDEAM_OneSite : public PairCDEAM
+ class PairEAMCD_OneSite : public PairEAMCD
{
public:
/// Constructor.
- PairCDEAM_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 1) {}
+ PairEAMCD_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 1) {}
};
/// The two-site concentration formulation of CD-EAM.
- class PairCDEAM_TwoSite : public PairCDEAM
+ class PairEAMCD_TwoSite : public PairEAMCD
{
public:
/// Constructor.
- PairCDEAM_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 2) {}
+ PairEAMCD_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 2) {}
};
}
diff --git a/src/Purge.list b/src/Purge.list
index cd4eb17dab..cb98636b1c 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -24,6 +24,9 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
+# renamed on 31 July 2018
+pair_cdeam.h
+pair_cdeam.cpp
# renamed on 20 July 2018
pair_body.h
pair_body.cpp
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 8b47eff624..6460a6185f 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -816,9 +816,9 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values)
x[nlocal][2] = coord[2];
sp[nlocal][3] = atof(values[2]);
- sp[nlocal][0] = atof(values[5]);
- sp[nlocal][1] = atof(values[6]);
- sp[nlocal][2] = atof(values[7]);
+ sp[nlocal][0] = atof(values[6]);
+ sp[nlocal][1] = atof(values[7]);
+ sp[nlocal][2] = atof(values[8]);
double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] +
sp[nlocal][1]*sp[nlocal][1] +
sp[nlocal][2]*sp[nlocal][2]);
diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp
index b67f62d53d..dc16190c98 100644
--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@@ -105,16 +105,16 @@ void ComputeSpin::compute_vector()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (atom->sp_flag) {
- mag[0] += sp[i][0];
- mag[1] += sp[i][1];
- mag[2] += sp[i][2];
- magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
- tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
- ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
- tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
- tempnum += tx*tx+ty*ty+tz*tz;
- tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2];
- countsp++;
+ mag[0] += sp[i][0];
+ mag[1] += sp[i][1];
+ mag[2] += sp[i][2];
+ magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]);
+ tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1];
+ ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2];
+ tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0];
+ tempnum += tx*tx+ty*ty+tz*tz;
+ tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2];
+ countsp++;
}
}
else error->all(FLERR,"Compute compute/spin requires atom/spin style");
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index b792969c5d..08e2c63e7f 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -65,6 +65,9 @@ PairSpinDmi::~PairSpinDmi()
memory->destroy(v_dmx);
memory->destroy(v_dmy);
memory->destroy(v_dmz);
+ memory->destroy(vmech_dmx);
+ memory->destroy(vmech_dmy);
+ memory->destroy(vmech_dmz);
memory->destroy(cutsq);
}
}
@@ -118,7 +121,7 @@ void PairSpinDmi::coeff(int narg, char **arg)
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
const double rij = force->numeric(FLERR,arg[3]);
- const double dm = (force->numeric(FLERR,arg[4]))/hbar;
+ const double dm = (force->numeric(FLERR,arg[4]));
double dmx = force->numeric(FLERR,arg[5]);
double dmy = force->numeric(FLERR,arg[6]);
double dmz = force->numeric(FLERR,arg[7]);
@@ -133,9 +136,12 @@ void PairSpinDmi::coeff(int narg, char **arg)
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_spin_dmi[i][j] = rij;
DM[i][j] = dm;
- v_dmx[i][j] = dmx * dm;
- v_dmy[i][j] = dmy * dm;
- v_dmz[i][j] = dmz * dm;
+ v_dmx[i][j] = dmx * dm / hbar;
+ v_dmy[i][j] = dmy * dm / hbar;
+ v_dmz[i][j] = dmz * dm / hbar;
+ vmech_dmx[i][j] = dmx * dm;
+ vmech_dmy[i][j] = dmy * dm;
+ vmech_dmz[i][j] = dmz * dm;
setflag[i][j] = 1;
count++;
}
@@ -187,9 +193,17 @@ void PairSpinDmi::init_style()
double PairSpinDmi::init_one(int i, int j)
{
-
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ DM[j][i] = DM[i][j];
+ v_dmx[j][i] = v_dmx[i][j];
+ v_dmy[j][i] = v_dmy[i][j];
+ v_dmz[j][i] = v_dmz[i][j];
+ vmech_dmx[j][i] = vmech_dmx[i][j];
+ vmech_dmy[j][i] = vmech_dmy[i][j];
+ vmech_dmz[j][i] = vmech_dmz[i][j];
+ cut_spin_dmi[j][i] = cut_spin_dmi[i][j];
+
return cut_spin_dmi_global;
}
@@ -210,7 +224,8 @@ void PairSpinDmi::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -264,20 +279,17 @@ void PairSpinDmi::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = rij[1] = rij[2] = 0.0;
- eij[0] = eij[1] = eij[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = rij[0]*inorm;
- eij[1] = rij[1]*inorm;
- eij[2] = rij[2]*inorm;
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype];
@@ -286,7 +298,7 @@ void PairSpinDmi::compute(int eflag, int vflag)
if (rsq <= local_cut2) {
compute_dmi(i,j,eij,fmi,spj);
if (lattice_flag) {
- compute_dmi_mech(fi);
+ compute_dmi_mech(i,j,rsq,eij,fi,spi,spj);
}
}
@@ -309,7 +321,7 @@ void PairSpinDmi::compute(int eflag, int vflag)
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -325,8 +337,8 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -358,14 +370,14 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = rij[0]*inorm;
- eij[1] = rij[1]*inorm;
- eij[2] = rij[2]*inorm;
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype];
@@ -390,23 +402,45 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
jtype = type[j];
dmix = eij[1]*v_dmz[itype][jtype] - eij[2]*v_dmy[itype][jtype];
- dmiy = eij[2]*v_dmx[itype][jtype] - eij[2]*v_dmz[itype][jtype];
+ dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype];
dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype];
- fmi[0] += (spj[1]*dmiz - spj[2]*dmiy);
- fmi[1] += (spj[2]*dmix - spj[0]*dmiz);
- fmi[2] += (spj[0]*dmiy - spj[1]*dmix);
+ fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy);
+ fmi[1] -= (spj[2]*dmix - spj[0]*dmiz);
+ fmi[2] -= (spj[0]*dmiy - spj[1]*dmix);
}
/* ----------------------------------------------------------------------
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinDmi::compute_dmi_mech(double fi[3])
+void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double eij[3],
+ double fi[3], double spi[3], double spj[3])
{
- fi[0] += 0.0;
- fi[1] += 0.0;
- fi[2] += 0.0;
+ int *type = atom->type;
+ int itype, jtype;
+ double dmix,dmiy,dmiz;
+ itype = type[i];
+ jtype = type[j];
+ double csx,csy,csz,cdmx,cdmy,cdmz,irij;
+
+ irij = 1.0/sqrt(rsq);
+
+ dmix = vmech_dmx[itype][jtype];
+ dmiy = vmech_dmy[itype][jtype];
+ dmiz = vmech_dmz[itype][jtype];
+
+ csx = (spi[1]*spj[2] - spi[2]*spj[1]);
+ csy = (spi[2]*spj[0] - spi[0]*spj[2]);
+ csz = (spi[0]*spj[1] - spi[1]*spj[0]);
+
+ cdmx = (dmiy*csz - dmiz*csy);
+ cdmy = (dmiz*csx - dmix*csz);
+ cdmz = (dmix*csy - dmiy*csz);
+
+ fi[0] += irij*cdmx;
+ fi[1] += irij*cdmy;
+ fi[2] += irij*cdmz;
}
/* ----------------------------------------------------------------------
@@ -428,6 +462,9 @@ void PairSpinDmi::allocate()
memory->create(v_dmx,n+1,n+1,"pair:DM_vector_x");
memory->create(v_dmy,n+1,n+1,"pair:DM_vector_y");
memory->create(v_dmz,n+1,n+1,"pair:DM_vector_z");
+ memory->create(vmech_dmx,n+1,n+1,"pair:DMmech_vector_x");
+ memory->create(vmech_dmy,n+1,n+1,"pair:DMmech_vector_y");
+ memory->create(vmech_dmz,n+1,n+1,"pair:DMmech_vector_z");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
@@ -451,6 +488,9 @@ void PairSpinDmi::write_restart(FILE *fp)
fwrite(&v_dmx[i][j],sizeof(double),1,fp);
fwrite(&v_dmy[i][j],sizeof(double),1,fp);
fwrite(&v_dmz[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmx[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmy[i][j],sizeof(double),1,fp);
+ fwrite(&vmech_dmz[i][j],sizeof(double),1,fp);
fwrite(&cut_spin_dmi[i][j],sizeof(double),1,fp);
}
}
@@ -478,12 +518,18 @@ void PairSpinDmi::read_restart(FILE *fp)
fread(&v_dmx[i][j],sizeof(double),1,fp);
fread(&v_dmy[i][j],sizeof(double),1,fp);
fread(&v_dmz[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmx[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmy[i][j],sizeof(double),1,fp);
+ fread(&vmech_dmz[i][j],sizeof(double),1,fp);
fread(&cut_spin_dmi[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmy[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&v_dmz[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmx[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmy[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&vmech_dmz[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_spin_dmi[i][j],1,MPI_DOUBLE,0,world);
}
}
diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h
index a309f0c8d5..68e42e879d 100644
--- a/src/SPIN/pair_spin_dmi.h
+++ b/src/SPIN/pair_spin_dmi.h
@@ -38,22 +38,23 @@ class PairSpinDmi : public PairSpin {
void compute_single_pair(int, double *);
void compute_dmi(int, int, double *, double *, double *);
- void compute_dmi_mech(double *);
+ void compute_dmi_mech(int, int, double, double *, double *, double *, double *);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
- double cut_spin_dmi_global; // short range pair cutoff
+ double cut_spin_dmi_global; // short range pair cutoff
protected:
- double **DM; // dmi coeff in eV
- double **v_dmx, **v_dmy, **v_dmz; // dmi direction
- double **cut_spin_dmi; // cutoff distance dmi
+ double **DM; // dmi coeff in eV
+ double **v_dmx, **v_dmy, **v_dmz; // dmi direction
+ double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction
+ double **cut_spin_dmi; // cutoff distance dmi
- int lattice_flag; // flag for mech force computation
- class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups
+ int lattice_flag; // flag for mech force computation
+ class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups
void allocate();
};
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index 1b7b36b6db..cc074bb97d 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -65,7 +65,7 @@ PairSpinExchange::~PairSpinExchange()
memory->destroy(J1_mech);
memory->destroy(J2);
memory->destroy(J3);
- memory->destroy(cutsq); // to be deleted
+ memory->destroy(cutsq); // to be implemented
}
}
@@ -134,8 +134,8 @@ void PairSpinExchange::coeff(int narg, char **arg)
count++;
}
}
- if (count == 0)
- error->all(FLERR,"Incorrect args in pair_style command");
+
+ if (count == 0) error->all(FLERR,"Incorrect args in pair_style command");
}
/* ----------------------------------------------------------------------
@@ -183,6 +183,12 @@ double PairSpinExchange::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ J1_mag[j][i] = J1_mag[i][j];
+ J1_mech[j][i] = J1_mech[i][j];
+ J2[j][i] = J2[i][j];
+ J3[j][i] = J3[i][j];
+ cut_spin_exchange[j][i] = cut_spin_exchange[i][j];
+
return cut_spin_exchange_global;
}
@@ -203,7 +209,8 @@ void PairSpinExchange::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -255,18 +262,17 @@ void PairSpinExchange::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype];
@@ -298,7 +304,7 @@ void PairSpinExchange::compute(int eflag, int vflag)
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -317,8 +323,8 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
double xi[3], rij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -351,15 +357,14 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= local_cut2) {
compute_exchange(i,j,rsq,fmi,spj);
}
-
}
}
@@ -390,7 +395,8 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3],
compute the mechanical force due to the exchange interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double rij[3], double fi[3], double spi[3], double spj[3])
+void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3],
+ double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
@@ -408,9 +414,9 @@ void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double ri
Jex_mech *= 8.0*Jex*rr*exp(-ra);
Jex_mech *= (spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]);
- fi[0] -= Jex_mech*rij[0];
- fi[1] -= Jex_mech*rij[1];
- fi[2] -= Jex_mech*rij[2];
+ fi[0] -= Jex_mech*eij[0];
+ fi[1] -= Jex_mech*eij[1];
+ fi[2] -= Jex_mech*eij[2];
}
/* ----------------------------------------------------------------------
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 315b691d17..6bc1f71947 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -187,8 +187,14 @@ void PairSpinMagelec::init_style()
double PairSpinMagelec::init_one(int i, int j)
{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
- if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ ME[j][i] = ME[i][j];
+ ME_mech[j][i] = ME_mech[i][j];
+ v_mex[j][i] = v_mex[i][j];
+ v_mey[j][i] = v_mey[i][j];
+ v_mez[j][i] = v_mez[i][j];
+ cut_spin_magelec[j][i] = cut_spin_magelec[i][j];
return cut_spin_magelec_global;
}
@@ -211,7 +217,8 @@ void PairSpinMagelec::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl, ecoul;
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spi[3], spj[3];
double fi[3], fmi[3];
double local_cut2;
@@ -263,18 +270,17 @@ void PairSpinMagelec::compute(int eflag, int vflag)
spj[2] = sp[j][2];
evdwl = 0.0;
-
fi[0] = fi[1] = fi[2] = 0.0;
fmi[0] = fmi[1] = fmi[2] = 0.0;
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype];
@@ -301,12 +307,12 @@ void PairSpinMagelec::compute(int eflag, int vflag)
}
if (eflag) {
- evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
+ evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]);
evdwl *= hbar;
} else evdwl = 0.0;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]);
+ evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz);
}
}
@@ -322,8 +328,8 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
double **x = atom->x;
double **sp = atom->sp;
double local_cut2;
-
- double xi[3], rij[3], eij[3];
+ double xi[3], eij[3];
+ double delx,dely,delz;
double spj[3];
int i,j,jnum,itype,jtype;
@@ -342,8 +348,6 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
xi[1] = x[i][1];
xi[2] = x[i][2];
- eij[0] = eij[1] = eij[2] = 0.0;
-
jlist = firstneigh[i];
jnum = numneigh[i];
@@ -358,14 +362,14 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
spj[1] = sp[j][1];
spj[2] = sp[j][2];
- rij[0] = x[j][0] - xi[0];
- rij[1] = x[j][1] - xi[1];
- rij[2] = x[j][2] - xi[2];
- rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ delx = xi[0] - x[j][0];
+ dely = xi[1] - x[j][1];
+ delz = xi[2] - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
inorm = 1.0/sqrt(rsq);
- eij[0] = inorm*rij[0];
- eij[1] = inorm*rij[1];
- eij[2] = inorm*rij[2];
+ eij[0] = -inorm*delx;
+ eij[1] = -inorm*dely;
+ eij[2] = -inorm*delz;
if (rsq <= local_cut2) {
compute_magelec(i,j,rsq,eij,fmi,spj);
@@ -380,36 +384,26 @@ void PairSpinMagelec::compute_magelec(int i, int j, double rsq, double eij[3], d
{
int *type = atom->type;
int itype, jtype;
+ double meix,meiy,meiz;
+ double vx,vy,vz;
itype = type[i];
jtype = type[j];
- double local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype];
-
- if (rsq <= local_cut2) {
- double meix,meiy,meiz;
- double rx, ry, rz;
- double vx, vy, vz;
-
- rx = eij[0];
- ry = eij[1];
- rz = eij[2];
-
- vx = v_mex[itype][jtype];
- vy = v_mey[itype][jtype];
- vz = v_mez[itype][jtype];
+ vx = v_mex[itype][jtype];
+ vy = v_mey[itype][jtype];
+ vz = v_mez[itype][jtype];
- meix = vy*rz - vz*ry;
- meiy = vz*rx - vx*rz;
- meiz = vx*ry - vy*rx;
+ meix = vy*eij[2] - vz*eij[1];
+ meiy = vz*eij[0] - vx*eij[2];
+ meiz = vx*eij[1] - vy*eij[0];
- meix *= ME[itype][jtype];
- meiy *= ME[itype][jtype];
- meiz *= ME[itype][jtype];
+ meix *= ME[itype][jtype];
+ meiy *= ME[itype][jtype];
+ meiz *= ME[itype][jtype];
- fmi[0] += spj[1]*meiz - spj[2]*meiy;
- fmi[1] += spj[2]*meix - spj[0]*meiz;
- fmi[2] += spj[0]*meiy - spj[1]*meix;
- }
+ fmi[0] += spj[1]*meiz - spj[2]*meiy;
+ fmi[1] += spj[2]*meix - spj[0]*meiz;
+ fmi[2] += spj[0]*meiy - spj[1]*meix;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
index 0daafad756..55f537cf4f 100644
--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@@ -193,8 +193,16 @@ void PairSpinNeel::init_style()
double PairSpinNeel::init_one(int i, int j)
{
-
- if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ g1[j][i] = g1[i][j];
+ g1_mech[j][i] = g1_mech[i][j];
+ g2[j][i] = g2[i][j];
+ g3[j][i] = g3[i][j];
+ q1[j][i] = q1[i][j];
+ q1_mech[j][i] = q1_mech[i][j];
+ q2[j][i] = q2[i][j];
+ q3[j][i] = q3[i][j];
return cut_spin_neel_global;
}
diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h
index 934d4a93ad..f60d7d2dca 100644
--- a/src/SPIN/pair_spin_neel.h
+++ b/src/SPIN/pair_spin_neel.h
@@ -51,9 +51,9 @@ class PairSpinNeel : public PairSpin {
// pseudo-dipolar and pseudo-quadrupolar coeff.
- double **g1, **g1_mech; // exchange coeffs gij
+ double **g1, **g1_mech; // neel coeffs gij
double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang
- double **q1, **q1_mech; // exchange coeffs qij
+ double **q1, **q1_mech; // neel coeffs qij
double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang
double **cut_spin_neel; // cutoff distance exchange
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 37e128f556..7fb8a27110 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -846,7 +846,7 @@ void FixBocs::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@@ -1508,7 +1508,7 @@ double FixBocs::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@@ -1539,15 +1539,21 @@ double FixBocs::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
- for (i = 0; i < 3; i++)
- if (p_flag[i])
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
+ lkt_press += kt;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i])
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ lkt_press += kt;
+ }
+ }
}
// extra contributions from thermostat chain for barostat
@@ -1880,15 +1886,14 @@ void FixBocs::nhc_temp_integrate()
void FixBocs::nhc_press_integrate()
{
- int ich,i;
+ int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
- double lkt_press = kt;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@@ -1912,14 +1917,24 @@ void FixBocs::nhc_press_integrate()
}
kecurrent = 0.0;
- for (i = 0; i < 3; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof = 0;
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
+ }
}
+ double lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;
diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh
deleted file mode 100755
index 2d42125ec3..0000000000
--- a/src/USER-MISC/Install.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-# Install/unInstall package files in LAMMPS
-# mode = 0/1/2 for uninstall/install/update
-
-mode=$1
-
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL
-
-# arg1 = file, arg2 = file it depends on
-
-action () {
- if (test $mode = 0) then
- rm -f ../$1
- elif (! cmp -s $1 ../$1) then
- if (test -z "$2" || test -e ../$2) then
- cp $1 ..
- if (test $mode = 2) then
- echo " updating src/$1"
- fi
- fi
- elif (test ! -n "$2") then
- if (test ! -e ../$2) then
- rm -f ../$1
- fi
- fi
-}
-
-# all package files
-# only a few files have dependencies
-
-for file in *.cpp *.h; do
- if (test $file = "pair_cdeam.cpp") then
- action pair_cdeam.cpp pair_eam_alloy.cpp
- elif (test $file = "pair_cdeam.h") then
- action pair_cdeam.h pair_eam_alloy.cpp
- else
- test -f ${file} && action $file
- fi
-done
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 68a6252d8d..0f9e7bf383 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -65,7 +65,6 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
-pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp
deleted file mode 100644
index 53d9036a61..0000000000
--- a/src/USER-MISC/pair_cdeam.cpp
+++ /dev/null
@@ -1,644 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Alexander Stukowski
- Technical University of Darmstadt,
- Germany Department of Materials Science
-------------------------------------------------------------------------- */
-
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include "pair_cdeam.h"
-#include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-// This is for debugging purposes. The ASSERT() macro is used in the code to check
-// if everything runs as expected. Change this to #if 0 if you don't need the checking.
-#if 0
- #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop())
-
- inline void my_noop() {}
- inline void my_failure(Error* error, const char* file, int line) {
- char str[1024];
- sprintf(str,"Assertion failure: File %s, line %i", file, line);
- error->one(FLERR,str);
- }
-#else
- #define ASSERT(cond)
-#endif
-
-#define MAXLINE 1024 // This sets the maximum line length in EAM input files.
-
-PairCDEAM::PairCDEAM(LAMMPS *lmp, int _cdeamVersion) : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion)
-{
- single_enable = 0;
- restartinfo = 0;
-
- rhoB = NULL;
- D_values = NULL;
- hcoeff = NULL;
-
- // Set communication buffer sizes needed by this pair style.
- if(cdeamVersion == 1) {
- comm_forward = 4;
- comm_reverse = 3;
- }
- else if(cdeamVersion == 2) {
- comm_forward = 3;
- comm_reverse = 2;
- }
- else {
- error->all(FLERR,"Invalid CD-EAM potential version.");
- }
-}
-
-PairCDEAM::~PairCDEAM()
-{
- memory->destroy(rhoB);
- memory->destroy(D_values);
- if(hcoeff) delete[] hcoeff;
-}
-
-void PairCDEAM::compute(int eflag, int vflag)
-{
- int i,j,ii,jj,inum,jnum,itype,jtype;
- double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
- double rsq,rhoip,rhojp,recip,phi;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- evdwl = 0.0;
- if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
-
- // Grow per-atom arrays if necessary
- if(atom->nmax > nmax) {
- memory->destroy(rho);
- memory->destroy(fp);
- memory->destroy(rhoB);
- memory->destroy(D_values);
- nmax = atom->nmax;
- memory->create(rho,nmax,"pair:rho");
- memory->create(rhoB,nmax,"pair:rhoB");
- memory->create(fp,nmax,"pair:fp");
- memory->create(D_values,nmax,"pair:D_values");
- }
-
- double **x = atom->x;
- double **f = atom->f;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int newton_pair = force->newton_pair;
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // Zero out per-atom arrays.
- int m = nlocal + atom->nghost;
- for(i = 0; i < m; i++) {
- rho[i] = 0.0;
- rhoB[i] = 0.0;
- D_values[i] = 0.0;
- }
-
- // Stage I
-
- // Compute rho and rhoB at each local atom site.
- // Additionally calculate the D_i values here if we are using the one-site formulation.
- // For the two-site formulation we have to calculate the D values in an extra loop (Stage II).
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
- double localrho = RhoOfR(index, jtype, itype);
- rho[i] += localrho;
- if(jtype == speciesB) rhoB[i] += localrho;
- if(newton_pair || j < nlocal) {
- localrho = RhoOfR(index, itype, jtype);
- rho[j] += localrho;
- if(itype == speciesB) rhoB[j] += localrho;
- }
-
- if(cdeamVersion == 1 && itype != jtype) {
- // Note: if the i-j interaction is not concentration dependent (because either
- // i or j are not species A or B) then its contribution to D_i and D_j should
- // be ignored.
- // This if-clause is only required for a ternary.
- if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) {
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
- D_values[i] += Phi_AB;
- if(newton_pair || j < nlocal)
- D_values[j] += Phi_AB;
- }
- }
- }
- }
- }
-
- // Communicate and sum densities.
- if(newton_pair) {
- communicationStage = 1;
- comm->reverse_comm_pair(this);
- }
-
- // fp = derivative of embedding energy at each atom
- // phi = embedding energy at each atom
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- EAMTableIndex index = rhoToTableIndex(rho[i]);
- fp[i] = FPrimeOfRho(index, type[i]);
- if(eflag) {
- phi = FofRho(index, type[i]);
- if (eflag_global) eng_vdwl += phi;
- if (eflag_atom) eatom[i] += phi;
- }
- }
-
- // Communicate derivative of embedding function and densities
- // and D_values (this for one-site formulation only).
- communicationStage = 2;
- comm->forward_comm_pair(this);
-
- // The electron densities may not drop to zero because then the concentration would no longer be defined.
- // But the concentration is not needed anyway if there is no interaction with another atom, which is the case
- // if the electron density is exactly zero. That's why the following lines have been commented out.
- //
- //for(i = 0; i < nlocal + atom->nghost; i++) {
- // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB))
- // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density.");
- //}
-
- // Stage II
- // This is only required for the original two-site formulation of the CD-EAM potential.
-
- if(cdeamVersion == 2) {
- // Compute intermediate value D_i for each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // This code line is required for ternary alloys.
- if(itype != speciesA && itype != speciesB) continue;
-
- double x_i = rhoB[i] / rho[i]; // Concentration at atom i.
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = type[j];
- if(itype == jtype) continue;
-
- // This code line is required for ternary alloys.
- if(jtype != speciesA && jtype != speciesB) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // The concentration independent part of the cross pair potential.
- double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r);
-
- // Average concentration of two sites
- double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]);
-
- // Calculate derivative of h(x_ij) polynomial function.
- double h_prime = evalHprime(x_ij);
-
- D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]);
- if(newton_pair || j < nlocal)
- D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]);
- }
- }
- }
-
- // Communicate and sum D values.
- if(newton_pair) {
- communicationStage = 3;
- comm->reverse_comm_pair(this);
- }
- communicationStage = 4;
- comm->forward_comm_pair(this);
- }
-
- // Stage III
-
- // Compute force acting on each atom.
- for(ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
-
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- // Concentration at site i
- double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i.
- // It will be replaced by the concentration at site i if atom i is either A or B.
-
- double D_i, h_prime_i;
-
- // This if-clause is only required for ternary alloys.
- if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) {
-
- // Compute local concentration at site i.
- x_i = rhoB[i]/rho[i];
- ASSERT(x_i >= 0 && x_i<=1.0);
-
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_i) polynomial function.
- h_prime_i = evalHprime(x_i);
- D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]);
- } else if(cdeamVersion == 2) {
- D_i = D_values[i];
- } else {
- ASSERT(false);
- }
- }
-
- for(jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if(rsq < cutforcesq) {
- jtype = type[j];
- double r = sqrt(rsq);
- const EAMTableIndex index = radiusToTableIndex(r);
-
- // rhoip = derivative of (density at atom j due to atom i)
- // rhojp = derivative of (density at atom i due to atom j)
- // psip needs both fp[i] and fp[j] terms since r_ij appears in two
- // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
- // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
- rhoip = RhoPrimeOfR(index, itype, jtype);
- rhojp = RhoPrimeOfR(index, jtype, itype);
- fpair = fp[i]*rhojp + fp[j]*rhoip;
- recip = 1.0/r;
-
- double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair
- // because atom j is not of species A nor B.
-
- // This code line is required for ternary alloy.
- if(jtype == speciesA || jtype == speciesB) {
- ASSERT(rho[i] != 0.0);
- ASSERT(rho[j] != 0.0);
-
- // Compute local concentration at site j.
- x_j = rhoB[j]/rho[j];
- ASSERT(x_j >= 0 && x_j<=1.0);
-
- double D_j=0.0;
- if(cdeamVersion == 1) {
- // Calculate derivative of h(x_j) polynomial function.
- double h_prime_j = evalHprime(x_j);
- D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]);
- } else if(cdeamVersion == 2) {
- D_j = D_values[j];
- } else {
- ASSERT(false);
- }
- double t2 = -rhoB[j];
- if(itype == speciesB) t2 += rho[j];
- fpair += D_j * rhoip * t2;
- }
-
- // This if-clause is only required for a ternary alloy.
- // Actually we don't need it at all because D_i should be zero anyway if
- // atom i has no concentration dependent interactions (because it is not species A or B).
- if(x_i != -1.0) {
- double t1 = -rhoB[i];
- if(jtype == speciesB) t1 += rho[i];
- fpair += D_i * rhojp * t1;
- }
-
- double phip;
- double phi = PhiOfR(index, itype, jtype, recip, phip);
- if(itype == jtype || x_i == -1.0 || x_j == -1.0) {
- // Case of no concentration dependence.
- fpair += phip;
- } else {
- // We have a concentration dependence for the i-j interaction.
- double h=0.0;
- if(cdeamVersion == 1) {
- // Calculate h(x_i) polynomial function.
- double h_i = evalH(x_i);
- // Calculate h(x_j) polynomial function.
- double h_j = evalH(x_j);
- h = 0.5 * (h_i + h_j);
- } else if(cdeamVersion == 2) {
- // Average concentration.
- double x_ij = 0.5 * (x_i + x_j);
- // Calculate h(x_ij) polynomial function.
- h = evalH(x_ij);
- } else {
- ASSERT(false);
- }
- fpair += h * phip;
- phi *= h;
- }
-
- // Divide by r_ij and negate to get forces from gradient.
- fpair /= -r;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if(newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if(eflag) evdwl = phi;
- if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- }
- }
- }
-
- if(vflag_fdotr) virial_fdotr_compute();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::coeff(int narg, char **arg)
-{
- PairEAMAlloy::coeff(narg, arg);
-
- // Make sure the EAM file is a CD-EAM binary alloy.
- if(setfl->nelements < 2)
- error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style.");
-
- // Read in the coefficients of the h polynomial from the end of the EAM file.
- read_h_coeff(arg[2]);
-
- // Determine which atom type is the A species and which is the B species in the alloy.
- // By default take the first element (index 0) in the EAM file as the A species
- // and the second element (index 1) in the EAM file as the B species.
- speciesA = -1;
- speciesB = -1;
- for(int i = 1; i <= atom->ntypes; i++) {
- if(map[i] == 0) {
- if(speciesA >= 0)
- error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type.");
- speciesA = i;
- }
- if(map[i] == 1) {
- if(speciesB >= 0)
- error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type.");
- speciesB = i;
- }
- }
- if(speciesA < 0)
- error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type.");
- if(speciesB < 0)
- error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type.");
-}
-
-/* ----------------------------------------------------------------------
- Reads in the h(x) polynomial coefficients
-------------------------------------------------------------------------- */
-void PairCDEAM::read_h_coeff(char *filename)
-{
- if(comm->me == 0) {
- // Open potential file
- FILE *fptr;
- char line[MAXLINE];
- char nextline[MAXLINE];
- fptr = force->open_potential(filename);
- if (fptr == NULL) {
- char str[128];
- sprintf(str,"Cannot open EAM potential file %s", filename);
- error->one(FLERR,str);
- }
-
- // h coefficients are stored at the end of the file.
- // Skip to last line of file.
- while(fgets(nextline, MAXLINE, fptr) != NULL) {
- strcpy(line, nextline);
- }
- char* ptr = strtok(line, " \t\n\r\f");
- int degree = atoi(ptr);
- nhcoeff = degree+1;
- hcoeff = new double[nhcoeff];
- int i = 0;
- while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) {
- hcoeff[i++] = atof(ptr);
- }
- if(i != nhcoeff || nhcoeff < 1)
- error->one(FLERR,"Failed to read h(x) function coefficients from EAM file.");
-
- // Close the potential file.
- fclose(fptr);
- }
-
- MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
- if(comm->me != 0) hcoeff = new double[nhcoeff];
- MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
-}
-
-
-/* ---------------------------------------------------------------------- */
-
-int PairCDEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
-{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- buf[m++] = D_values[j];
- }
- return m;
- }
- else if(cdeamVersion == 2) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = fp[j];
- buf[m++] = rho[j];
- buf[m++] = rhoB[j];
- }
- return m;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 4) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = D_values[j];
- }
- return m;
- }
- else return 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::unpack_forward_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
- if(communicationStage == 2) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- D_values[i] = buf[m++];
- }
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- fp[i] = buf[m++];
- rho[i] = buf[m++];
- rhoB[i] = buf[m++];
- }
- } else {
- ASSERT(false);
- }
- }
- else if(communicationStage == 4) {
- for(i = first; i < last; i++) {
- D_values[i] = buf[m++];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-int PairCDEAM::pack_reverse_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
-
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- buf[m++] = D_values[i];
- }
- return m;
- }
- else if(cdeamVersion == 2) {
- for(i = first; i < last; i++) {
- buf[m++] = rho[i];
- buf[m++] = rhoB[i];
- }
- return m;
- }
- else { ASSERT(false); return 0; }
- }
- else if(communicationStage == 3) {
- for(i = first; i < last; i++) {
- buf[m++] = D_values[i];
- }
- return m;
- }
- else return 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf)
-{
- int i,j,m;
-
- m = 0;
- if(communicationStage == 1) {
- if(cdeamVersion == 1) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- D_values[j] += buf[m++];
- }
- } else if(cdeamVersion == 2) {
- for(i = 0; i < n; i++) {
- j = list[i];
- rho[j] += buf[m++];
- rhoB[j] += buf[m++];
- }
- } else {
- ASSERT(false);
- }
- }
- else if(communicationStage == 3) {
- for(i = 0; i < n; i++) {
- j = list[i];
- D_values[j] += buf[m++];
- }
- }
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-double PairCDEAM::memory_usage()
-{
- double bytes = 2 * nmax * sizeof(double);
- return PairEAMAlloy::memory_usage() + bytes;
-}
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 186376d952..73c70420c5 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -798,7 +798,7 @@ void FixNH::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@@ -1446,7 +1446,7 @@ double FixNH::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@@ -1477,15 +1477,21 @@ double FixNH::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
- for (i = 0; i < 3; i++)
- if (p_flag[i])
+ for (i = 0; i < 3; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
+ lkt_press += kt;
+ }
+ }
if (pstyle == TRICLINIC) {
- for (i = 3; i < 6; i++)
- if (p_flag[i])
+ for (i = 3; i < 6; i++) {
+ if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ lkt_press += kt;
+ }
+ }
}
// extra contributions from thermostat chain for barostat
@@ -1818,15 +1824,15 @@ void FixNH::nhc_temp_integrate()
void FixNH::nhc_press_integrate()
{
- int ich,i;
+ int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
- double lkt_press = kt;
+ double lkt_press;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
- double nkt = atom->natoms * kt;
+ double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@@ -1850,14 +1856,22 @@ void FixNH::nhc_press_integrate()
}
kecurrent = 0.0;
+ pdof = 0;
for (i = 0; i < 3; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
- if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ if (p_flag[i]) {
+ kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ pdof++;
+ }
}
+ lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;
diff --git a/src/variable.cpp b/src/variable.cpp
index 86296b4b40..f005221400 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -1576,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Mismatched compute in variable formula",ivar);
+ } else print_var_error(FLERR,
+ "Mismatched compute in variable formula",ivar);
// ----------------
// fix
@@ -1584,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) {
if (domain->box_exist == 0)
- print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
+ print_var_error(FLERR,"Variable evaluation before "
+ "simulation box is defined",ivar);
// uppercase used to force access of
// global vector vs global scalar, and global array vs global vector
@@ -1667,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (index1 > fix->size_array_rows &&
fix->size_array_rows_variable == 0)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (index2 > fix->size_array_cols)
- print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at a "
+ "compatible time",ivar);
value1 = fix->compute_array(index1-1,index2-1);
if (tree) {
@@ -1688,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
if (tree == NULL)
- print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "equal-style variable formula",ivar);
if (treetype == ATOM)
- print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar);
+ print_var_error(FLERR,"Fix global vector in "
+ "atom-style variable formula",ivar);
if (fix->size_vector == 0)
- print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
+ print_var_error(FLERR,"Variable formula "
+ "fix vector is zero length",ivar);
int nvec = fix->size_vector;
double *vec;
@@ -1726,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Fix global vector in "
"atom-style variable formula",ivar);
if (fix->size_array_rows == 0)
- print_var_error(FLERR,"Variable formula fix array is zero length",ivar);
+ print_var_error(FLERR,"Variable formula fix array is "
+ "zero length",ivar);
int nvec = fix->size_array_rows;
double *vec;
@@ -1785,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1805,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
fix->size_peratom_cols > 0) {
if (tree == NULL)
- print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Per-atom fix in "
+ "equal-style variable formula",ivar);
if (index1 > fix->size_peratom_cols)
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 &&
update->ntimestep % fix->peratom_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
Tree *newtree = new Tree();
newtree->type = ATOMARRAY;
@@ -1878,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
char *var = retrieve(word+2);
if (var == NULL)
- print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar);
+ print_var_error(FLERR,"Invalid variable evaluation in "
+ "variable formula",ivar);
if (tree) {
Tree *newtree = new Tree();
newtree->type = VALUE;
@@ -1977,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
double *vec;
int nvec = compute_vector(ivar,&vec);
if (index <= 0 || index > nvec)
- print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
+ print_var_error(FLERR,"Invalid index into "
+ "vector-style variable",ivar);
int m = index; // convert from tagint to int
if (tree) {
@@ -1989,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
} else argstack[nargstack++] = vec[m-1];
- } else print_var_error(FLERR,"Mismatched variable in variable formula",ivar);
+ } else print_var_error(FLERR,"Mismatched variable in "
+ "variable formula",ivar);
// ----------------
// math/group/special function or atom value/vector or
@@ -2194,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (value2 == 0.0)
argstack[nargstack++] = 1.0;
else if ((value1 == 0.0) && (value2 < 0.0))
- print_var_error(FLERR,"Invalid power expression in variable formula",ivar);
+ print_var_error(FLERR,"Invalid power expression in "
+ "variable formula",ivar);
else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
@@ -3368,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LN;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log(value1);
}
} else if (strcmp(word,"log") == 0) {
@@ -3377,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (tree) newtree->type = LOG;
else {
if (value1 <= 0.0)
- print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar);
+ print_var_error(FLERR,"Log of zero/negative value in "
+ "variable formula",ivar);
argstack[nargstack++] = log10(value1);
}
} else if (strcmp(word,"abs") == 0) {
@@ -3482,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use ramp in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = RAMP;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3617,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 2)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use vdisplace in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = VDISPLACE;
else {
double delta = update->ntimestep - update->beginstep;
@@ -3629,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use swiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3644,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg != 3)
print_var_error(FLERR,"Invalid math function in variable formula",ivar);
if (update->whichflag == 0)
- print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar);
+ print_var_error(FLERR,"Cannot use cwiggle in "
+ "variable formula between runs",ivar);
if (tree) newtree->type = CWIGGLE;
else {
if (values[0] == 0.0)
@@ -3709,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
- else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"mass") == 0) {
@@ -3719,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
- else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar));
+ else if (narg == 2)
+ value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
} else if (strcmp(word,"xcm") == 0) {
@@ -3732,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = xcm[0];
else if (strcmp(args[1],"y") == 0) value = xcm[1];
else if (strcmp(args[1],"z") == 0) value = xcm[2];
@@ -3748,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
int iregion = region_function(args[2],ivar);
double masstotal = group->mass(igroup,iregion);
group->vcm(igroup,masstotal,vcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = vcm[0];
else if (strcmp(args[1],"y") == 0) value = vcm[1];
else if (strcmp(args[1],"z") == 0) value = vcm[2];
@@ -3767,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
- else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar));
+ else if (narg == 3)
+ group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
else if (strcmp(args[1],"xmax") == 0) value = minmax[1];
@@ -3789,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
value = group->gyration(igroup,masstotal,xcm,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
} else if (strcmp(word,"ke") == 0) {
if (narg == 1) value = group->ke(igroup);
@@ -3808,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->angmom(igroup,xcm,lmom,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = lmom[0];
else if (strcmp(args[1],"y") == 0) value = lmom[1];
else if (strcmp(args[1],"z") == 0) value = lmom[2];
@@ -3826,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->torque(igroup,xcm,tq,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = tq[0];
else if (strcmp(args[1],"y") == 0) value = tq[1];
else if (strcmp(args[1],"z") == 0) value = tq[2];
@@ -3844,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
double masstotal = group->mass(igroup,iregion);
group->xcm(igroup,masstotal,xcm,iregion);
group->inertia(igroup,xcm,inertia,iregion);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"xx") == 0) value = inertia[0][0];
else if (strcmp(args[1],"yy") == 0) value = inertia[1][1];
else if (strcmp(args[1],"zz") == 0) value = inertia[2][2];
@@ -3869,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
group->angmom(igroup,xcm,angmom,iregion);
group->inertia(igroup,xcm,inertia,iregion);
group->omega(angmom,inertia,omega);
- } else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid group function in "
+ "variable formula",ivar);
if (strcmp(args[1],"x") == 0) value = omega[0];
else if (strcmp(args[1],"y") == 0) value = omega[1];
else if (strcmp(args[1],"z") == 0) value = omega[2];
@@ -3924,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
Tree **treestack, int &ntreestack,
double *argstack, int &nargstack, int ivar)
{
- double value,xvalue,sx,sy,sxx,sxy;
+ bigint sx,sxx;
+ double value,xvalue,sy,sxy;
// word not a match to any special function
@@ -4020,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
- if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
+ if (ifix < 0)
+ print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_vector;
nstride = 1;
} else if (index && fix->array_flag) {
@@ -4032,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
print_var_error(FLERR,"Variable formula fix array "
"is accessed out-of-range",ivar);
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
- print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar);
+ print_var_error(FLERR,"Fix in variable not computed at "
+ "compatible time",ivar);
nvec = fix->size_array_rows;
nstride = fix->size_array_cols;
} else print_var_error(FLERR,"Mismatched fix in variable formula",ivar);
@@ -4048,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
if (index)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
ivar = find(&args[0][2]);
if (ivar < 0)
- print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
if (style[ivar] != VECTOR)
print_var_error(FLERR,"Mis-matched special function variable "
"in variable formula",ivar);
@@ -4062,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
nvec = compute_vector(ivar,&vec);
nstride = 1;
- } else print_var_error(FLERR,"Invalid special function in variable formula",ivar);
+ } else print_var_error(FLERR,"Invalid special function in "
+ "variable formula",ivar);
value = 0.0;
- if (method == SLOPE) sx = sy = sxx = sxy = 0.0;
- if (method == XMIN) value = BIG;
- if (method == XMAX) value = -BIG;
+ if (method == SLOPE) {
+ sx = sxx = 0;
+ sy = sxy = 0.0;
+ }
+ else if (method == XMIN) value = BIG;
+ else if (method == XMAX) value = -BIG;
if (compute) {
double *vec;
@@ -4084,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += vec[j];
else if (method == TRAP) value += vec[j];
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += vec[j];
- sxx += xvalue*xvalue;
- sxy += xvalue*vec[j];
+ sxx += i*i;
+ sxy += i*vec[j];
}
j += nstride;
}
@@ -4107,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) {
@@ -4134,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (method == AVE) value += one;
else if (method == TRAP) value += one;
else if (method == SLOPE) {
- if (nvec > 1) xvalue = (double) i / (nvec-1);
- else xvalue = 0.0;
- sx += xvalue;
+ sx += i;
sy += one;
- sxx += xvalue*xvalue;
- sxy += xvalue*one;
+ sxx += i*i;
+ sxy += i*one;
}
}
if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1];
@@ -4148,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (method == AVE) value /= nvec;
if (method == SLOPE) {
- double numerator = sxy - sx*sy;
- double denominator = sxx - sx*sx;
- if (denominator != 0.0) value = numerator/denominator / nvec;
+ double numerator = nvec*sxy - sx*sy;
+ double denominator = nvec*sxx - sx*sx;
+ if (denominator != 0.0) value = numerator/denominator;
else value = BIG;
}
@@ -4169,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"gmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Gmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4186,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"rmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Rmask function in equal-style "
+ "variable formula",ivar);
if (narg != 1)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4202,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"grmask") == 0) {
if (tree == NULL)
- print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Grmask function in equal-style "
+ "variable formula",ivar);
if (narg != 2)
print_var_error(FLERR,"Invalid special function in variable formula",ivar);
@@ -4228,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
int ivar = find(args[0]);
if (ivar < 0)
- print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar);
+ print_var_error(FLERR,"Variable ID in "
+ "variable formula does not exist",ivar);
// SCALARFILE has single current value, read next one
// save value in tree or on argstack
@@ -4253,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (style[ivar] == ATOMFILE) {
if (tree == NULL)
- print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar);
+ print_var_error(FLERR,"Atomfile variable in "
+ "equal-style variable formula",ivar);
double *result;
memory->create(result,atom->nlocal,"variable:result");
@@ -4271,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
newtree->nextra = 0;
treestack[ntreestack++] = newtree;
- } else print_var_error(FLERR,"Invalid variable style in special function next",ivar);
+ } else print_var_error(FLERR,"Invalid variable style in "
+ "special function next",ivar);
} else if (strcmp(word,"is_active") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_active() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0;
@@ -4293,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_available") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_available() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0;
@@ -4311,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"is_defined") == 0) {
if (narg != 2)
- print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar);
+ print_var_error(FLERR,"Invalid is_defined() function in "
+ "variable formula",ivar);
Info info(lmp);
value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0;
diff --git a/src/version.h b/src/version.h
index 90a21631d9..b95c259dd6 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Jul 2018"
+#define LAMMPS_VERSION "2 Aug 2018"
diff --git a/tools/emacs/README.md b/tools/emacs/README.md
new file mode 100644
index 0000000000..75504a7000
--- /dev/null
+++ b/tools/emacs/README.md
@@ -0,0 +1,82 @@
+# GNU Emacs Syntax Highlighting
+
+> Copyright (C) 2010-2018 Aidan Thompson <athomps at sandia.gov>
+> Copyright (C) 2018 Rohit Goswami <r95g10 at gmail.com>
+
+The `lammps-mode.el` file provided in this directory will enable syntax
+highlighting for the lammps script syntax in GNU Emacs. The groupings of
+commands were originally copied from `tools/vim`.
+
+## Installation
+**Requirements: GNU Emacs 24.\***
+
+### Obtaining the Package
+
+#### MELPA
+
+The easiest installation method is via MELPA and it is advisable to use one of
+the many [MELPA installation methods](https://melpa.org/#/getting-started).
+
+For example, with [use-package](https://github.com/jwiegley/use-package) one can
+simply use the following:
+
+``` emacs-lisp
+(use-package lammps-mode)
+```
+
+#### Manually
+
+Assuming for some reason you have downloaded the file to `~/.emacs.d/lisp` you
+would do the following (kanged [from here](http://ergoemacs.org/emacs/emacs_installing_packages.html)):
+
+``` emacs-lisp
+;; Tell emacs where is your personal elisp lib dir
+(add-to-list 'load-path "~/.emacs.d/lisp/")
+
+;; load the package.
+(load "lammps-mode")
+```
+
+### Autoloading \& Auto-recognition
+
+To automatically turn on the LAMMPS mode for editing your input scripts,
+use the following line as the **first** line of your script:
+```
+# -*- lammps -*-
+```
+
+For automatically switching on the LAMMPS mode based on filename patterns,
+e.g. for `in.*` and `*.lmp` files, add the following code to your `.emacs`:
+
+``` emacs-lisp
+(autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t)
+(setq auto-mode-alist (append auto-mode-alist
+ '(("in\\." . lammps-mode))
+ '(("\\.lmp\\'" . lammps-mode))
+ ))
+```
+
+## Status
+
+By far not all commands are included in the syntax file (lammps-mode.el). You
+can easily add new ones to the existing classes.
+
+## Implementation Details
+
+`lammps-mode` is derived from `shell-script-mode` which provides some basic
+syntax highlighting of strings, comments, etc.
+
+The MELPA recipe used for this package is simply:
+
+``` emacs-lisp
+(lammps-mode :fetcher github :repo "HaoZeke/lammps-mode")
+```
+
+## Caveats
+
+* Does not work with Xemacs [See [this comment](https://github.com/lammps/lammps/pull/1022#issuecomment-408871233)]
+
+## License
+
+[GNU GPL v2](https://github.com/HaoZeke/lammps-mode/blob/master/LICENSE).
+Check the file for more details.
diff --git a/tools/emacs/README.txt b/tools/emacs/README.txt
deleted file mode 100644
index 8dfc37cb85..0000000000
--- a/tools/emacs/README.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-=== Emacs Syntax Highlighting ===
-Created by Aidan Thompson 12/2010
-===============================
-
-The lammps.el file provided in this directory will enable syntax
-highlighting for the lammps script syntax in emacs. The groupings
-of commands were copied from tools/vim. The simulation scripts have to
-end on *.lmp or start with in.* (see lammps.el). By far not all
-commands are included in the syntax file (lammps.el).
-You can easily add new ones to the existing classes.
-'lammps-mode' is derived from 'shell-script-mode' which provides
-some basic syntax highlighting of strings, comments, etc.
-
-=To enable the highlighting:
-============================
-(0) Create/edit the emacs init file ~/.emacs to contain:
-
-(load "~/.emacs.d/lammps")
-
-This file may also be called ~/.emacs.el, or ~/.emacs.d/init.el
-
-(1) Copy lammps.el to the directory ~/.emacs.d
-
diff --git a/tools/emacs/lammps.el b/tools/emacs/lammps-mode.el
similarity index 73%
rename from tools/emacs/lammps.el
rename to tools/emacs/lammps-mode.el
index d1ebebbbbf..37e8a32116 100644
--- a/tools/emacs/lammps.el
+++ b/tools/emacs/lammps-mode.el
@@ -1,7 +1,48 @@
-;; LAMMPS auto-mode
+;;; lammps-mode.el --- basic syntax highlighting for LAMMPS files
+
+;; Copyright (C) 2010-18 Aidan Thompson
+;; Copyright (C) 2018 Rohit Goswami
+
+;; Author: Aidan Thompson <athomps at sandia.gov>
+;; Maintainer: Rohit Goswami <r95g10 at gmail.com>
+;; Created: December 4, 2010
+;; Modified: July 30, 2018
+;; Version: 1.5.0
+;; Keywords: languages, faces
+;; Homepage: https://github.com/lammps/lammps/tree/master/tools/emacs
+;; Package-Requires: ((emacs "24.4"))
+
+;; This file is not part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 2 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License along
+;; with this program; if not, write to the Free Software Foundation, Inc.,
+;; 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+;;; Commentary:
;; translation of keyword classes from tools/vim
;; see http://xahlee.org/emacs/elisp_syntax_coloring.html
+;; Put this in your .emacs file to enable autoloading of lammps-mode
+;; and auto-recognition of "in.*" and "*.lmp" files:
+;;
+;; (autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t)
+;; (setq auto-mode-alist (append auto-mode-alist
+;; '(("in\\." . lammps-mode))
+;; '(("\\.lmp\\'" . lammps-mode))
+;; ))
+;;
+
+;;; Code:
;; define several keyword classes
(defvar lammps-output
'("log"
@@ -136,6 +177,8 @@
(defvar lammps-variable-regexp
"\\$\\({[a-zA-Z0-9_]+}\\)\\|\\$[A-Za-z]")
+(defvar lammps-font-lock-keywords)
+
;; clear memory
(setq lammps-output nil)
(setq lammps-read nil)
@@ -151,8 +194,7 @@
;; create the list for font-lock.
;; each class of keyword is given a particular face
-(setq
- lammps-font-lock-keywords
+(setq lammps-font-lock-keywords
`((,lammps-output-regexp . font-lock-function-name-face)
(,lammps-read-regexp . font-lock-preprocessor-face)
(,lammps-lattice-regexp . font-lock-type-face)
@@ -199,12 +241,5 @@
(setq lammps-comment-regexp nil)
(setq lammps-variable-regexp nil))
-;; apply it to specified filename patterns
-(setq
- auto-mode-alist
- (append
- auto-mode-alist
- '(("in\\." . lammps-mode))
- '(("\\.lmp\\'" . lammps-mode))
- ))
-
+(provide 'lammps-mode)
+;;; lammps-mode.el ends here
--
GitLab
From b97195d48f69d984005b81d33da4fc161e3806f8 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 6 Aug 2018 15:58:53 -0600
Subject: [PATCH 072/332] CMake: download ScaFaCoS, compile and link it -
required resorting, as Fortran MPI is required
---
cmake/CMakeLists.txt | 103 +++++++++++++++++++++++++++++++------------
1 file changed, 75 insertions(+), 28 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 401bdca99c..b2cc7e613d 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -115,6 +115,34 @@ set(LAMMPS_LINK_LIBS)
set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
+ KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
+ SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
+ USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
+ USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
+ USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS
+ USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
+set(OTHER_PACKAGES CORESHELL QEQ)
+foreach(PKG ${DEFAULT_PACKAGES})
+ option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+ option(PKG_${PKG} "Build ${PKG} Package" OFF)
+endforeach()
+
+######################################################
+# packages with special compiler needs or external libs
+######################################################
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+ enable_language(Fortran)
+endif()
+
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+ enable_language(C)
+endif()
+
+# do MPI detection after language activation, if MPI for these language is required
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if(BUILD_MPI)
@@ -154,22 +182,6 @@ if(ENABLE_TESTING)
enable_testing()
endif(ENABLE_TESTING)
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
- SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
- USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
- USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
- USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS
- USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
-set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ)
-foreach(PKG ${DEFAULT_PACKAGES})
- option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
- option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-
macro(pkg_depends PKG1 PKG2)
if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
@@ -182,17 +194,7 @@ pkg_depends(MPIIO MPI)
pkg_depends(USER-ATC MANYBODY)
pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
-
-######################################################
-# packages with special compiler needs or external libs
-######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
- enable_language(Fortran)
-endif()
-
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
- enable_language(C)
-endif()
+pkg_depends(USER-SCAFACOS MPI)
find_package(OpenMP QUIET)
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
@@ -350,10 +352,55 @@ if(PKG_LATTE)
endif()
if(PKG_USER-SCAFACOS)
+ find_package(GSL REQUIRED)
+ option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
+ if(DOWNLOAD_SCAFACOS)
+ include(ExternalProject)
+ ExternalProject_Add(scafacos_build
+ URL https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz
+ URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f
+ CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+ --disable-doc
+ --enable-fcs-solvers=fmm,p2nfft,direct,ewald
+ FC=${CMAKE_MPI_Fortran_COMPILER}
+ CXX=${CMAKE_MPI_CXX_COMPILER}
+ CC=${CMAKE_MPI_C_COMPILER}
+ F77=
+ )
+ ExternalProject_get_property(scafacos_build INSTALL_DIR)
+ set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
+ set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
+ list(APPEND LAMMPS_DEPS scafacos_build)
+ # list and order from pkg_config file of ScaFaCoS build
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+ list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+ #list(APPEND LAMMPS_LINK_LIBS gsl)
+ #list(APPEND LAMMPS_LINK_LIBS gslcblas)
+ list(APPEND LAMMPS_LINK_LIBS m)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+ list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+ list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+# -L${libdir} -lfcs4fortran -lfcs -lfcs_direct -lfcs_ewald -lfcs_fmm -lfcs_p2nfft -lgsl -lgslcblas -lm -lfcs_near -lfcs_gridsort -lfcs_resort -lfcs_common -lfcs_pnfft -lfcs_pfft -lfcs_fftw3_mpi -lfcs_fftw3 -L/projects/opt/centos7/mpich/3.2-gcc_6.2.0/lib -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../.. -lmpifort -lmpi -lgfortran -lm -lquadmath
+#libfcs4fortran.a libfcs_common.a libfcs_direct.la libfcs_fftw3.a libfcs_fftw3_mpi.la libfcs_gridsort.a libfcs_near.a libfcs_p2nfft.la libfcs_pnfft.a libfcs_resort.la
+#libfcs4fortran.la libfcs_common.la libfcs_ewald.a libfcs_fftw3.la libfcs_fmm.a libfcs_gridsort.la libfcs_near.la libfcs_pfft.a libfcs_pnfft.la pkgconfig
+#libfcs.a libfcs_direct.a libfcs_ewald.la libfcs_fftw3_mpi.a libfcs_fmm.la libfcs.la libfcs_p2nfft.a libfcs_pfft.la libfcs_resort.a
+ else()
FIND_PACKAGE(PkgConfig REQUIRED)
PKG_CHECK_MODULES(SCAFACOS scafacos)
- include_directories(${SCAFACOS_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+ endif()
+ include_directories(${SCAFACOS_INCLUDE_DIRS})
endif()
if(PKG_USER-MOLFILE)
--
GitLab
From 953b2837739501df789721655447c6c14a6236f7 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 6 Aug 2018 15:59:46 -0600
Subject: [PATCH 073/332] updated URL for tarball download
---
lib/scafacos/Install.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
index df82780438..4e00e805d1 100644
--- a/lib/scafacos/Install.py
+++ b/lib/scafacos/Install.py
@@ -29,8 +29,8 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation
# settings
-version = "scafacos-0.9"
-url = "https://gigamove.rz.rwth-aachen.de/d/id/fTmrTm4EUAUSAp/dd/100"
+version = "scafacos-1.0.0"
+url = "https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz"
#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version
# print error message or help
--
GitLab
From 0a27b7065b0476e1fc3c9834bf783a7278b4053d Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Mon, 6 Aug 2018 16:01:39 -0600
Subject: [PATCH 074/332] bug fixes: ScaFaCoS returns virial as 9-value array,
requires copies to Lammps 6-value array; fixed error in compuation of
per-atom energy calculation
---
src/USER-SCAFACOS/scafacos.cpp | 22 ++++++++++++++++++++--
src/USER-SCAFACOS/scafacos.h | 2 ++
2 files changed, 22 insertions(+), 2 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index d4b106b26c..27828b1da1 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -219,7 +219,25 @@ void Scafacos::compute(int eflag, int vflag)
if (vflag_global)
{
- fcs_get_virial(fcs,virial);
+ fcs_get_virial(fcs,virial_int);
+ /*
+ printf(" %lf %lf %lf \n %lf %lf %lf \n %lf %lf %lf \n ",
+ virial_int[0],
+ virial_int[1],
+ virial_int[2],
+ virial_int[3],
+ virial_int[4],
+ virial_int[5],
+ virial_int[6],
+ virial_int[7],
+ virial_int[8]);
+ */
+ virial[0] = virial_int[0];
+ virial[1] = virial_int[1];
+ virial[2] = virial_int[2];
+ virial[3] = virial_int[4];
+ virial[4] = virial_int[5];
+ virial[5] = virial_int[8];
}
// apply Efield to each particle
@@ -240,7 +258,7 @@ void Scafacos::compute(int eflag, int vflag)
if (eflag_atom) {
for (int i = 0; i < nlocal; i++)
- eatom[i] = qscale * epot[i];
+ eatom[i] = 0.5 * qscale * q[i] * epot[i];
}
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index 857036bb7a..8f7c46dc6b 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -57,6 +57,8 @@ class Scafacos : public KSpace {
fcs_int old_periodicity[3];
fcs_int old_natoms;
+ fcs_float virial_int[9];
+
void check_result(FCSResult);
void setup_handle();
bool box_has_changed();
--
GitLab
From ba693a74be0b785818ae592d82daf0282871ebb0 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Tue, 7 Aug 2018 12:27:32 -0600
Subject: [PATCH 075/332] Add contribute method to pair_table_kokkos
---
src/KOKKOS/pair_table_kokkos.cpp | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index 7b06f814bb..b72df04c5f 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -128,21 +128,25 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
ff(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
else Kokkos::parallel_for(list->inum,ff);
+ ff.contribute();
} else if (neighflag == HALFTHREAD) {
PairComputeFunctor<PairTableKokkos<DeviceType>,HALFTHREAD,false,S_TableCompute<DeviceType,TABSTYLE> >
ff(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
else Kokkos::parallel_for(list->inum,ff);
+ ff.contribute();
} else if (neighflag == HALF) {
PairComputeFunctor<PairTableKokkos<DeviceType>,HALF,false,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
} else if (neighflag == N2) {
PairComputeFunctor<PairTableKokkos<DeviceType>,N2,false,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
}
} else {
if (neighflag == FULL) {
@@ -150,21 +154,25 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
} else if (neighflag == HALFTHREAD) {
PairComputeFunctor<PairTableKokkos<DeviceType>,HALFTHREAD,true,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
} else if (neighflag == HALF) {
PairComputeFunctor<PairTableKokkos<DeviceType>,HALF,true,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
} else if (neighflag == N2) {
PairComputeFunctor<PairTableKokkos<DeviceType>,N2,true,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
+ f.contribute();
}
}
--
GitLab
From a944d1c913350cbe4378637a5f458b251bc5334e Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 7 Aug 2018 14:26:53 -0600
Subject: [PATCH 076/332] fixed missing REQUIRED and introduced the compilation
of internal sub-libraries (FFTW,PFFT,PNFFT)
---
cmake/CMakeLists.txt | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index b2cc7e613d..0ec2d2086c 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -361,7 +361,10 @@ if(PKG_USER-SCAFACOS)
URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
--disable-doc
- --enable-fcs-solvers=fmm,p2nfft,direct,ewald
+ --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+ --with-internal-fftw
+ --with-internal-pfft
+ --with-internal-pnfft
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
@@ -377,9 +380,8 @@ if(PKG_USER-SCAFACOS)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
- #list(APPEND LAMMPS_LINK_LIBS gsl)
- #list(APPEND LAMMPS_LINK_LIBS gslcblas)
list(APPEND LAMMPS_LINK_LIBS m)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
@@ -391,13 +393,9 @@ if(PKG_USER-SCAFACOS)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
-# -L${libdir} -lfcs4fortran -lfcs -lfcs_direct -lfcs_ewald -lfcs_fmm -lfcs_p2nfft -lgsl -lgslcblas -lm -lfcs_near -lfcs_gridsort -lfcs_resort -lfcs_common -lfcs_pnfft -lfcs_pfft -lfcs_fftw3_mpi -lfcs_fftw3 -L/projects/opt/centos7/mpich/3.2-gcc_6.2.0/lib -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/projects/opt/centos7/gcc/6.2.0/packages/gcc-6.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/../../.. -lmpifort -lmpi -lgfortran -lm -lquadmath
-#libfcs4fortran.a libfcs_common.a libfcs_direct.la libfcs_fftw3.a libfcs_fftw3_mpi.la libfcs_gridsort.a libfcs_near.a libfcs_p2nfft.la libfcs_pnfft.a libfcs_resort.la
-#libfcs4fortran.la libfcs_common.la libfcs_ewald.a libfcs_fftw3.la libfcs_fmm.a libfcs_gridsort.la libfcs_near.la libfcs_pfft.a libfcs_pnfft.la pkgconfig
-#libfcs.a libfcs_direct.a libfcs_ewald.la libfcs_fftw3_mpi.a libfcs_fmm.la libfcs.la libfcs_p2nfft.a libfcs_pfft.la libfcs_resort.a
else()
FIND_PACKAGE(PkgConfig REQUIRED)
- PKG_CHECK_MODULES(SCAFACOS scafacos)
+ PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
endif()
include_directories(${SCAFACOS_INCLUDE_DIRS})
--
GitLab
From cdde51d8af3d38679fbd311e942fd94359305560 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 7 Aug 2018 14:29:04 -0600
Subject: [PATCH 077/332] fixed example so that P3M also works, changed
tolerance type in the FMM example
---
examples/USER/scafacos/data.NaCl | 22 +++++++++++-----------
examples/USER/scafacos/in.scafacos.fmm | 2 +-
2 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/examples/USER/scafacos/data.NaCl b/examples/USER/scafacos/data.NaCl
index 23807e23d5..2fd6077983 100644
--- a/examples/USER/scafacos/data.NaCl
+++ b/examples/USER/scafacos/data.NaCl
@@ -4,9 +4,9 @@ LAMMPS Description
2 atom types
-0 2 xlo xhi
-0 2 ylo yhi
-0 2 zlo zhi
+0 1 xlo xhi
+0 1 ylo yhi
+0 1 zlo zhi
Masses
@@ -15,11 +15,11 @@ Masses
Atoms
-1 2 1 0 0 0
-2 1 -1 1 0 0
-3 1 -1 0 1 0
-4 2 1 1 1 0
-5 1 -1 0 0 1
-6 2 1 1 0 1
-7 2 1 0 1 1
-8 1 -1 1 1 1
+1 2 1 0.25 0.25 0.25
+2 1 -1 0.75 0.25 0.25
+3 1 -1 0.25 0.75 0.25
+4 2 1 0.75 0.75 0.25
+5 1 -1 0.25 0.25 0.75
+6 2 1 0.75 0.25 0.75
+7 2 1 0.25 0.75 0.75
+8 1 -1 0.75 0.75 0.75
diff --git a/examples/USER/scafacos/in.scafacos.fmm b/examples/USER/scafacos/in.scafacos.fmm
index 18d7464fb8..054188ede2 100644
--- a/examples/USER/scafacos/in.scafacos.fmm
+++ b/examples/USER/scafacos/in.scafacos.fmm
@@ -29,7 +29,7 @@ pair_coeff * *
#fix 2 all scafacos p3m tolerance field 0.001
kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos tolerance energy
timestep 0.005
thermo 10
--
GitLab
From eb86ec3eea994ad1828f5db9b7e2db11ba5ff91b Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 7 Aug 2018 15:03:48 -0600
Subject: [PATCH 078/332] added support for p3m, added check for compatible
tolerance / method combinations (should they not be caught by ScaFaCoS
itself)
---
src/USER-SCAFACOS/scafacos.cpp | 80 ++++++++++++++++++++++------------
1 file changed, 51 insertions(+), 29 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 27828b1da1..fdbd5e34e0 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -96,10 +96,13 @@ Scafacos::~Scafacos()
void Scafacos::init()
{
// error checks
- if (screen && me == 0) fprintf(screen,"Setting up ScaFaCoS with solver %s ...\n",method);
- if (logfile && me == 0) fprintf(logfile,"Setting up ScaFaCoS with solver %s ...\n",method);
+ if (screen && me == 0) fprintf(screen,
+ "Setting up ScaFaCoS with solver %s ...\n",method);
+ if (logfile && me == 0) fprintf(logfile,
+ "Setting up ScaFaCoS with solver %s ...\n",method);
- if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q");
+ if (!atom->q_flag) error->all(FLERR,
+ "Kspace style requires atom attribute q");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
@@ -111,7 +114,8 @@ void Scafacos::init()
error->all(FLERR,"Scafacos atom count exceeds 2B");
if (atom->molecular > 0)
- error->all(FLERR,"Cannot use Scafacos with molecular charged systems yet");
+ error->all(FLERR,
+ "Cannot use Scafacos with molecular charged systems yet");
// one-time initialization of ScaFaCoS
@@ -204,34 +208,16 @@ void Scafacos::compute(int eflag, int vflag)
if (vflag_global)
{
fcs_set_compute_virial(fcs,1);
+ if (strcmp(method,"p3m") == 0)
+ error->all(FLERR,"ScaFaCoS p3m does not support the computation of virial");
}
- /*
- if (strcmp(method,"p3m")==0)
- {
- result = fcs_tune(fcs,nlocal,&x[0][0],q);
- check_result(result);
- }
- */
-
result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
check_result(result);
if (vflag_global)
{
fcs_get_virial(fcs,virial_int);
- /*
- printf(" %lf %lf %lf \n %lf %lf %lf \n %lf %lf %lf \n ",
- virial_int[0],
- virial_int[1],
- virial_int[2],
- virial_int[3],
- virial_int[4],
- virial_int[5],
- virial_int[6],
- virial_int[7],
- virial_int[8]);
- */
virial[0] = virial_int[0];
virial[1] = virial_int[1];
virial[2] = virial_int[2];
@@ -277,7 +263,8 @@ int Scafacos::modify_param(int narg, char **arg)
if (strcmp(arg[0],"scafacos") != 0) return 0;
if (strcmp(arg[1],"tolerance") == 0) {
- if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (tolerance)");
+ if (narg < 3) error->all(FLERR,
+ "Illegal kspace_modify command (tolerance)");
if (strcmp(arg[2],"energy") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
else if (strcmp(arg[2],"energy_rel") == 0)
@@ -290,7 +277,39 @@ int Scafacos::modify_param(int narg, char **arg)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
else if (strcmp(arg[2],"potential_rel") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
- else error->all(FLERR,"Illegal kspace_modify command (tolerance argument)");
+ else error->all(FLERR,
+ "Illegal kspace_modify command (tolerance argument)");
+ // check if method is compatatible to chosen tolerance type
+ if(
+ (
+ strcmp(method,"fmm") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
+ tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL
+ )
+ ) &&
+ (
+ strcmp(method,"p2nfft") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
+ tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL
+ )
+ ) &&
+ (
+ strcmp(method,"p3m") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD
+ )
+ ) &&
+ (
+ strcmp(method,"ewald") == 0 &&
+ (
+ tolerance_type != FCS_TOLERANCE_TYPE_FIELD
+ )
+ )
+ )
+ error->all(FLERR,"Illegal kspace_modify command \
+ (invalid tolerance / method combination)");
return 3;
}
@@ -300,9 +319,12 @@ int Scafacos::modify_param(int narg, char **arg)
// 1 -> inhomogenous system (more internal tuning is provided (sequential!))
if (strcmp(arg[1],"fmm_tuning") == 0)
{
- if (screen && me == 0) fprintf(screen,"ScaFaCoS setting fmm inhomogen tuning ...\n");
- if (logfile && me == 0) fprintf(logfile,"ScaFaCoS setting fmm inhomogen tuning ...\n");
- if (narg < 3) error->all(FLERR,"Illegal kspace_modify command (fmm_tuning)");
+ if (screen && me == 0) fprintf(screen,
+ "ScaFaCoS setting fmm inhomogen tuning ...\n");
+ if (logfile && me == 0) fprintf(logfile,
+ "ScaFaCoS setting fmm inhomogen tuning ...\n");
+ if (narg < 3) error->all(FLERR,
+ "Illegal kspace_modify command (fmm_tuning)");
fmm_tuning_flag = atoi(arg[2]);
return 3;
}
--
GitLab
From 48fd8b46ee49b8b56d0c9470a4114091b2d7a25b Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 7 Aug 2018 15:04:37 -0600
Subject: [PATCH 079/332] cleaned documentation, added p3m entry for allowed
tolerance type
---
doc/src/kspace_modify.txt | 15 +++------------
doc/src/kspace_style.txt | 1 +
2 files changed, 4 insertions(+), 12 deletions(-)
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 57cff18d7e..b05bd6dccb 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -346,17 +346,12 @@ the per-atom electric field, this effectively sets a tolerance on the
forces, simimlar to other LAMMPS KSpace styles, as explained on the
"kspace_style"_kspace_style.html doc page.
-RENE: Also, can you explain more what is the difference between energy
-(total) and potential (per-atom)? Which one is more vs less accurate?
-Does potential mean that the maximum of any atom's energy error is <
-tolerance? I.e. it is a max across all per-atom values? Ditto for
-field, since it is computed on a per-atom basis?
-
Note that not all ScaFaCoS solvers support all tolerance types.
These are the allowed values for each method:
fmm = energy and energy_rel
p2nfft = field (1d-,2d-,3d-periodic systems) or potential (0d-periodic)
+p3m = field
ewald = field
direct = has no tolerance tuning :ul
@@ -364,17 +359,13 @@ If the tolerance type is not changed, the default values for the
tolerance type are the first values in the above list, e.g. energy
is the default tolerance type for the fmm solver.
-RENE: Does the code (LAMMPS or Scafacos) generate an error
-if an unsupported tolerance is specified for a method?
-
The {fmm_tuning} option is only relevant when using the FMM method.
It activates (value=1) or deactivates (value=0) an internal tuning
mechanism for the FMM solver. The tuning operation runs sequentially
and can be very time-consuming. Usually it is not needed for systems
with a homogenous charge distribution. The default for this option is
-therefore {0}.
-
-RENE: is the tuning a one-time (start-up) operation if enabled?
+therefore {0}. The FMM internal tuning is performed once, when the
+solver is set up.
:line
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index cff196ed69..9e26f8e2e4 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -251,6 +251,7 @@ These are the ScaFaCoS methods currently available from LAMMPS:
{p2nfft} = FFT-based Coulomb solver
{ewald} = Ewald summation
{direct} = direct O(N^2) summation
+{p3m} = PPPM
We plan to support additional ScaFaCoS solvers from LAMMPS in the
future. For an overview of the included solvers, refer to
--
GitLab
From 7f5476b4081eccbf6f9ddf398ea3f46e92204535 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 8 Aug 2018 14:04:41 -0600
Subject: [PATCH 080/332] removed deprecated log files (will be replaced with
more current ones)
---
.../log.23Jul18.scafacos.cw.g++.ewald.16 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.ewald.8 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.fmm.1 | 99 ----------------
.../log.23Jul18.scafacos.cw.g++.fmm.16 | 99 ----------------
.../log.23Jul18.scafacos.cw.g++.fmm.2 | 99 ----------------
.../log.23Jul18.scafacos.cw.g++.fmm.4 | 99 ----------------
.../log.23Jul18.scafacos.cw.g++.fmm.8 | 99 ----------------
.../log.23Jul18.scafacos.cw.g++.p2nfft.1 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.p2nfft.16 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.p2nfft.2 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.p2nfft.4 | 92 ---------------
.../log.23Jul18.scafacos.cw.g++.p2nfft.8 | 92 ---------------
.../log.23Jul18.scafacos.g++.ewald.16 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.ewald.8 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.fmm.1 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.fmm.16 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.fmm.2 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.fmm.4 | 102 ----------------
.../scafacos/log.23Jul18.scafacos.g++.fmm.8 | 102 ----------------
.../log.23Jul18.scafacos.g++.p2nfft.1 | 102 ----------------
.../log.23Jul18.scafacos.g++.p2nfft.16 | 102 ----------------
.../log.23Jul18.scafacos.g++.p2nfft.2 | 102 ----------------
.../log.23Jul18.scafacos.g++.p2nfft.4 | 102 ----------------
.../log.23Jul18.scafacos.g++.p2nfft.8 | 102 ----------------
.../log.23Jul18.scafacos.hsph.g++.direct.1 | 105 -----------------
.../log.23Jul18.scafacos.hsph.g++.direct.2 | 105 -----------------
.../log.23Jul18.scafacos.hsph.g++.direct.4 | 105 -----------------
.../log.23Jul18.scafacos.hsph.g++.direct.8 | 105 -----------------
.../log.23Jul18.scafacos.hsph.g++.fmm.1 | 109 ------------------
.../log.23Jul18.scafacos.hsph.g++.fmm.2 | 109 ------------------
.../log.23Jul18.scafacos.hsph.g++.fmm.4 | 109 ------------------
.../log.23Jul18.scafacos.hsph.g++.fmm.8 | 109 ------------------
.../log.23Jul18.scafacos.hsph.g++.p2nfft.1 | 107 -----------------
.../log.23Jul18.scafacos.hsph.g++.p2nfft.2 | 107 -----------------
.../log.23Jul18.scafacos.hsph.g++.p2nfft.4 | 107 -----------------
.../log.23Jul18.scafacos.hsph.g++.p2nfft.8 | 107 -----------------
36 files changed, 3647 deletions(-)
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
delete mode 100644 examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
deleted file mode 100644
index ffdc7e3a3c..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.16
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos ewald 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver ewald ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49647271 0 0.49647271 0
- 10 300 0.061254978 0.014582562 0.44286522 0.02180093 0.46466616 0
- 20 300 0.12240911 0.058693359 0.37869251 0.087746571 0.46643909 0
- 30 300 0.18348265 0.13468789 0.26730177 0.2013584 0.46866017 0
- 40 300 0.24441123 0.50949535 0.083356437 0.76169555 0.84505198 0
- 50 300 0.30493236 1.1731116 -0.055261984 1.7538018 1.6985399 0
- 60 300 0.36615515 1.3589639 -0.33351524 2.031651 1.6981358 0
- 70 300 0.42717433 1.6482648 -0.76570045 2.4641559 1.6984554 0
- 80 300 0.48137259 2.8640899 -2.4038488 4.2818144 1.8779656 0
- 90 300 0.5323379 93.168442 -2.5911448 139.28682 136.69568 0
- 100 300 0.5756321 94.146897 -1.3480439 140.74961 139.40157 0
-Loop time of 0.575655 on 16 procs for 100 steps with 300 atoms
-
-Performance: 75045.007 tau/day, 173.715 timesteps/s
-98.7% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.2159e-05 | 1.739e-05 | 2.3127e-05 | 0.0 | 0.00
-Kspace | 0.57008 | 0.57086 | 0.57137 | 0.1 | 99.17
-Neigh | 0.00025606 | 0.00061357 | 0.001369 | 0.0 | 0.11
-Comm | 0.0023558 | 0.0027267 | 0.003104 | 0.4 | 0.47
-Output | 0.00029898 | 0.00032344 | 0.00037599 | 0.0 | 0.06
-Modify | 8.2493e-05 | 0.00014143 | 0.00021815 | 0.0 | 0.02
-Other | | 0.0009701 | | | 0.17
-
-Nlocal: 18.75 ave 39 max 6 min
-Histogram: 6 1 1 0 1 2 2 1 1 1
-Nghost: 122.812 ave 195 max 63 min
-Histogram: 8 0 0 0 0 0 0 1 3 4
-Neighs: 160.625 ave 598 max 13 min
-Histogram: 8 2 1 1 1 0 0 2 0 1
-
-Total # of neighbors = 2570
-Ave neighs/atom = 8.56667
-Neighbor list builds = 23
-Dangerous builds = 16
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
deleted file mode 100644
index 52d887f475..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.ewald.8
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos ewald 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver ewald ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49647271 0 0.49647271 0
- 10 300 0.067519665 0.014718629 0.45088339 0.02200435 0.47288774 0
- 20 300 0.13502312 0.05922597 0.38470912 0.088542825 0.47325194 0
- 30 300 0.20248008 0.13587829 0.27058048 0.20313804 0.47371852 0
- 40 300 0.26985955 0.51353118 0.088432648 0.76772911 0.85616176 0
- 50 300 0.33801103 1.1760001 -0.058088247 1.7581201 1.7000319 0
- 60 300 0.40665984 1.3627885 -0.33736672 2.0373688 1.7000021 0
- 70 300 0.47533679 1.6529365 -0.77082139 2.4711401 1.7003187 0
- 80 300 0.54396391 2.9569837 -2.4624654 4.4206907 1.9582253 0
- 90 300 0.61429667 81.642726 -2.5370215 122.05588 119.51885 0
- 100 300 0.68513632 85.047974 -1.128107 127.14672 126.01861 0
-Loop time of 0.685155 on 8 procs for 100 steps with 300 atoms
-
-Performance: 63051.442 tau/day, 145.952 timesteps/s
-99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.0967e-05 | 1.4216e-05 | 1.8358e-05 | 0.0 | 0.00
-Kspace | 0.67942 | 0.67981 | 0.6803 | 0.0 | 99.22
-Neigh | 0.00073242 | 0.0010653 | 0.0015635 | 0.8 | 0.16
-Comm | 0.0029492 | 0.0031102 | 0.0033047 | 0.2 | 0.45
-Output | 0.00021768 | 0.00023454 | 0.00028443 | 0.0 | 0.03
-Modify | 0.00016046 | 0.00018132 | 0.00019431 | 0.0 | 0.03
-Other | | 0.0007433 | | | 0.11
-
-Nlocal: 37.5 ave 46 max 31 min
-Histogram: 2 0 0 2 1 0 2 0 0 1
-Nghost: 203.875 ave 212 max 192 min
-Histogram: 1 0 1 0 0 2 1 0 0 3
-Neighs: 321.625 ave 599 max 112 min
-Histogram: 1 2 0 1 1 0 1 1 0 1
-
-Total # of neighbors = 2573
-Ave neighs/atom = 8.57667
-Neighbor list builds = 23
-Dangerous builds = 16
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
deleted file mode 100644
index 47e0be01ce..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.1
+++ /dev/null
@@ -1,99 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-kspace_style scafacos fmm 1.0e-3
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49646402 0 0.49646402 0
- 10 300 0.036603451 0.015455559 0.47335833 0.02310606 0.49646439 0
- 20 300 0.073534727 0.06229069 0.40334177 0.093124582 0.49646635 0
- 30 300 0.10984373 0.14310163 0.28254277 0.21393694 0.49647971 0
- 40 300 0.14610171 0.52929788 0.089669015 0.79130033 0.88096934 0
- 50 300 0.18255496 1.1963022 -0.082792461 1.7884718 1.7056794 0
- 60 300 0.2194376 1.3928167 -0.37659239 2.082261 1.7056686 0
- 70 300 0.25588369 1.7069009 -0.84571914 2.5518169 1.7060978 0
- 80 300 0.29101205 15.358343 -3.368063 22.960722 19.592659 0
- 90 300 0.32697225 42.280432 -2.1623864 63.209247 61.04686 0
- 100 300 0.36395645 41.48079 -0.89904529 62.013782 61.114736 0
-Loop time of 0.363968 on 1 procs for 100 steps with 300 atoms
-
-Performance: 118691.709 tau/day, 274.749 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.2875e-05 | 1.2875e-05 | 1.2875e-05 | 0.0 | 0.00
-Kspace | 0.35715 | 0.35715 | 0.35715 | 0.0 | 98.13
-Neigh | 0.0039768 | 0.0039768 | 0.0039768 | 0.0 | 1.09
-Comm | 0.0012023 | 0.0012023 | 0.0012023 | 0.0 | 0.33
-Output | 0.0001502 | 0.0001502 | 0.0001502 | 0.0 | 0.04
-Modify | 0.0009768 | 0.0009768 | 0.0009768 | 0.0 | 0.27
-Other | | 0.0005031 | | | 0.14
-
-Nlocal: 300 ave 300 max 300 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 374 ave 374 max 374 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2459 ave 2459 max 2459 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2459
-Ave neighs/atom = 8.19667
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
deleted file mode 100644
index f104355d87..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.16
+++ /dev/null
@@ -1,99 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-kspace_style scafacos fmm 1.0e-3
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49646402 0 0.49646402 0
- 10 300 0.018873215 0.015455559 0.47335833 0.02310606 0.49646439 0
- 20 300 0.035197735 0.06229069 0.40334177 0.093124582 0.49646635 0
- 30 300 0.051513195 0.14310163 0.28254277 0.21393694 0.49647971 0
- 40 300 0.067400217 0.52929788 0.089669015 0.79130033 0.88096934 0
- 50 300 0.083569527 1.1963022 -0.082792461 1.7884718 1.7056794 0
- 60 300 0.099931955 1.3928167 -0.37659239 2.082261 1.7056686 0
- 70 300 0.11602688 1.7069009 -0.84571914 2.5518169 1.7060978 0
- 80 300 0.13271379 15.358343 -3.368063 22.960722 19.592659 0
- 90 300 0.15055513 42.280432 -2.1623864 63.209247 61.04686 0
- 100 300 0.16817498 41.48079 -0.89904529 62.013782 61.114736 0
-Loop time of 0.168194 on 16 procs for 100 steps with 300 atoms
-
-Performance: 256846.586 tau/day, 594.552 timesteps/s
-97.7% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.4544e-05 | 2.0206e-05 | 2.6941e-05 | 0.0 | 0.01
-Kspace | 0.16313 | 0.16373 | 0.16423 | 0.1 | 97.34
-Neigh | 0.00016737 | 0.00039591 | 0.00084519 | 0.0 | 0.24
-Comm | 0.0021157 | 0.0026083 | 0.0032525 | 0.7 | 1.55
-Output | 0.00026298 | 0.00030228 | 0.00035977 | 0.0 | 0.18
-Modify | 0.00010705 | 0.00015062 | 0.00020647 | 0.0 | 0.09
-Other | | 0.0009913 | | | 0.59
-
-Nlocal: 18.75 ave 36 max 6 min
-Histogram: 4 3 1 0 0 1 2 1 2 2
-Nghost: 127 ave 196 max 71 min
-Histogram: 8 0 0 0 0 0 0 1 6 1
-Neighs: 153.688 ave 491 max 10 min
-Histogram: 8 1 1 1 1 1 0 0 0 3
-
-Total # of neighbors = 2459
-Ave neighs/atom = 8.19667
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
deleted file mode 100644
index 43ded2d4da..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.2
+++ /dev/null
@@ -1,99 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-kspace_style scafacos fmm 1.0e-3
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49646402 0 0.49646402 0
- 10 300 0.021326542 0.015455559 0.47335833 0.02310606 0.49646439 0
- 20 300 0.043129683 0.06229069 0.40334177 0.093124582 0.49646635 0
- 30 300 0.064425707 0.14310163 0.28254277 0.21393694 0.49647971 0
- 40 300 0.085822344 0.52929788 0.089669015 0.79130033 0.88096934 0
- 50 300 0.10737753 1.1963022 -0.082792461 1.7884718 1.7056794 0
- 60 300 0.12947297 1.3928167 -0.37659239 2.082261 1.7056686 0
- 70 300 0.15108895 1.7069009 -0.84571914 2.5518169 1.7060978 0
- 80 300 0.17378163 15.358343 -3.368063 22.960722 19.592659 0
- 90 300 0.19809985 42.280432 -2.1623864 63.209247 61.04686 0
- 100 300 0.22268319 41.48079 -0.89904529 62.013782 61.114736 0
-Loop time of 0.222696 on 2 procs for 100 steps with 300 atoms
-
-Performance: 193986.156 tau/day, 449.042 timesteps/s
-98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.1683e-05 | 1.5378e-05 | 1.9073e-05 | 0.0 | 0.01
-Kspace | 0.21627 | 0.2168 | 0.21734 | 0.1 | 97.35
-Neigh | 0.0016344 | 0.0021609 | 0.0026875 | 1.1 | 0.97
-Comm | 0.0022857 | 0.0023286 | 0.0023715 | 0.1 | 1.05
-Output | 0.00015521 | 0.00019228 | 0.00022936 | 0.0 | 0.09
-Modify | 0.00052834 | 0.00054049 | 0.00055265 | 0.0 | 0.24
-Other | | 0.0006541 | | | 0.29
-
-Nlocal: 150 ave 159 max 141 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost: 392 ave 395 max 389 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs: 1229.5 ave 1773 max 686 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 2459
-Ave neighs/atom = 8.19667
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
deleted file mode 100644
index 12c74993e9..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.4
+++ /dev/null
@@ -1,99 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-kspace_style scafacos fmm 1.0e-3
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49646402 0 0.49646402 0
- 10 300 0.017563343 0.015455559 0.47335833 0.02310606 0.49646439 0
- 20 300 0.034884214 0.06229069 0.40334177 0.093124582 0.49646635 0
- 30 300 0.052014828 0.14310163 0.28254277 0.21393694 0.49647971 0
- 40 300 0.069101095 0.52929788 0.089669015 0.79130033 0.88096934 0
- 50 300 0.085633039 1.1963022 -0.082792461 1.7884718 1.7056794 0
- 60 300 0.10165119 1.3928167 -0.37659239 2.082261 1.7056686 0
- 70 300 0.11729789 1.7069009 -0.84571914 2.5518169 1.7060978 0
- 80 300 0.1342802 15.358343 -3.368063 22.960722 19.592659 0
- 90 300 0.15266848 42.280432 -2.1623864 63.209247 61.04686 0
- 100 300 0.17004442 41.48079 -0.89904529 62.013782 61.114736 0
-Loop time of 0.170072 on 4 procs for 100 steps with 300 atoms
-
-Performance: 254010.216 tau/day, 587.987 timesteps/s
-98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.5497e-05 | 1.6868e-05 | 1.9789e-05 | 0.0 | 0.01
-Kspace | 0.16417 | 0.16472 | 0.16507 | 0.1 | 96.86
-Neigh | 0.00082564 | 0.0012031 | 0.0015855 | 0.9 | 0.71
-Comm | 0.0026572 | 0.0029335 | 0.003197 | 0.4 | 1.72
-Output | 0.00019169 | 0.00021791 | 0.00026536 | 0.0 | 0.13
-Modify | 0.00031304 | 0.00032955 | 0.00035334 | 0.0 | 0.19
-Other | | 0.0006474 | | | 0.38
-
-Nlocal: 75 ave 81 max 70 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 282.5 ave 290 max 274 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Neighs: 614.75 ave 981 max 285 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 2459
-Ave neighs/atom = 8.19667
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
deleted file mode 100644
index 1fea13cd13..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.fmm.8
+++ /dev/null
@@ -1,99 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-kspace_style scafacos fmm 1.0e-3
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49646402 0 0.49646402 0
- 10 300 0.016258478 0.015455559 0.47335833 0.02310606 0.49646439 0
- 20 300 0.031442165 0.06229069 0.40334177 0.093124582 0.49646635 0
- 30 300 0.046462774 0.14310163 0.28254277 0.21393694 0.49647971 0
- 40 300 0.061176538 0.52929788 0.089669015 0.79130033 0.88096934 0
- 50 300 0.076244354 1.1963022 -0.082792461 1.7884718 1.7056794 0
- 60 300 0.091396809 1.3928167 -0.37659239 2.082261 1.7056686 0
- 70 300 0.10625911 1.7069009 -0.84571914 2.5518169 1.7060978 0
- 80 300 0.1204896 15.358343 -3.368063 22.960722 19.592659 0
- 90 300 0.13657618 42.280432 -2.1623864 63.209247 61.04686 0
- 100 300 0.15163732 41.48079 -0.89904529 62.013782 61.114736 0
-Loop time of 0.151654 on 8 procs for 100 steps with 300 atoms
-
-Performance: 284858.554 tau/day, 659.395 timesteps/s
-97.7% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.3828e-05 | 1.6987e-05 | 1.955e-05 | 0.0 | 0.01
-Kspace | 0.14633 | 0.14689 | 0.14725 | 0.1 | 96.86
-Neigh | 0.00047135 | 0.00067887 | 0.00094771 | 0.0 | 0.45
-Comm | 0.0027649 | 0.0029218 | 0.0032592 | 0.3 | 1.93
-Output | 0.00022578 | 0.00024724 | 0.00030136 | 0.0 | 0.16
-Modify | 0.00018954 | 0.00021681 | 0.0002358 | 0.0 | 0.14
-Other | | 0.0006794 | | | 0.45
-
-Nlocal: 37.5 ave 45 max 31 min
-Histogram: 1 1 1 1 1 0 1 0 1 1
-Nghost: 200 ave 209 max 189 min
-Histogram: 1 0 0 0 1 4 0 0 0 2
-Neighs: 307.375 ave 514 max 115 min
-Histogram: 2 1 0 1 1 0 0 0 1 2
-
-Total # of neighbors = 2459
-Ave neighs/atom = 8.19667
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
deleted file mode 100644
index bd9325dc4b..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.1
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49683273 0 0.49683273 0
- 10 300 0.082981586 0.015479312 0.47369009 0.023141571 0.49683166 0
- 20 300 0.16677213 0.062386358 0.40356181 0.093267605 0.49682941 0
- 30 300 0.2506392 0.14331637 0.2825636 0.21425798 0.49682157 0
- 40 300 0.33466673 0.53041843 0.089505208 0.79297556 0.88248077 0
- 50 300 0.41812825 1.1948397 -0.083317439 1.7862853 1.7029679 0
- 60 300 0.50167894 1.3915614 -0.37745551 2.0803842 1.7029287 0
- 70 300 0.58574796 1.7061978 -0.84746071 2.5507657 1.703305 0
- 80 300 0.6700325 20.692093 -3.32971 30.93468 27.60497 0
- 90 300 0.75608635 48.999403 -2.1632167 73.254107 71.090891 0
- 100 300 0.84190726 51.199785 -0.81127924 76.543678 75.732399 0
-Loop time of 0.841921 on 1 procs for 100 steps with 300 atoms
-
-Performance: 51311.251 tau/day, 118.776 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.1206e-05 | 1.1206e-05 | 1.1206e-05 | 0.0 | 0.00
-Kspace | 0.835 | 0.835 | 0.835 | 0.0 | 99.18
-Neigh | 0.0040102 | 0.0040102 | 0.0040102 | 0.0 | 0.48
-Comm | 0.0012431 | 0.0012431 | 0.0012431 | 0.0 | 0.15
-Output | 0.0001545 | 0.0001545 | 0.0001545 | 0.0 | 0.02
-Modify | 0.0010202 | 0.0010202 | 0.0010202 | 0.0 | 0.12
-Other | | 0.000484 | | | 0.06
-
-Nlocal: 300 ave 300 max 300 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 381 ave 381 max 381 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2461 ave 2461 max 2461 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 2461
-Ave neighs/atom = 8.20333
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
deleted file mode 100644
index 1e385c5fda..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.16
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49683273 0 0.49683273 0
- 10 300 0.029647827 0.015479312 0.47369009 0.023141571 0.49683166 0
- 20 300 0.059298515 0.062386358 0.40356181 0.093267605 0.49682941 0
- 30 300 0.088926077 0.14331637 0.2825636 0.21425798 0.49682157 0
- 40 300 0.11850166 0.53041843 0.089505208 0.79297556 0.88248077 0
- 50 300 0.14820433 1.1948397 -0.083317439 1.7862853 1.7029679 0
- 60 300 0.17807317 1.3915614 -0.37745551 2.0803842 1.7029287 0
- 70 300 0.20803642 1.7061978 -0.84746071 2.5507657 1.703305 0
- 80 300 0.23797083 20.692093 -3.32971 30.93468 27.60497 0
- 90 300 0.26835561 48.999403 -2.1632167 73.254107 71.090891 0
- 100 300 0.29766583 51.199785 -0.81127924 76.543678 75.732399 0
-Loop time of 0.297693 on 16 procs for 100 steps with 300 atoms
-
-Performance: 145116.000 tau/day, 335.917 timesteps/s
-98.8% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.1683e-05 | 1.6928e-05 | 2.4557e-05 | 0.0 | 0.01
-Kspace | 0.29245 | 0.29325 | 0.29366 | 0.1 | 98.51
-Neigh | 0.00017214 | 0.00042973 | 0.0010228 | 0.0 | 0.14
-Comm | 0.0021176 | 0.0024613 | 0.0028479 | 0.5 | 0.83
-Output | 0.00028467 | 0.00033538 | 0.00041103 | 0.0 | 0.11
-Modify | 8.893e-05 | 0.00015014 | 0.00027537 | 0.0 | 0.05
-Other | | 0.001048 | | | 0.35
-
-Nlocal: 18.75 ave 33 max 6 min
-Histogram: 2 6 0 0 0 0 2 1 2 3
-Nghost: 128.875 ave 198 max 71 min
-Histogram: 7 1 0 0 0 0 0 1 5 2
-Neighs: 153.812 ave 490 max 14 min
-Histogram: 8 0 3 0 1 1 0 0 1 2
-
-Total # of neighbors = 2461
-Ave neighs/atom = 8.20333
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
deleted file mode 100644
index 3f54069ffd..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.2
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49683273 0 0.49683273 0
- 10 300 0.049199581 0.015479312 0.47369009 0.023141571 0.49683166 0
- 20 300 0.09860301 0.062386358 0.40356181 0.093267605 0.49682941 0
- 30 300 0.14826894 0.14331637 0.2825636 0.21425798 0.49682157 0
- 40 300 0.19769144 0.53041843 0.089505208 0.79297556 0.88248077 0
- 50 300 0.24735355 1.1948397 -0.083317439 1.7862853 1.7029679 0
- 60 300 0.29692888 1.3915614 -0.37745551 2.0803842 1.7029287 0
- 70 300 0.34639764 1.7061978 -0.84746071 2.5507657 1.703305 0
- 80 300 0.39633083 20.692093 -3.32971 30.93468 27.60497 0
- 90 300 0.44779778 48.999403 -2.1632167 73.254107 71.090891 0
- 100 300 0.49988627 51.199785 -0.81127924 76.543678 75.732399 0
-Loop time of 0.499909 on 2 procs for 100 steps with 300 atoms
-
-Performance: 86415.782 tau/day, 200.037 timesteps/s
-99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 9.0599e-06 | 1.3709e-05 | 1.8358e-05 | 0.0 | 0.00
-Kspace | 0.49314 | 0.49365 | 0.49416 | 0.1 | 98.75
-Neigh | 0.0016146 | 0.0021083 | 0.0026021 | 1.1 | 0.42
-Comm | 0.002754 | 0.0028276 | 0.0029013 | 0.1 | 0.57
-Output | 0.00015783 | 0.00019348 | 0.00022912 | 0.0 | 0.04
-Modify | 0.00049257 | 0.00049472 | 0.00049686 | 0.0 | 0.10
-Other | | 0.0006217 | | | 0.12
-
-Nlocal: 150 ave 157 max 143 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost: 399 ave 402 max 396 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs: 1230.5 ave 1756 max 705 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 2461
-Ave neighs/atom = 8.20333
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
deleted file mode 100644
index 8b94402658..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.4
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49683273 0 0.49683273 0
- 10 300 0.031973124 0.015479312 0.47369009 0.023141571 0.49683166 0
- 20 300 0.064628601 0.062386358 0.40356181 0.093267605 0.49682941 0
- 30 300 0.096747875 0.14331637 0.2825636 0.21425798 0.49682157 0
- 40 300 0.12864041 0.53041843 0.089505208 0.79297556 0.88248077 0
- 50 300 0.161134 1.1948397 -0.083317439 1.7862853 1.7029679 0
- 60 300 0.19359422 1.3915614 -0.37745551 2.0803842 1.7029287 0
- 70 300 0.22573543 1.7061978 -0.84746071 2.5507657 1.703305 0
- 80 300 0.25922132 20.692093 -3.32971 30.93468 27.60497 0
- 90 300 0.29452014 48.999403 -2.1632167 73.254107 71.090891 0
- 100 300 0.33031607 51.199785 -0.81127924 76.543678 75.732399 0
-Loop time of 0.330333 on 4 procs for 100 steps with 300 atoms
-
-Performance: 130777.056 tau/day, 302.725 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.0014e-05 | 1.3471e-05 | 1.5497e-05 | 0.0 | 0.00
-Kspace | 0.32504 | 0.3255 | 0.3258 | 0.1 | 98.54
-Neigh | 0.00083303 | 0.0011883 | 0.0015609 | 0.8 | 0.36
-Comm | 0.0024087 | 0.0025436 | 0.0026674 | 0.2 | 0.77
-Output | 0.00017405 | 0.00020278 | 0.00024986 | 0.0 | 0.06
-Modify | 0.00028658 | 0.00031012 | 0.00033331 | 0.0 | 0.09
-Other | | 0.0005748 | | | 0.17
-
-Nlocal: 75 ave 81 max 69 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Nghost: 287 ave 296 max 278 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Neighs: 615.25 ave 964 max 286 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 2461
-Ave neighs/atom = 8.20333
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
deleted file mode 100644
index 3de3c25017..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.cw.g++.p2nfft.8
+++ /dev/null
@@ -1,92 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-
-units lj
-atom_style charge
-
-read_data data.cloud_wall
- orthogonal box = (0 0 0) to (10 10 10)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 300 atoms
-
-velocity all set 0.0 0.0 0.0 mom no
-
-pair_style zero 1.0
-pair_coeff * *
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-
-thermo_style custom step atoms cpu temp pe ke etotal ecoul
-
-run_style verlet
-
-#dump simple all custom 1000 id x y z vx vy vz
-#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
-#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
-#dump_modify dmpvtk pad 7
-
-thermo 10
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 10 10 10
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
-Step Atoms CPU Temp PotEng KinEng TotEng E_coul
- 0 300 0 0 0.49683273 0 0.49683273 0
- 10 300 0.023941755 0.015479312 0.47369009 0.023141571 0.49683166 0
- 20 300 0.047938108 0.062386358 0.40356181 0.093267605 0.49682941 0
- 30 300 0.071953773 0.14331637 0.2825636 0.21425798 0.49682157 0
- 40 300 0.095941782 0.53041843 0.089505208 0.79297556 0.88248077 0
- 50 300 0.12011361 1.1948397 -0.083317439 1.7862853 1.7029679 0
- 60 300 0.14433384 1.3915614 -0.37745551 2.0803842 1.7029287 0
- 70 300 0.16875505 1.7061978 -0.84746071 2.5507657 1.703305 0
- 80 300 0.193331 20.692093 -3.32971 30.93468 27.60497 0
- 90 300 0.21844888 48.999403 -2.1632167 73.254107 71.090891 0
- 100 300 0.24417853 51.199785 -0.81127924 76.543678 75.732399 0
-Loop time of 0.244198 on 8 procs for 100 steps with 300 atoms
-
-Performance: 176905.349 tau/day, 409.503 timesteps/s
-99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 9.7752e-06 | 1.4246e-05 | 1.955e-05 | 0.0 | 0.01
-Kspace | 0.23946 | 0.23972 | 0.24009 | 0.0 | 98.17
-Neigh | 0.00049043 | 0.00071204 | 0.00095773 | 0.0 | 0.29
-Comm | 0.0025063 | 0.0026675 | 0.0027597 | 0.2 | 1.09
-Output | 0.00019646 | 0.00021604 | 0.00026321 | 0.0 | 0.09
-Modify | 0.00017905 | 0.0001913 | 0.00020766 | 0.0 | 0.08
-Other | | 0.0006773 | | | 0.28
-
-Nlocal: 37.5 ave 42 max 33 min
-Histogram: 2 1 0 1 0 0 1 0 1 2
-Nghost: 202.25 ave 212 max 194 min
-Histogram: 1 0 2 1 0 2 0 1 0 1
-Neighs: 307.625 ave 505 max 129 min
-Histogram: 3 0 0 1 1 0 0 0 1 2
-
-Total # of neighbors = 2461
-Ave neighs/atom = 8.20333
-Neighbor list builds = 15
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
deleted file mode 100644
index f2223064e0..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.16
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 4 MPI processor grid
- 4096 atoms
- Time spent = 0.000503302 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos ewald 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver ewald ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87413076 0 1.3753199 1.4996338
- 10 1.5001167 -0.84976141 0 1.3998642 1.4997504
- 20 1.5002402 -0.84977464 0 1.4000363 1.499874
- 30 1.5003611 -0.84978325 0 1.4002089 1.4999948
- 40 1.5004736 -0.84977869 0 1.4003823 1.5001073
- 50 1.5005703 -0.8497468 0 1.4005591 1.5002039
- 60 1.5006418 -0.84967646 0 1.4007366 1.5002754
- 70 1.5006785 -0.84955497 0 1.4009132 1.5003121
- 80 1.5006711 -0.849369 0 1.4010881 1.5003047
- 90 1.500611 -0.84910811 0 1.4012589 1.5002446
- 100 1.5004911 -0.84870167 0 1.4014854 1.5001247
-Loop time of 46.4857 on 16 procs for 100 steps with 4096 atoms
-
-Performance: 929.317 tau/day, 2.151 timesteps/s
-99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00023437 | 0.00024788 | 0.00026894 | 0.0 | 0.00
-Kspace | 46.476 | 46.476 | 46.476 | 0.0 | 99.98
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0062859 | 0.0067717 | 0.0072649 | 0.3 | 0.01
-Output | 0.0004127 | 0.00044075 | 0.00050807 | 0.0 | 0.00
-Modify | 0.00099325 | 0.0010343 | 0.0010939 | 0.1 | 0.00
-Other | | 0.001459 | | | 0.00
-
-Nlocal: 256 ave 256 max 256 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Nghost: 1265 ave 1265 max 1265 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Neighs: 4096 ave 4096 max 4096 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:47
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
deleted file mode 100644
index 8d3702a8b3..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.ewald.8
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000281811 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos ewald 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver ewald ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87413076 0 1.3753199 1.4996338
- 10 1.5001095 -0.85040058 0 1.3992143 1.4997433
- 20 1.5002258 -0.85039456 0 1.3993947 1.4998595
- 30 1.5003395 -0.85038368 0 1.3995761 1.4999732
- 40 1.5004452 -0.85035944 0 1.3997589 1.5000789
- 50 1.5005354 -0.85030783 0 1.3999457 1.500169
- 60 1.5006008 -0.85021779 0 1.4001339 1.5002344
- 70 1.500632 -0.8500769 0 1.4003215 1.5002656
- 80 1.5006197 -0.84987187 0 1.4005081 1.5002533
- 90 1.5005554 -0.84959251 0 1.400691 1.500189
- 100 1.500432 -0.84916846 0 1.4009301 1.5000657
-Loop time of 86.1477 on 8 procs for 100 steps with 4096 atoms
-
-Performance: 501.464 tau/day, 1.161 timesteps/s
-99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.000314 | 0.00033289 | 0.00035048 | 0.0 | 0.00
-Kspace | 86.136 | 86.136 | 86.136 | 0.0 | 99.99
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0069821 | 0.0073864 | 0.0077834 | 0.3 | 0.01
-Output | 0.00038719 | 0.00041264 | 0.00047517 | 0.0 | 0.00
-Modify | 0.0018711 | 0.0019454 | 0.0020905 | 0.1 | 0.00
-Other | | 0.001762 | | | 0.00
-
-Nlocal: 512 ave 512 max 512 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Nghost: 1685 ave 1685 max 1685 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Neighs: 8192 ave 8192 max 8192 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:01:28
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
deleted file mode 100644
index 0749de3832..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.1
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 1 by 1 MPI processor grid
- 4096 atoms
- Time spent = 0.000584364 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87378819 0 1.3756625 1.4996338
- 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
- 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
- 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
- 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
- 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
- 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
- 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
- 80 1.4995842 -0.87316464 0 1.3756624 1.499218
- 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
- 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
-Loop time of 5.26537 on 1 procs for 100 steps with 4096 atoms
-
-Performance: 8204.550 tau/day, 18.992 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0011349 | 0.0011349 | 0.0011349 | 0.0 | 0.02
-Kspace | 5.2375 | 5.2375 | 5.2375 | 0.0 | 99.47
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0090225 | 0.0090225 | 0.0090225 | 0.0 | 0.17
-Output | 0.0004127 | 0.0004127 | 0.0004127 | 0.0 | 0.01
-Modify | 0.012851 | 0.012851 | 0.012851 | 0.0 | 0.24
-Other | | 0.004441 | | | 0.08
-
-Nlocal: 4096 ave 4096 max 4096 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 5165 ave 5165 max 5165 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 65536 ave 65536 max 65536 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:06
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
deleted file mode 100644
index 6af26f7b81..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.16
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 4 MPI processor grid
- 4096 atoms
- Time spent = 0.000507593 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87378819 0 1.3756625 1.4996338
- 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
- 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
- 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
- 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
- 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
- 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
- 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
- 80 1.4995842 -0.87316464 0 1.3756624 1.499218
- 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
- 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
-Loop time of 0.570389 on 16 procs for 100 steps with 4096 atoms
-
-Performance: 75737.813 tau/day, 175.319 timesteps/s
-99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00024104 | 0.00025283 | 0.00029206 | 0.0 | 0.04
-Kspace | 0.56153 | 0.56176 | 0.56189 | 0.0 | 98.49
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0055203 | 0.0057825 | 0.0061858 | 0.2 | 1.01
-Output | 0.00038505 | 0.00040831 | 0.00048184 | 0.0 | 0.07
-Modify | 0.00096965 | 0.00099662 | 0.0010159 | 0.0 | 0.17
-Other | | 0.001192 | | | 0.21
-
-Nlocal: 256 ave 256 max 256 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Nghost: 1265 ave 1265 max 1265 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Neighs: 4096 ave 4096 max 4096 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
deleted file mode 100644
index bcc61485ca..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.2
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 1 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000455141 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87378819 0 1.3756625 1.4996338
- 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
- 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
- 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
- 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
- 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
- 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
- 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
- 80 1.4995842 -0.87316464 0 1.3756624 1.499218
- 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
- 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
-Loop time of 2.73149 on 2 procs for 100 steps with 4096 atoms
-
-Performance: 15815.560 tau/day, 36.610 timesteps/s
-99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00070763 | 0.00071537 | 0.00072312 | 0.0 | 0.03
-Kspace | 2.7111 | 2.7112 | 2.7112 | 0.0 | 99.26
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0096555 | 0.0097489 | 0.0098424 | 0.1 | 0.36
-Output | 0.00036025 | 0.0003823 | 0.00040436 | 0.0 | 0.01
-Modify | 0.0063472 | 0.0064594 | 0.0065715 | 0.1 | 0.24
-Other | | 0.00299 | | | 0.11
-
-Nlocal: 2048 ave 2048 max 2048 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-Nghost: 3685 ave 3685 max 3685 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-Neighs: 32768 ave 32768 max 32768 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:04
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
deleted file mode 100644
index 54e010c8fd..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.4
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 2 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000329494 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87378819 0 1.3756625 1.4996338
- 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
- 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
- 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
- 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
- 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
- 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
- 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
- 80 1.4995842 -0.87316464 0 1.3756624 1.499218
- 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
- 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
-Loop time of 1.53742 on 4 procs for 100 steps with 4096 atoms
-
-Performance: 28099.005 tau/day, 65.044 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00044894 | 0.00045562 | 0.0004611 | 0.0 | 0.03
-Kspace | 1.5223 | 1.5225 | 1.5225 | 0.0 | 99.03
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0085156 | 0.0086777 | 0.0088782 | 0.1 | 0.56
-Output | 0.00034738 | 0.0003686 | 0.0004015 | 0.0 | 0.02
-Modify | 0.0032606 | 0.0033693 | 0.0034289 | 0.1 | 0.22
-Other | | 0.002084 | | | 0.14
-
-Nlocal: 1024 ave 1024 max 1024 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost: 2525 ave 2525 max 2525 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 16384 ave 16384 max 16384 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
deleted file mode 100644
index d5d38d6804..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.fmm.8
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000284672 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87378819 0 1.3756625 1.4996338
- 10 1.5000004 -0.87378882 0 1.3756625 1.4996342
- 20 1.4999998 -0.87378782 0 1.3756625 1.4996336
- 30 1.4999934 -0.87377823 0 1.3756625 1.4996272
- 40 1.4999745 -0.87374997 0 1.3756625 1.4996083
- 50 1.4999347 -0.87369019 0 1.3756625 1.4995685
- 60 1.4998637 -0.87358381 0 1.3756625 1.4994975
- 70 1.4997506 -0.87341428 0 1.3756624 1.4993845
- 80 1.4995842 -0.87316464 0 1.3756624 1.499218
- 90 1.4993536 -0.87281897 0 1.3756624 1.4989876
- 100 1.4990503 -0.87236411 0 1.3756624 1.4986843
-Loop time of 0.902102 on 8 procs for 100 steps with 4096 atoms
-
-Performance: 47888.152 tau/day, 110.852 timesteps/s
-99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00030732 | 0.00031349 | 0.00032663 | 0.0 | 0.03
-Kspace | 0.89112 | 0.89138 | 0.8916 | 0.0 | 98.81
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0064399 | 0.0066807 | 0.0070164 | 0.2 | 0.74
-Output | 0.00034571 | 0.00036666 | 0.00041723 | 0.0 | 0.04
-Modify | 0.0018673 | 0.0019273 | 0.0020192 | 0.1 | 0.21
-Other | | 0.001431 | | | 0.16
-
-Nlocal: 512 ave 512 max 512 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Nghost: 1685 ave 1685 max 1685 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Neighs: 8192 ave 8192 max 8192 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:02
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
deleted file mode 100644
index d8b782e41d..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.1
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 1 by 1 MPI processor grid
- 4096 atoms
- Time spent = 0.000631332 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.723 | 3.723 | 3.723 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87394226 0 1.3755084 1.4996338
- 10 1.5000144 -0.87365638 0 1.375816 1.4996482
- 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
- 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
- 40 1.5000313 -0.8736496 0 1.375848 1.4996651
- 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
- 60 1.4999432 -0.87350118 0 1.3758644 1.499577
- 70 1.499838 -0.87333517 0 1.3758726 1.4994719
- 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
- 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
- 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
-Loop time of 9.59682 on 1 procs for 100 steps with 4096 atoms
-
-Performance: 4501.489 tau/day, 10.420 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0011375 | 0.0011375 | 0.0011375 | 0.0 | 0.01
-Kspace | 9.5688 | 9.5688 | 9.5688 | 0.0 | 99.71
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.009017 | 0.009017 | 0.009017 | 0.0 | 0.09
-Output | 0.0004344 | 0.0004344 | 0.0004344 | 0.0 | 0.00
-Modify | 0.012987 | 0.012987 | 0.012987 | 0.0 | 0.14
-Other | | 0.004481 | | | 0.05
-
-Nlocal: 4096 ave 4096 max 4096 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 5165 ave 5165 max 5165 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 65536 ave 65536 max 65536 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:10
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
deleted file mode 100644
index 43bcfb6770..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.16
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 4 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 4 MPI processor grid
- 4096 atoms
- Time spent = 0.000500917 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.401 | 3.401 | 3.401 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87394226 0 1.3755084 1.4996338
- 10 1.5000144 -0.87365638 0 1.375816 1.4996482
- 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
- 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
- 40 1.5000313 -0.8736496 0 1.375848 1.4996651
- 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
- 60 1.4999432 -0.87350118 0 1.3758644 1.499577
- 70 1.499838 -0.87333517 0 1.3758726 1.4994719
- 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
- 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
- 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
-Loop time of 1.20528 on 16 procs for 100 steps with 4096 atoms
-
-Performance: 35842.175 tau/day, 82.968 timesteps/s
-99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00021839 | 0.00025332 | 0.00029278 | 0.0 | 0.02
-Kspace | 1.1945 | 1.1948 | 1.195 | 0.0 | 99.13
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0066545 | 0.0069329 | 0.0072389 | 0.2 | 0.58
-Output | 0.0003922 | 0.00042732 | 0.00054955 | 0.0 | 0.04
-Modify | 0.0010166 | 0.0011965 | 0.0014412 | 0.3 | 0.10
-Other | | 0.001724 | | | 0.14
-
-Nlocal: 256 ave 256 max 256 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Nghost: 1265 ave 1265 max 1265 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-Neighs: 4096 ave 4096 max 4096 min
-Histogram: 16 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
deleted file mode 100644
index 9f4f44153b..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.2
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 1 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.00044775 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.634 | 3.634 | 3.634 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87394226 0 1.3755084 1.4996338
- 10 1.5000144 -0.87365638 0 1.375816 1.4996482
- 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
- 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
- 40 1.5000313 -0.8736496 0 1.375848 1.4996651
- 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
- 60 1.4999432 -0.87350118 0 1.3758644 1.499577
- 70 1.499838 -0.87333517 0 1.3758726 1.4994719
- 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
- 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
- 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
-Loop time of 5.14681 on 2 procs for 100 steps with 4096 atoms
-
-Performance: 8393.542 tau/day, 19.429 timesteps/s
-99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00070882 | 0.00072873 | 0.00074863 | 0.0 | 0.01
-Kspace | 5.1257 | 5.1258 | 5.1258 | 0.0 | 99.59
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.010188 | 0.010291 | 0.010394 | 0.1 | 0.20
-Output | 0.00042391 | 0.00044322 | 0.00046253 | 0.0 | 0.01
-Modify | 0.0063772 | 0.006551 | 0.0067248 | 0.2 | 0.13
-Other | | 0.003026 | | | 0.06
-
-Nlocal: 2048 ave 2048 max 2048 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-Nghost: 3685 ave 3685 max 3685 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-Neighs: 32768 ave 32768 max 32768 min
-Histogram: 2 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:05
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
deleted file mode 100644
index d6a78bb193..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.4
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 1 by 2 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000317335 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.497 | 3.497 | 3.497 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87394226 0 1.3755084 1.4996338
- 10 1.5000144 -0.87365638 0 1.375816 1.4996482
- 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
- 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
- 40 1.5000313 -0.8736496 0 1.375848 1.4996651
- 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
- 60 1.4999432 -0.87350118 0 1.3758644 1.499577
- 70 1.499838 -0.87333517 0 1.3758726 1.4994719
- 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
- 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
- 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
-Loop time of 2.94274 on 4 procs for 100 steps with 4096 atoms
-
-Performance: 14680.187 tau/day, 33.982 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00048852 | 0.00049287 | 0.00050163 | 0.0 | 0.02
-Kspace | 2.9277 | 2.9279 | 2.928 | 0.0 | 99.49
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0081494 | 0.0083126 | 0.0084655 | 0.1 | 0.28
-Output | 0.00034475 | 0.00040233 | 0.00043464 | 0.0 | 0.01
-Modify | 0.0034239 | 0.0035145 | 0.0036252 | 0.1 | 0.12
-Other | | 0.00216 | | | 0.07
-
-Nlocal: 1024 ave 1024 max 1024 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost: 2525 ave 2525 max 2525 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 16384 ave 16384 max 16384 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
deleted file mode 100644
index 70716bbcbd..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.g++.p2nfft.8
+++ /dev/null
@@ -1,102 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.NaCl
- orthogonal box = (0 0 0) to (2 2 2)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 8 atoms
-
-replicate 8 8 8
- orthogonal box = (0 0 0) to (16 16 16)
- 2 by 2 by 2 MPI processor grid
- 4096 atoms
- Time spent = 0.000422239 secs
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance field
-
-timestep 0.005
-thermo 10
-
-run 100
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 16 16 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.416 | 3.416 | 3.416 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.87394226 0 1.3755084 1.4996338
- 10 1.5000144 -0.87365638 0 1.375816 1.4996482
- 20 1.5000284 -0.87366526 0 1.3758281 1.4996622
- 30 1.5000364 -0.87366516 0 1.3758401 1.4996702
- 40 1.5000313 -0.8736496 0 1.375848 1.4996651
- 50 1.5000039 -0.87360069 0 1.3758558 1.4996377
- 60 1.4999432 -0.87350118 0 1.3758644 1.499577
- 70 1.499838 -0.87333517 0 1.3758726 1.4994719
- 80 1.4996772 -0.87308644 0 1.3758801 1.4993111
- 90 1.4994505 -0.87274307 0 1.3758836 1.4990844
- 100 1.4991498 -0.8722911 0 1.3758846 1.4987838
-Loop time of 1.75933 on 8 procs for 100 steps with 4096 atoms
-
-Performance: 24554.819 tau/day, 56.840 timesteps/s
-99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00030684 | 0.00031838 | 0.00032926 | 0.0 | 0.02
-Kspace | 1.7474 | 1.7477 | 1.748 | 0.0 | 99.34
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0068667 | 0.0072413 | 0.0075011 | 0.2 | 0.41
-Output | 0.00036955 | 0.00038695 | 0.00044942 | 0.0 | 0.02
-Modify | 0.0018206 | 0.0019438 | 0.0020213 | 0.1 | 0.11
-Other | | 0.001739 | | | 0.10
-
-Nlocal: 512 ave 512 max 512 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Nghost: 1685 ave 1685 max 1685 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-Neighs: 8192 ave 8192 max 8192 min
-Histogram: 8 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 65536
-Ave neighs/atom = 16
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:02
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
deleted file mode 100644
index 37d12bb37d..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.1
+++ /dev/null
@@ -1,105 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos direct 0.001
-
-timestep 0.005
-thermo 1
-run 20
-Setting up ScaFaCoS with solver direct ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777512 0 272.51604 0.17489112
- 5 286.36222 -4.382053 0 424.73173 0.26957567
- 6 481.42206 -4.3095567 0 717.1014 0.4532011
- 7 488.59167 -3.8685194 0 728.2861 0.45995044
- 8 497.85287 -3.0417966 0 742.99073 0.46866874
- 9 499.61615 -3.419003 0 745.2558 0.47032866
- 10 502.63684 -2.8360961 0 750.36521 0.47317227
- 11 504.4846 -2.7628105 0 753.20736 0.47491172
- 12 506.54485 -2.8460356 0 756.21142 0.47685119
- 13 508.27211 -2.730935 0 758.91482 0.4784772
- 14 510.57045 -2.6094877 0 762.48033 0.48064081
- 15 513.14798 -2.7150827 0 766.23717 0.48306726
- 16 515.78124 -2.3961811 0 770.50201 0.48554615
- 17 515.70265 -2.2982683 0 770.48215 0.48547216
- 18 515.7081 -2.1515983 0 770.63699 0.4854773
- 19 515.74906 -2.0581436 0 770.79182 0.48551586
- 20 515.70883 -1.8922577 0 770.89742 0.48547798
-Loop time of 0.52055 on 1 procs for 20 steps with 1000 atoms
-
-Performance: 16597.836 tau/day, 38.421 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
-Kspace | 0.35879 | 0.35879 | 0.35879 | 0.0 | 68.93
-Neigh | 0.15946 | 0.15946 | 0.15946 | 0.0 | 30.63
-Comm | 0.00024056 | 0.00024056 | 0.00024056 | 0.0 | 0.05
-Output | 0.00034761 | 0.00034761 | 0.00034761 | 0.0 | 0.07
-Modify | 0.00071192 | 0.00071192 | 0.00071192 | 0.0 | 0.14
-Other | | 0.0007269 | | | 0.14
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 247817 ave 247817 max 247817 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
deleted file mode 100644
index 7a22e62bce..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.2
+++ /dev/null
@@ -1,105 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos direct 0.001
-
-timestep 0.005
-thermo 1
-run 20
-Setting up ScaFaCoS with solver direct ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777512 0 272.51604 0.17489112
- 5 286.36222 -4.382053 0 424.73173 0.26957567
- 6 481.42206 -4.3095567 0 717.1014 0.4532011
- 7 488.59167 -3.8685194 0 728.2861 0.45995044
- 8 497.85287 -3.0417966 0 742.99073 0.46866874
- 9 499.61615 -3.419003 0 745.2558 0.47032866
- 10 502.63684 -2.8360961 0 750.36521 0.47317227
- 11 504.4846 -2.7628105 0 753.20736 0.47491172
- 12 506.54485 -2.8460356 0 756.21142 0.47685119
- 13 508.27211 -2.730935 0 758.91482 0.4784772
- 14 510.57045 -2.6094877 0 762.48033 0.48064081
- 15 513.14798 -2.7150827 0 766.23717 0.48306726
- 16 515.78124 -2.3961811 0 770.50201 0.48554615
- 17 515.70265 -2.2982683 0 770.48215 0.48547216
- 18 515.7081 -2.1515983 0 770.63699 0.4854773
- 19 515.74906 -2.0581436 0 770.79182 0.48551586
- 20 515.70883 -1.8922577 0 770.89742 0.48547798
-Loop time of 0.330519 on 2 procs for 20 steps with 1000 atoms
-
-Performance: 26140.700 tau/day, 60.511 timesteps/s
-99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0002749 | 0.00027692 | 0.00027895 | 0.0 | 0.08
-Kspace | 0.21565 | 0.24173 | 0.26782 | 5.3 | 73.14
-Neigh | 0.058644 | 0.084906 | 0.11117 | 9.0 | 25.69
-Comm | 0.002033 | 0.0022832 | 0.0025334 | 0.5 | 0.69
-Output | 0.00035667 | 0.0004549 | 0.00055313 | 0.0 | 0.14
-Modify | 0.0004704 | 0.00050521 | 0.00054002 | 0.0 | 0.15
-Other | | 0.0003613 | | | 0.11
-
-Nlocal: 500 ave 516 max 484 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost: 456.5 ave 475 max 438 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs: 123908 ave 172139 max 75678 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
deleted file mode 100644
index 51d0f8c47e..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.4
+++ /dev/null
@@ -1,105 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos direct 0.001
-
-timestep 0.005
-thermo 1
-run 20
-Setting up ScaFaCoS with solver direct ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777512 0 272.51604 0.17489112
- 5 286.36222 -4.382053 0 424.73173 0.26957567
- 6 481.42206 -4.3095567 0 717.1014 0.4532011
- 7 488.59167 -3.8685194 0 728.2861 0.45995044
- 8 497.85287 -3.0417966 0 742.99073 0.46866874
- 9 499.61615 -3.419003 0 745.2558 0.47032866
- 10 502.63684 -2.8360961 0 750.36521 0.47317227
- 11 504.4846 -2.7628105 0 753.20736 0.47491172
- 12 506.54485 -2.8460356 0 756.21142 0.47685119
- 13 508.27211 -2.730935 0 758.91482 0.4784772
- 14 510.57045 -2.6094877 0 762.48033 0.48064081
- 15 513.14798 -2.7150827 0 766.23717 0.48306726
- 16 515.78124 -2.3961811 0 770.50201 0.48554615
- 17 515.70265 -2.2982683 0 770.48215 0.48547216
- 18 515.7081 -2.1515983 0 770.63699 0.4854773
- 19 515.74906 -2.0581436 0 770.79182 0.48551586
- 20 515.70883 -1.8922577 0 770.89742 0.48547798
-Loop time of 0.197141 on 4 procs for 20 steps with 1000 atoms
-
-Performance: 43826.435 tau/day, 101.450 timesteps/s
-99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0002718 | 0.00027621 | 0.00028539 | 0.0 | 0.14
-Kspace | 0.12861 | 0.14654 | 0.16542 | 3.7 | 74.33
-Neigh | 0.027906 | 0.046895 | 0.064943 | 6.6 | 23.79
-Comm | 0.0022087 | 0.0024236 | 0.0026295 | 0.4 | 1.23
-Output | 0.0003252 | 0.00044608 | 0.0006001 | 0.0 | 0.23
-Modify | 0.00016618 | 0.0001756 | 0.00018811 | 0.0 | 0.09
-Other | | 0.0003839 | | | 0.19
-
-Nlocal: 250 ave 259 max 238 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Nghost: 672.25 ave 683 max 663 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 61954.2 ave 97157 max 25016 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
deleted file mode 100644
index 90119a101b..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.direct.8
+++ /dev/null
@@ -1,105 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos direct 0.001
-
-timestep 0.005
-thermo 1
-run 20
-Setting up ScaFaCoS with solver direct ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777512 0 272.51604 0.17489112
- 5 286.36222 -4.382053 0 424.73173 0.26957567
- 6 481.42206 -4.3095567 0 717.1014 0.4532011
- 7 488.59167 -3.8685194 0 728.2861 0.45995044
- 8 497.85287 -3.0417966 0 742.99073 0.46866874
- 9 499.61615 -3.419003 0 745.2558 0.47032866
- 10 502.63684 -2.8360961 0 750.36521 0.47317227
- 11 504.4846 -2.7628105 0 753.20736 0.47491172
- 12 506.54485 -2.8460356 0 756.21142 0.47685119
- 13 508.27211 -2.730935 0 758.91482 0.4784772
- 14 510.57045 -2.6094877 0 762.48033 0.48064081
- 15 513.14798 -2.7150827 0 766.23717 0.48306726
- 16 515.78124 -2.3961811 0 770.50201 0.48554615
- 17 515.70265 -2.2982683 0 770.48215 0.48547216
- 18 515.7081 -2.1515983 0 770.63699 0.4854773
- 19 515.74906 -2.0581436 0 770.79182 0.48551586
- 20 515.70883 -1.8922577 0 770.89742 0.48547798
-Loop time of 0.107014 on 8 procs for 20 steps with 1000 atoms
-
-Performance: 80736.875 tau/day, 186.891 timesteps/s
-98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00027704 | 0.00029281 | 0.00035691 | 0.0 | 0.27
-Kspace | 0.069458 | 0.07877 | 0.089146 | 2.5 | 73.61
-Neigh | 0.013525 | 0.024156 | 0.033524 | 4.7 | 22.57
-Comm | 0.002552 | 0.0029828 | 0.0033691 | 0.5 | 2.79
-Output | 0.00037909 | 0.00051123 | 0.00070429 | 0.0 | 0.48
-Modify | 8.9645e-05 | 9.5487e-05 | 0.000103 | 0.0 | 0.09
-Other | | 0.0002059 | | | 0.19
-
-Nlocal: 125 ave 133 max 113 min
-Histogram: 2 0 0 0 0 1 1 0 2 2
-Nghost: 773.625 ave 788 max 764 min
-Histogram: 1 1 2 1 1 0 0 0 1 1
-Neighs: 30977.1 ave 50690 max 10447 min
-Histogram: 1 1 1 0 1 1 0 0 2 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
deleted file mode 100644
index 432ea72b67..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.1
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417141 0 1.6235786 0.00141207
- 1 18.780412 -10.770009 0 17.372438 0.017679504
- 2 65.294131 -11.084501 0 86.758754 0.06146659
- 3 121.92555 -7.0612033 0 175.64423 0.11477827
- 4 185.71165 -5.8781334 0 272.41077 0.17482523
- 5 286.28339 -4.3800108 0 424.61565 0.26950146
- 6 481.28097 -4.3052012 0 716.89433 0.45306828
- 7 487.26022 -3.8672741 0 726.29216 0.45869703
- 8 493.65478 -3.0242687 0 736.71742 0.46471675
- 9 495.66203 -3.4336343 0 739.31592 0.46660633
- 10 498.41831 -2.8837072 0 743.99613 0.46920104
- 11 499.20944 -2.7724783 0 745.29287 0.46994579
- 12 500.97345 -2.8281484 0 747.88057 0.4716064
- 13 507.46412 -2.7752775 0 757.65971 0.47771658
- 14 525.35729 -2.5749814 0 784.67292 0.49456085
- 15 563.9578 -2.9982381 0 842.09253 0.5308986
- 16 645.47602 -2.5519203 0 964.69389 0.60763822
- 17 647.09276 -2.2568468 0 967.41166 0.60916019
- 18 647.12596 -2.2791003 0 967.43915 0.60919144
- 19 647.24862 -2.2495226 0 967.65253 0.60930691
- 20 647.51175 -2.0239179 0 968.27244 0.60955462
-Loop time of 0.644143 on 1 procs for 20 steps with 1000 atoms
-
-Performance: 13413.173 tau/day, 31.049 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00027657 | 0.00027657 | 0.00027657 | 0.0 | 0.04
-Kspace | 0.4788 | 0.4788 | 0.4788 | 0.0 | 74.33
-Neigh | 0.16279 | 0.16279 | 0.16279 | 0.0 | 25.27
-Comm | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.03
-Output | 0.00054836 | 0.00054836 | 0.00054836 | 0.0 | 0.09
-Modify | 0.00075102 | 0.00075102 | 0.00075102 | 0.0 | 0.12
-Other | | 0.000757 | | | 0.12
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 244342 ave 244342 max 244342 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 244342
-Ave neighs/atom = 244.342
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
deleted file mode 100644
index 4d4b1100e3..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.2
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417141 0 1.6235786 0.00141207
- 1 18.780412 -10.770009 0 17.372438 0.017679504
- 2 65.294131 -11.084501 0 86.758754 0.06146659
- 3 121.92555 -7.0612033 0 175.64423 0.11477827
- 4 185.71165 -5.8781334 0 272.41077 0.17482523
- 5 286.28339 -4.3800108 0 424.61565 0.26950146
- 6 481.28097 -4.3052012 0 716.89433 0.45306828
- 7 487.26022 -3.8672741 0 726.29216 0.45869703
- 8 493.65478 -3.0242687 0 736.71742 0.46471675
- 9 495.66203 -3.4336343 0 739.31592 0.46660633
- 10 498.41831 -2.8837072 0 743.99613 0.46920104
- 11 499.20944 -2.7724783 0 745.29287 0.46994579
- 12 500.97345 -2.8281484 0 747.88057 0.4716064
- 13 507.46412 -2.7752775 0 757.65971 0.47771658
- 14 525.35729 -2.5749814 0 784.67292 0.49456085
- 15 563.9578 -2.9982381 0 842.09253 0.5308986
- 16 645.47602 -2.5519203 0 964.69389 0.60763822
- 17 647.09276 -2.2568468 0 967.41166 0.60916019
- 18 647.12596 -2.2791003 0 967.43915 0.60919144
- 19 647.24862 -2.2495226 0 967.65253 0.60930691
- 20 647.51175 -2.0239179 0 968.27244 0.60955462
-Loop time of 0.563049 on 2 procs for 20 steps with 1000 atoms
-
-Performance: 15345.024 tau/day, 35.521 timesteps/s
-99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00024986 | 0.00026596 | 0.00028205 | 0.0 | 0.05
-Kspace | 0.45103 | 0.47692 | 0.50281 | 3.7 | 84.70
-Neigh | 0.055771 | 0.081813 | 0.10785 | 9.1 | 14.53
-Comm | 0.0022206 | 0.0024507 | 0.0026808 | 0.5 | 0.44
-Output | 0.00050044 | 0.00061882 | 0.00073719 | 0.0 | 0.11
-Modify | 0.00029945 | 0.00044227 | 0.00058508 | 0.0 | 0.08
-Other | | 0.0005381 | | | 0.10
-
-Nlocal: 500 ave 509 max 491 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost: 455.5 ave 467 max 444 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs: 122171 ave 171834 max 72508 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 244342
-Ave neighs/atom = 244.342
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
deleted file mode 100644
index 9634a0174b..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.4
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417141 0 1.6235786 0.00141207
- 1 18.780412 -10.770009 0 17.372438 0.017679504
- 2 65.294131 -11.084501 0 86.758754 0.06146659
- 3 121.92555 -7.0612033 0 175.64423 0.11477827
- 4 185.71165 -5.8781334 0 272.41077 0.17482523
- 5 286.28339 -4.3800108 0 424.61565 0.26950146
- 6 481.28097 -4.3052012 0 716.89433 0.45306828
- 7 487.26022 -3.8672741 0 726.29216 0.45869703
- 8 493.65478 -3.0242687 0 736.71742 0.46471675
- 9 495.66203 -3.4336343 0 739.31592 0.46660633
- 10 498.41831 -2.8837072 0 743.99613 0.46920104
- 11 499.20944 -2.7724783 0 745.29287 0.46994579
- 12 500.97345 -2.8281484 0 747.88057 0.4716064
- 13 507.46412 -2.7752775 0 757.65971 0.47771658
- 14 525.35729 -2.5749814 0 784.67292 0.49456085
- 15 563.9578 -2.9982381 0 842.09253 0.5308986
- 16 645.47602 -2.5519203 0 964.69389 0.60763822
- 17 647.09276 -2.2568468 0 967.41166 0.60916019
- 18 647.12596 -2.2791003 0 967.43915 0.60919144
- 19 647.24862 -2.2495226 0 967.65253 0.60930691
- 20 647.51175 -2.0239179 0 968.27244 0.60955462
-Loop time of 0.508149 on 4 procs for 20 steps with 1000 atoms
-
-Performance: 17002.884 tau/day, 39.359 timesteps/s
-99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00024509 | 0.00026453 | 0.00028753 | 0.0 | 0.05
-Kspace | 0.43933 | 0.45836 | 0.47734 | 2.2 | 90.20
-Neigh | 0.025956 | 0.045068 | 0.064242 | 7.2 | 8.87
-Comm | 0.002799 | 0.0030612 | 0.0033174 | 0.4 | 0.60
-Output | 0.00047231 | 0.00058293 | 0.00076509 | 0.0 | 0.11
-Modify | 0.00016856 | 0.0002442 | 0.00042009 | 0.0 | 0.05
-Other | | 0.0005655 | | | 0.11
-
-Nlocal: 250 ave 259 max 240 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost: 668.75 ave 679 max 657 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Neighs: 61085.5 ave 95363 max 24964 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-
-Total # of neighbors = 244342
-Ave neighs/atom = 244.342
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
deleted file mode 100644
index a6a020b031..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.fmm.8
+++ /dev/null
@@ -1,109 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos fmm 0.001
-kspace_modify scafacos tolerance energy_rel
-kspace_modify scafacos fmm_tuning 1
-ScaFaCoS setting fmm inhomogen tuning ...3
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver fmm ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417141 0 1.6235786 0.00141207
- 1 18.780412 -10.770009 0 17.372438 0.017679504
- 2 65.294131 -11.084501 0 86.758754 0.06146659
- 3 121.92555 -7.0612033 0 175.64423 0.11477827
- 4 185.71165 -5.8781334 0 272.41077 0.17482523
- 5 286.28339 -4.3800108 0 424.61565 0.26950146
- 6 481.28097 -4.3052012 0 716.89433 0.45306828
- 7 487.26022 -3.8672741 0 726.29216 0.45869703
- 8 493.65478 -3.0242687 0 736.71742 0.46471675
- 9 495.66203 -3.4336343 0 739.31592 0.46660633
- 10 498.41831 -2.8837072 0 743.99613 0.46920104
- 11 499.20944 -2.7724783 0 745.29287 0.46994579
- 12 500.97345 -2.8281484 0 747.88057 0.4716064
- 13 507.46412 -2.7752775 0 757.65971 0.47771658
- 14 525.35729 -2.5749814 0 784.67292 0.49456085
- 15 563.9578 -2.9982381 0 842.09253 0.5308986
- 16 645.47602 -2.5519203 0 964.69389 0.60763822
- 17 647.09276 -2.2568468 0 967.41166 0.60916019
- 18 647.12596 -2.2791003 0 967.43915 0.60919144
- 19 647.24862 -2.2495226 0 967.65253 0.60930691
- 20 647.51175 -2.0239179 0 968.27244 0.60955462
-Loop time of 0.494261 on 8 procs for 20 steps with 1000 atoms
-
-Performance: 17480.630 tau/day, 40.464 timesteps/s
-99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00027752 | 0.00030088 | 0.0003736 | 0.0 | 0.06
-Kspace | 0.45443 | 0.46295 | 0.47316 | 1.0 | 93.67
-Neigh | 0.014408 | 0.02515 | 0.034048 | 4.6 | 5.09
-Comm | 0.0036254 | 0.0041741 | 0.0048032 | 0.6 | 0.84
-Output | 0.00072742 | 0.0009357 | 0.0012984 | 0.0 | 0.19
-Modify | 0.00011778 | 0.00015756 | 0.00019836 | 0.0 | 0.03
-Other | | 0.000589 | | | 0.12
-
-Nlocal: 125 ave 137 max 111 min
-Histogram: 1 1 0 0 0 2 2 1 0 1
-Nghost: 768.875 ave 788 max 761 min
-Histogram: 4 0 2 0 0 0 1 0 0 1
-Neighs: 30542.8 ave 48077 max 10011 min
-Histogram: 1 1 1 0 1 1 0 0 0 3
-
-Total # of neighbors = 244342
-Ave neighs/atom = 244.342
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
deleted file mode 100644
index f9192cdfaf..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.1
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance potential
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777511 0 272.51603 0.17489112
- 5 286.36221 -4.3820531 0 424.73172 0.26957566
- 6 481.42203 -4.3095567 0 717.10136 0.45320108
- 7 488.59165 -3.8685193 0 728.28607 0.45995042
- 8 497.85288 -3.0417938 0 742.99075 0.46866875
- 9 499.61619 -3.4190063 0 745.25585 0.47032869
- 10 502.63691 -2.8360951 0 750.36531 0.47317234
- 11 504.4847 -2.7628089 0 753.20751 0.47491181
- 12 506.54494 -2.8460319 0 756.21157 0.47685128
- 13 508.2722 -2.7309328 0 758.91497 0.47847729
- 14 510.57053 -2.6094792 0 762.48045 0.48064089
- 15 513.14804 -2.7150819 0 766.23726 0.48306731
- 16 515.78127 -2.3961749 0 770.50206 0.48554618
- 17 515.70267 -2.2982581 0 770.48219 0.48547219
- 18 515.70813 -2.1516075 0 770.63702 0.48547732
- 19 515.74908 -2.0581483 0 770.79185 0.48551588
- 20 515.70881 -1.892235 0 770.89742 0.48547797
-Loop time of 1.34132 on 1 procs for 20 steps with 1000 atoms
-
-Performance: 6441.409 tau/day, 14.911 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00028849 | 0.00028849 | 0.00028849 | 0.0 | 0.02
-Kspace | 1.1744 | 1.1744 | 1.1744 | 0.0 | 87.56
-Neigh | 0.16435 | 0.16435 | 0.16435 | 0.0 | 12.25
-Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02
-Output | 0.00051928 | 0.00051928 | 0.00051928 | 0.0 | 0.04
-Modify | 0.00079513 | 0.00079513 | 0.00079513 | 0.0 | 0.06
-Other | | 0.0007439 | | | 0.06
-
-Nlocal: 1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 247817 ave 247817 max 247817 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
deleted file mode 100644
index 4db3e28dbf..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.2
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 1 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance potential
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777511 0 272.51603 0.17489112
- 5 286.36221 -4.3820531 0 424.73172 0.26957566
- 6 481.42203 -4.3095567 0 717.10136 0.45320108
- 7 488.59165 -3.8685193 0 728.28607 0.45995042
- 8 497.85288 -3.0417938 0 742.99075 0.46866875
- 9 499.61619 -3.4190063 0 745.25585 0.47032869
- 10 502.63691 -2.8360951 0 750.36531 0.47317234
- 11 504.4847 -2.7628089 0 753.20751 0.47491181
- 12 506.54494 -2.8460319 0 756.21157 0.47685128
- 13 508.2722 -2.7309328 0 758.91497 0.47847729
- 14 510.57053 -2.6094792 0 762.48045 0.48064089
- 15 513.14804 -2.7150819 0 766.23726 0.48306731
- 16 515.78127 -2.3961749 0 770.50206 0.48554618
- 17 515.70267 -2.2982581 0 770.48219 0.48547219
- 18 515.70813 -2.1516075 0 770.63702 0.48547732
- 19 515.74908 -2.0581483 0 770.79185 0.48551588
- 20 515.70881 -1.892235 0 770.89742 0.48547797
-Loop time of 0.858675 on 2 procs for 20 steps with 1000 atoms
-
-Performance: 10062.016 tau/day, 23.292 timesteps/s
-100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00026321 | 0.00026667 | 0.00027013 | 0.0 | 0.03
-Kspace | 0.74531 | 0.77182 | 0.79833 | 3.0 | 89.89
-Neigh | 0.055915 | 0.082578 | 0.10924 | 9.3 | 9.62
-Comm | 0.0021703 | 0.002401 | 0.0026317 | 0.5 | 0.28
-Output | 0.00048423 | 0.00061262 | 0.000741 | 0.0 | 0.07
-Modify | 0.00034285 | 0.0004636 | 0.00058436 | 0.0 | 0.05
-Other | | 0.0005329 | | | 0.06
-
-Nlocal: 500 ave 516 max 484 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost: 456.5 ave 475 max 438 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs: 123908 ave 172139 max 75678 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
deleted file mode 100644
index 3a2d653106..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.4
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance potential
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777511 0 272.51603 0.17489112
- 5 286.36221 -4.3820531 0 424.73172 0.26957566
- 6 481.42203 -4.3095567 0 717.10136 0.45320108
- 7 488.59165 -3.8685193 0 728.28607 0.45995042
- 8 497.85288 -3.0417938 0 742.99075 0.46866875
- 9 499.61619 -3.4190063 0 745.25585 0.47032869
- 10 502.63691 -2.8360951 0 750.36531 0.47317234
- 11 504.4847 -2.7628089 0 753.20751 0.47491181
- 12 506.54494 -2.8460319 0 756.21157 0.47685128
- 13 508.2722 -2.7309328 0 758.91497 0.47847729
- 14 510.57053 -2.6094792 0 762.48045 0.48064089
- 15 513.14804 -2.7150819 0 766.23726 0.48306731
- 16 515.78127 -2.3961749 0 770.50206 0.48554618
- 17 515.70267 -2.2982581 0 770.48219 0.48547219
- 18 515.70813 -2.1516075 0 770.63702 0.48547732
- 19 515.74908 -2.0581483 0 770.79185 0.48551588
- 20 515.70881 -1.892235 0 770.89742 0.48547797
-Loop time of 0.540235 on 4 procs for 20 steps with 1000 atoms
-
-Performance: 15993.051 tau/day, 37.021 timesteps/s
-99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00025725 | 0.00028253 | 0.00031233 | 0.0 | 0.05
-Kspace | 0.47152 | 0.48989 | 0.50709 | 1.9 | 90.68
-Neigh | 0.028196 | 0.045694 | 0.064338 | 6.3 | 8.46
-Comm | 0.0026579 | 0.003028 | 0.0033965 | 0.5 | 0.56
-Output | 0.00049663 | 0.00064254 | 0.00084853 | 0.0 | 0.12
-Modify | 0.00019264 | 0.0002293 | 0.00030923 | 0.0 | 0.04
-Other | | 0.0004709 | | | 0.09
-
-Nlocal: 250 ave 259 max 238 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Nghost: 672.25 ave 683 max 663 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 61954.2 ave 97157 max 25016 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
deleted file mode 100644
index 08e68531a9..0000000000
--- a/examples/USER/scafacos/log.23Jul18.scafacos.hsph.g++.p2nfft.8
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (29 Jun 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-# Point dipoles in a 2d box
-
-units lj
-atom_style charge
-
-read_data data.hammersley_shphere
- orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
- 2 by 2 by 2 MPI processor grid
- reading atoms ...
- 1000 atoms
-change_box all boundary f f f
-
-velocity all create 1.5 49893
-
-neighbor 1.0 bin
-neigh_modify delay 0
-
-fix 1 all nve
-
-# LAMMPS computes pairwise and long-range Coulombics
-
-#pair_style coul/long 3.0
-#pair_coeff * *
-#kspace_style pppm 1.0e-3
-
-# Scafacos computes entire long-range Coulombics
-# use dummy pair style to perform atom sorting
-
-pair_style zero 1.0
-pair_coeff * *
-
-#fix 2 all scafacos p3m tolerance field 0.001
-
-kspace_style scafacos p2nfft 0.001
-kspace_modify scafacos tolerance potential
-
-timestep 0.005
-thermo 1
-
-run 20
-Setting up ScaFaCoS with solver p2nfft ...
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2
- ghost atom cutoff = 2
- binsize = 1, bins = 102 102 102
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair zero, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 1.5 -0.62417787 0 1.6235721 0.00141207
- 1 18.780041 -10.770002 0 17.371889 0.017679155
- 2 65.289192 -11.084705 0 86.751149 0.06146194
- 3 121.92987 -7.0625759 0 175.64933 0.11478234
- 4 185.78164 -5.8777511 0 272.51603 0.17489112
- 5 286.36221 -4.3820531 0 424.73172 0.26957566
- 6 481.42203 -4.3095567 0 717.10136 0.45320108
- 7 488.59165 -3.8685193 0 728.28607 0.45995042
- 8 497.85288 -3.0417938 0 742.99075 0.46866875
- 9 499.61619 -3.4190063 0 745.25585 0.47032869
- 10 502.63691 -2.8360951 0 750.36531 0.47317234
- 11 504.4847 -2.7628089 0 753.20751 0.47491181
- 12 506.54494 -2.8460319 0 756.21157 0.47685128
- 13 508.2722 -2.7309328 0 758.91497 0.47847729
- 14 510.57053 -2.6094792 0 762.48045 0.48064089
- 15 513.14804 -2.7150819 0 766.23726 0.48306731
- 16 515.78127 -2.3961749 0 770.50206 0.48554618
- 17 515.70267 -2.2982581 0 770.48219 0.48547219
- 18 515.70813 -2.1516075 0 770.63702 0.48547732
- 19 515.74908 -2.0581483 0 770.79185 0.48551588
- 20 515.70881 -1.892235 0 770.89742 0.48547797
-Loop time of 0.317433 on 8 procs for 20 steps with 1000 atoms
-
-Performance: 27218.342 tau/day, 63.005 timesteps/s
-99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.00027013 | 0.00028479 | 0.00029206 | 0.0 | 0.09
-Kspace | 0.27742 | 0.28666 | 0.29702 | 1.4 | 90.31
-Neigh | 0.014795 | 0.025382 | 0.03481 | 4.8 | 8.00
-Comm | 0.0034907 | 0.0038758 | 0.0042439 | 0.5 | 1.22
-Output | 0.00055361 | 0.00073573 | 0.0010755 | 0.0 | 0.23
-Modify | 0.00012279 | 0.00014156 | 0.00016165 | 0.0 | 0.04
-Other | | 0.0003535 | | | 0.11
-
-Nlocal: 125 ave 133 max 113 min
-Histogram: 2 0 0 0 0 1 1 0 2 2
-Nghost: 773.625 ave 788 max 764 min
-Histogram: 1 1 2 1 1 0 0 0 1 1
-Neighs: 30977.1 ave 50690 max 10447 min
-Histogram: 1 1 1 0 1 1 0 0 2 1
-
-Total # of neighbors = 247817
-Ave neighs/atom = 247.817
-Neighbor list builds = 19
-Dangerous builds = 18
-Total wall time: 0:00:00
--
GitLab
From fc93a79fdd04234f041aab2a9f7f07d5242585a0 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 8 Aug 2018 14:05:28 -0600
Subject: [PATCH 081/332] updated to support ScaFaCoS 1.0.1
---
cmake/CMakeLists.txt | 5 +++--
lib/scafacos/Install.py | 6 +++---
src/USER-SCAFACOS/scafacos.cpp | 22 ++++++++++++++++++++++
3 files changed, 28 insertions(+), 5 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index a03548c712..9f1f3a7526 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -360,8 +360,8 @@ if(PKG_USER-SCAFACOS)
if(DOWNLOAD_SCAFACOS)
include(ExternalProject)
ExternalProject_Add(scafacos_build
- URL https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz
- URL_MD5 c75d75d8a4cb9757faddb8b205a2b20f
+ URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+ URL_MD5 bd46d74e3296bd8a444d731bb10c1738
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
--disable-doc
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
@@ -389,6 +389,7 @@ if(PKG_USER-SCAFACOS)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+ list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py
index 4e00e805d1..d23e8a3686 100644
--- a/lib/scafacos/Install.py
+++ b/lib/scafacos/Install.py
@@ -29,8 +29,8 @@ make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation
# settings
-version = "scafacos-1.0.0"
-url = "https://github.com/scafacos/scafacos/releases/download/v1.0.0/scafacos-1.0.0.tar.gz"
+version = "scafacos-1.0.1"
+url = "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz"
#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version
# print error message or help
@@ -147,7 +147,7 @@ if buildflag:
if buildflag:
print("Building Scafacos ...")
- cmd = 'cd "%s"; CC=mpicc FC=mpif90 CXX=mpicxx ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald > log.txt; make -j; make install' % homedir
+ cmd = 'cd "%s"; ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77= > log.txt; make -j; make install' % homedir
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index fdbd5e34e0..5832f5b052 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -150,6 +150,17 @@ void Scafacos::init()
fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
}
+ // for the FMM at least one particle is required per process
+ if (strcmp(method,"fmm") == 0)
+ {
+ int empty = (nlocal==0)?1:0;
+ MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
+ if (empty > 0)
+ fcs_set_redistribute(fcs,1);
+ else
+ fcs_set_redistribute(fcs,0);
+ }
+
result = fcs_tune(fcs,nlocal,&x[0][0],q);
check_result(result);
// more useful here, since the parameters should be tuned now
@@ -172,6 +183,17 @@ void Scafacos::compute(int eflag, int vflag)
const double qscale = qqrd2e;
+ // for the FMM at least one particle is required per process
+ if (strcmp(method,"fmm"))
+ {
+ int empty = (nlocal==0)?1:0;
+ MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
+ if (empty > 0)
+ fcs_set_redistribute(fcs,1);
+ else
+ fcs_set_redistribute(fcs,0);
+ }
+
if (eflag || vflag) ev_setup(eflag,vflag);
else
{
--
GitLab
From 2a5e550bdacb74abba6136db9a8c4b80e147774f Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 8 Aug 2018 15:02:19 -0600
Subject: [PATCH 082/332] updated log files
---
.../log.08Aug18.scafacos.cw.g++.ewald.16 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.ewald.8 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.fmm.1 | 99 ++++++++++++++++
.../log.08Aug18.scafacos.cw.g++.fmm.16 | 99 ++++++++++++++++
.../log.08Aug18.scafacos.cw.g++.fmm.2 | 99 ++++++++++++++++
.../log.08Aug18.scafacos.cw.g++.fmm.4 | 99 ++++++++++++++++
.../log.08Aug18.scafacos.cw.g++.fmm.8 | 99 ++++++++++++++++
.../log.08Aug18.scafacos.cw.g++.p2nfft.1 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.p2nfft.16 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.p2nfft.2 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.p2nfft.4 | 92 +++++++++++++++
.../log.08Aug18.scafacos.cw.g++.p2nfft.8 | 92 +++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.ewald.1 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.ewald.16 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.ewald.2 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.ewald.4 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.ewald.8 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.fmm.1 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.fmm.16 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.fmm.2 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.fmm.4 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.fmm.8 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.p2nfft.1 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.p2nfft.16 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.p2nfft.2 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.p2nfft.4 | 102 ++++++++++++++++
.../log.08Aug18.scafacos.g++.p2nfft.8 | 102 ++++++++++++++++
.../scafacos/log.08Aug18.scafacos.g++.p3m.2 | 0
.../log.08Aug18.scafacos.hsph.g++.direct.1 | 105 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.direct.2 | 105 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.direct.4 | 105 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.direct.8 | 105 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.fmm.1 | 109 ++++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.fmm.2 | 109 ++++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.fmm.4 | 109 ++++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.fmm.8 | 109 ++++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.p2nfft.1 | 107 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.p2nfft.2 | 107 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.p2nfft.4 | 107 +++++++++++++++++
.../log.08Aug18.scafacos.hsph.g++.p2nfft.8 | 107 +++++++++++++++++
40 files changed, 3953 insertions(+)
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4
create mode 100644 examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16
new file mode 100644
index 0000000000..20d3faaf7f
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49647271 0 0.49647271 0 0
+ 10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861
+ 20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314
+ 30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679
+ 40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911
+ 50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037
+ 60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302
+ 70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118
+ 80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288
+ 90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364
+ 100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922
+Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms
+
+Performance: 102047.913 tau/day, 236.222 timesteps/s
+99.2% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01
+Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04
+Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13
+Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54
+Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07
+Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03
+Other | | 0.000758 | | | 0.18
+
+Nlocal: 18.75 ave 39 max 6 min
+Histogram: 6 1 1 0 1 2 2 1 1 1
+Nghost: 122.812 ave 195 max 63 min
+Histogram: 8 0 0 0 0 0 0 1 3 4
+Neighs: 160.625 ave 598 max 13 min
+Histogram: 8 2 1 1 1 0 0 2 0 1
+
+Total # of neighbors = 2570
+Ave neighs/atom = 8.56667
+Neighbor list builds = 23
+Dangerous builds = 16
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8
new file mode 100644
index 0000000000..d26138522a
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49647271 0 0.49647271 0 0
+ 10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087
+ 20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565
+ 30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608
+ 40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582
+ 50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403
+ 60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376
+ 70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802
+ 80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814
+ 90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175
+ 100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344
+Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms
+
+Performance: 74052.598 tau/day, 171.418 timesteps/s
+99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01
+Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17
+Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16
+Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48
+Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04
+Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03
+Other | | 0.00065 | | | 0.11
+
+Nlocal: 37.5 ave 46 max 31 min
+Histogram: 2 0 0 2 1 0 2 0 0 1
+Nghost: 203.875 ave 212 max 192 min
+Histogram: 1 0 1 0 0 2 1 0 0 3
+Neighs: 321.625 ave 599 max 112 min
+Histogram: 1 2 0 1 1 0 1 1 0 1
+
+Total # of neighbors = 2573
+Ave neighs/atom = 8.57667
+Neighbor list builds = 23
+Dangerous builds = 16
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1
new file mode 100644
index 0000000000..714ce85a5f
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1
@@ -0,0 +1,99 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
+ 10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
+ 20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
+ 30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
+ 40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
+ 50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
+ 60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
+ 70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
+ 80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
+ 90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
+ 100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
+Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms
+
+Performance: 68029.122 tau/day, 157.475 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01
+Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01
+Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56
+Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16
+Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02
+Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16
+Other | | 0.0004218 | | | 0.07
+
+Nlocal: 300 ave 300 max 300 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 374 ave 374 max 374 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2459 ave 2459 max 2459 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16
new file mode 100644
index 0000000000..c9c1e0d155
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16
@@ -0,0 +1,99 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
+ 10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
+ 20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
+ 30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
+ 40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
+ 50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
+ 60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
+ 70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
+ 80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
+ 90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
+ 100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
+Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms
+
+Performance: 183509.107 tau/day, 424.790 timesteps/s
+97.9% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02
+Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31
+Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15
+Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97
+Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16
+Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06
+Other | | 0.0007878 | | | 0.33
+
+Nlocal: 18.75 ave 36 max 6 min
+Histogram: 4 3 1 0 0 1 2 1 2 2
+Nghost: 127 ave 196 max 71 min
+Histogram: 8 0 0 0 0 0 0 1 6 1
+Neighs: 153.688 ave 491 max 10 min
+Histogram: 8 1 1 1 1 1 0 0 0 3
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2
new file mode 100644
index 0000000000..1a9bc77146
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2
@@ -0,0 +1,99 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
+ 10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
+ 20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
+ 30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
+ 40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
+ 50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
+ 60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
+ 70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
+ 80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
+ 90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
+ 100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
+Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms
+
+Performance: 110479.760 tau/day, 255.740 timesteps/s
+99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02
+Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67
+Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50
+Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51
+Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04
+Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13
+Other | | 0.0004461 | | | 0.11
+
+Nlocal: 150 ave 159 max 141 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 392 ave 395 max 389 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 1229.5 ave 1773 max 686 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4
new file mode 100644
index 0000000000..eae3f2b840
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4
@@ -0,0 +1,99 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
+ 10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
+ 20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
+ 30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
+ 40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
+ 50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
+ 60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
+ 70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
+ 80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
+ 90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
+ 100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
+Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms
+
+Performance: 148735.741 tau/day, 344.296 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02
+Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41
+Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37
+Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84
+Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09
+Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11
+Other | | 0.0004706 | | | 0.16
+
+Nlocal: 75 ave 81 max 70 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 282.5 ave 290 max 274 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs: 614.75 ave 981 max 285 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8
new file mode 100644
index 0000000000..feb7e2a5a6
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8
@@ -0,0 +1,99 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+kspace_style scafacos fmm 1.0e-3
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
+ 10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
+ 20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
+ 30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
+ 40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
+ 50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
+ 60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
+ 70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
+ 80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
+ 90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
+ 100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
+Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms
+
+Performance: 147513.337 tau/day, 341.466 timesteps/s
+98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02
+Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25
+Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21
+Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09
+Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11
+Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08
+Other | | 0.0007486 | | | 0.26
+
+Nlocal: 37.5 ave 45 max 31 min
+Histogram: 1 1 1 1 1 0 1 0 1 1
+Nghost: 200 ave 209 max 189 min
+Histogram: 1 0 0 0 1 4 0 0 0 2
+Neighs: 307.375 ave 514 max 115 min
+Histogram: 2 1 0 1 1 0 0 0 1 2
+
+Total # of neighbors = 2459
+Ave neighs/atom = 8.19667
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1
new file mode 100644
index 0000000000..f47f24edee
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
+ 10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
+ 20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
+ 30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
+ 40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
+ 50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
+ 60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
+ 70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
+ 80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
+ 90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
+ 100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
+Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms
+
+Performance: 59891.733 tau/day, 138.638 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01
+Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13
+Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49
+Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14
+Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02
+Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14
+Other | | 0.0004385 | | | 0.06
+
+Nlocal: 300 ave 300 max 300 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 381 ave 381 max 381 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2461 ave 2461 max 2461 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16
new file mode 100644
index 0000000000..d6e7cbea37
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
+ 10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
+ 20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
+ 30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
+ 40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
+ 50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
+ 60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
+ 70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
+ 80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
+ 90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
+ 100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
+Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms
+
+Performance: 272716.448 tau/day, 631.288 timesteps/s
+99.4% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02
+Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74
+Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22
+Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26
+Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21
+Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08
+Other | | 0.0007506 | | | 0.47
+
+Nlocal: 18.75 ave 33 max 6 min
+Histogram: 2 6 0 0 0 0 2 1 2 3
+Nghost: 128.875 ave 198 max 71 min
+Histogram: 7 1 0 0 0 0 0 1 5 2
+Neighs: 153.812 ave 490 max 14 min
+Histogram: 8 0 3 0 1 1 0 0 1 2
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2
new file mode 100644
index 0000000000..fb863797f3
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
+ 10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
+ 20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
+ 30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
+ 40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
+ 50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
+ 60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
+ 70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
+ 80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
+ 90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
+ 100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
+Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms
+
+Performance: 97092.373 tau/day, 224.751 timesteps/s
+100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02
+Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84
+Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44
+Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45
+Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04
+Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11
+Other | | 0.0004425 | | | 0.10
+
+Nlocal: 150 ave 157 max 143 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 399 ave 402 max 396 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 1230.5 ave 1756 max 705 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4
new file mode 100644
index 0000000000..d5a07e0324
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
+ 10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
+ 20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
+ 30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
+ 40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
+ 50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
+ 60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
+ 70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
+ 80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
+ 90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
+ 100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
+Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms
+
+Performance: 153805.254 tau/day, 356.031 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02
+Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56
+Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39
+Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72
+Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07
+Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10
+Other | | 0.0004173 | | | 0.15
+
+Nlocal: 75 ave 81 max 69 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost: 287 ave 296 max 278 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 615.25 ave 964 max 286 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8
new file mode 100644
index 0000000000..a6f9228673
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8
@@ -0,0 +1,92 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+ orthogonal box = (0 0 0) to (10 10 10)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 300 atoms
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 10 10 10
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes
+Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
+ 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
+ 10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
+ 20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
+ 30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
+ 40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
+ 50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
+ 60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
+ 70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
+ 80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
+ 90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
+ 100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
+Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms
+
+Performance: 216363.074 tau/day, 500.840 timesteps/s
+99.4% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02
+Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08
+Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31
+Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12
+Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12
+Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09
+Other | | 0.0005245 | | | 0.26
+
+Nlocal: 37.5 ave 42 max 33 min
+Histogram: 2 1 0 1 0 0 1 0 1 2
+Nghost: 202.25 ave 212 max 194 min
+Histogram: 1 0 2 1 0 2 0 1 0 1
+Neighs: 307.625 ave 505 max 129 min
+Histogram: 3 0 0 1 1 0 0 0 1 2
+
+Total # of neighbors = 2461
+Ave neighs/atom = 8.20333
+Neighbor list builds = 15
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1
new file mode 100644
index 0000000000..13212ede0c
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 1 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000498772 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475938 0 0.50185691 11.99707
+ 10 1.500011 -1.747529 0 0.50193816 11.997158
+ 20 1.5000023 -1.7475152 0 0.50193898 11.997089
+ 30 1.4999308 -1.747404 0 0.50194285 11.996517
+ 40 1.4997722 -1.7471622 0 0.50194686 11.995248
+ 50 1.4995835 -1.746878 0 0.50194808 11.993739
+ 60 1.4996054 -1.7469114 0 0.50194749 11.993914
+ 70 1.5004341 -1.7481558 0 0.50194592 12.000543
+ 80 1.5033218 -1.7524875 0 0.50194458 12.023638
+ 90 1.5108306 -1.7637462 0 0.50194636 12.083694
+ 100 1.5292479 -1.7913449 0 0.50196695 12.230996
+Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms
+
+Performance: 38.530 tau/day, 0.089 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00
+Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00
+Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00
+Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00
+Other | | 0.00418 | | | 0.00
+
+Nlocal: 4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9728 ave 9728 max 9728 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 524288 ave 524288 max 524288 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:18:57
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16
new file mode 100644
index 0000000000..2fc46da3cd
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000462294 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475938 0 0.50185691 -nan
+ 10 1.500011 -1.747529 0 0.50193816 -nan
+ 20 1.5000023 -1.7475152 0 0.50193898 -nan
+ 30 1.4999308 -1.747404 0 0.50194285 -nan
+ 40 1.4997722 -1.7471622 0 0.50194686 -nan
+ 50 1.4995835 -1.746878 0 0.50194808 -nan
+ 60 1.4996054 -1.7469114 0 0.50194749 -nan
+ 70 1.5004341 -1.7481558 0 0.50194592 -nan
+ 80 1.5033218 -1.7524875 0 0.50194458 -nan
+ 90 1.5108306 -1.7637462 0 0.50194636 -nan
+ 100 1.5292479 -1.7913449 0 0.50196695 -nan
+Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 538.132 tau/day, 1.246 timesteps/s
+99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00
+Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01
+Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00
+Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00
+Other | | 0.001511 | | | 0.00
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 2816 ave 2816 max 2816 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 32768 ave 32768 max 32768 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:22
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2
new file mode 100644
index 0000000000..b6bf41de24
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000344753 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475938 0 0.50185691 11.99707
+ 10 1.500011 -1.747529 0 0.50193816 11.997158
+ 20 1.5000023 -1.7475152 0 0.50193898 11.997089
+ 30 1.4999308 -1.747404 0 0.50194285 11.996517
+ 40 1.4997722 -1.7471622 0 0.50194686 11.995248
+ 50 1.4995835 -1.746878 0 0.50194808 11.993739
+ 60 1.4996054 -1.7469114 0 0.50194749 11.993914
+ 70 1.5004341 -1.7481558 0 0.50194592 12.000543
+ 80 1.5033218 -1.7524875 0 0.50194458 12.023638
+ 90 1.5108306 -1.7637462 0 0.50194636 12.083694
+ 100 1.5292479 -1.7913449 0 0.50196695 12.230996
+Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms
+
+Performance: 76.218 tau/day, 0.176 timesteps/s
+100.0% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00
+Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00
+Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00
+Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00
+Other | | 0.002497 | | | 0.00
+
+Nlocal: 2048 ave 2048 max 2048 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 7168 ave 7168 max 7168 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 262144 ave 262144 max 262144 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:09:38
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4
new file mode 100644
index 0000000000..26c1953afa
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000261068 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475938 0 0.50185691 -nan
+ 10 1.500011 -1.747529 0 0.50193816 -nan
+ 20 1.5000023 -1.7475152 0 0.50193898 -nan
+ 30 1.4999308 -1.747404 0 0.50194285 -nan
+ 40 1.4997722 -1.7471622 0 0.50194686 -nan
+ 50 1.4995835 -1.746878 0 0.50194808 -nan
+ 60 1.4996054 -1.7469114 0 0.50194749 -nan
+ 70 1.5004341 -1.7481558 0 0.50194592 -nan
+ 80 1.5033218 -1.7524875 0 0.50194458 -nan
+ 90 1.5108306 -1.7637462 0 0.50194636 -nan
+ 100 1.5292479 -1.7913449 0 0.50196695 -nan
+Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms
+
+Performance: 145.948 tau/day, 0.338 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00
+Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00
+Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00
+Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00
+Other | | 0.001821 | | | 0.00
+
+Nlocal: 1024 ave 1024 max 1024 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5120 ave 5120 max 5120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 131072 ave 131072 max 131072 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:05:02
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8
new file mode 100644
index 0000000000..4a1a5b91ed
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000232935 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos ewald 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver ewald ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475938 0 0.50185691 -nan
+ 10 1.500011 -1.747529 0 0.50193816 -nan
+ 20 1.5000023 -1.7475152 0 0.50193898 -nan
+ 30 1.4999308 -1.747404 0 0.50194285 -nan
+ 40 1.4997722 -1.7471622 0 0.50194686 -nan
+ 50 1.4995835 -1.746878 0 0.50194808 -nan
+ 60 1.4996054 -1.7469114 0 0.50194749 -nan
+ 70 1.5004341 -1.7481558 0 0.50194592 -nan
+ 80 1.5033218 -1.7524875 0 0.50194458 -nan
+ 90 1.5108306 -1.7637462 0 0.50194636 -nan
+ 100 1.5292479 -1.7913449 0 0.50196695 -nan
+Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 279.720 tau/day, 0.647 timesteps/s
+99.9% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00
+Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01
+Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00
+Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00
+Other | | 0.001309 | | | 0.00
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 3584 ave 3584 max 3584 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 65536 ave 65536 max 65536 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:38
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1
new file mode 100644
index 0000000000..598585ae95
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 1 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000518799 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475646 0 0.50188608 10.44368
+ 10 1.5000016 -1.7475671 0 0.50188602 10.44369
+ 20 1.4999827 -1.7475388 0 0.50188592 10.443564
+ 30 1.4999016 -1.7474173 0 0.5018858 10.443023
+ 40 1.4997356 -1.7471685 0 0.50188572 10.441917
+ 50 1.4995414 -1.7468771 0 0.5018858 10.440623
+ 60 1.4995587 -1.7469027 0 0.50188622 10.440739
+ 70 1.5003837 -1.7481389 0 0.50188727 10.446238
+ 80 1.5032684 -1.7524625 0 0.50188958 10.465466
+ 90 1.5107749 -1.763714 0 0.50189507 10.515502
+ 100 1.52919 -1.791306 0 0.50191895 10.638261
+Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms
+
+Performance: 1244.749 tau/day, 2.881 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00
+Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04
+Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00
+Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03
+Other | | 0.004232 | | | 0.01
+
+Nlocal: 4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9728 ave 9728 max 9728 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 524288 ave 524288 max 524288 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16
new file mode 100644
index 0000000000..4bd0c3d4f3
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000400543 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475646 0 0.50188608 10.44368
+ 10 1.5000016 -1.7475671 0 0.50188602 10.44369
+ 20 1.4999827 -1.7475388 0 0.50188592 10.443564
+ 30 1.4999016 -1.7474173 0 0.5018858 10.443023
+ 40 1.4997356 -1.7471685 0 0.50188572 10.441917
+ 50 1.4995414 -1.7468771 0 0.5018858 10.440623
+ 60 1.4995587 -1.7469027 0 0.50188622 10.440739
+ 70 1.5003837 -1.7481389 0 0.50188727 10.446238
+ 80 1.5032684 -1.7524625 0 0.50188958 10.465466
+ 90 1.5107749 -1.763714 0 0.50189507 10.515502
+ 100 1.52919 -1.791306 0 0.50191895 10.638261
+Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 10194.102 tau/day, 23.597 timesteps/s
+99.6% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01
+Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29
+Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01
+Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02
+Other | | 0.002255 | | | 0.05
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 2816 ave 2816 max 2816 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 32768 ave 32768 max 32768 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2
new file mode 100644
index 0000000000..50dcc99393
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.0003407 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475646 0 0.50188608 10.44368
+ 10 1.5000016 -1.7475671 0 0.50188602 10.44369
+ 20 1.4999827 -1.7475388 0 0.50188592 10.443564
+ 30 1.4999016 -1.7474173 0 0.5018858 10.443023
+ 40 1.4997356 -1.7471685 0 0.50188572 10.441917
+ 50 1.4995414 -1.7468771 0 0.5018858 10.440623
+ 60 1.4995587 -1.7469027 0 0.50188622 10.440739
+ 70 1.5003837 -1.7481389 0 0.50188727 10.446238
+ 80 1.5032684 -1.7524625 0 0.50188958 10.465466
+ 90 1.5107749 -1.763714 0 0.50189507 10.515502
+ 100 1.52919 -1.791306 0 0.50191895 10.638261
+Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms
+
+Performance: 2408.014 tau/day, 5.574 timesteps/s
+99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01
+Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10
+Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00
+Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03
+Other | | 0.002716 | | | 0.02
+
+Nlocal: 2048 ave 2048 max 2048 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 7168 ave 7168 max 7168 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 262144 ave 262144 max 262144 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:19
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4
new file mode 100644
index 0000000000..27fdfcedcb
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000270367 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475646 0 0.50188608 10.44368
+ 10 1.5000016 -1.7475671 0 0.50188602 10.44369
+ 20 1.4999827 -1.7475388 0 0.50188592 10.443564
+ 30 1.4999016 -1.7474173 0 0.5018858 10.443023
+ 40 1.4997356 -1.7471685 0 0.50188572 10.441917
+ 50 1.4995414 -1.7468771 0 0.5018858 10.440623
+ 60 1.4995587 -1.7469027 0 0.50188622 10.440739
+ 70 1.5003837 -1.7481389 0 0.50188727 10.446238
+ 80 1.5032684 -1.7524625 0 0.50188958 10.465466
+ 90 1.5107749 -1.763714 0 0.50189507 10.515502
+ 100 1.52919 -1.791306 0 0.50191895 10.638261
+Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms
+
+Performance: 4286.533 tau/day, 9.923 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01
+Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15
+Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00
+Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03
+Other | | 0.002214 | | | 0.02
+
+Nlocal: 1024 ave 1024 max 1024 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5120 ave 5120 max 5120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 131072 ave 131072 max 131072 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:11
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8
new file mode 100644
index 0000000000..02a5528c59
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000236988 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7475646 0 0.50188608 10.44368
+ 10 1.5000016 -1.7475671 0 0.50188602 10.44369
+ 20 1.4999827 -1.7475388 0 0.50188592 10.443564
+ 30 1.4999016 -1.7474173 0 0.5018858 10.443023
+ 40 1.4997356 -1.7471685 0 0.50188572 10.441917
+ 50 1.4995414 -1.7468771 0 0.5018858 10.440623
+ 60 1.4995587 -1.7469027 0 0.50188622 10.440739
+ 70 1.5003837 -1.7481389 0 0.50188727 10.446238
+ 80 1.5032684 -1.7524625 0 0.50188958 10.465466
+ 90 1.5107749 -1.763714 0 0.50189507 10.515502
+ 100 1.52919 -1.791306 0 0.50191895 10.638261
+Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 7247.876 tau/day, 16.777 timesteps/s
+99.8% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01
+Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25
+Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01
+Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03
+Other | | 0.001971 | | | 0.03
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 3584 ave 3584 max 3584 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 65536 ave 65536 max 65536 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:07
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1
new file mode 100644
index 0000000000..1876a0e52b
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 1 MPI processor grid
+ 4096 atoms
+ Time spent = 0.00049448 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7477245 0 0.50172614 10.443537
+ 10 1.5000176 -1.7475898 0 0.50188725 10.443798
+ 20 1.5000161 -1.7475262 0 0.50194874 10.443843
+ 30 1.4999486 -1.7474019 0 0.50197176 10.443413
+ 40 1.4997889 -1.7471525 0 0.50198161 10.442357
+ 50 1.4995945 -1.7468614 0 0.50198122 10.441061
+ 60 1.499609 -1.7468813 0 0.50198309 10.44116
+ 70 1.5004314 -1.7481179 0 0.50197962 10.446638
+ 80 1.5033149 -1.7524495 0 0.50197233 10.46585
+ 90 1.5108219 -1.7637095 0 0.50197005 10.515883
+ 100 1.529239 -1.7913105 0 0.501988 10.638649
+Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms
+
+Performance: 2385.257 tau/day, 5.521 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01
+Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08
+Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00
+Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06
+Other | | 0.004455 | | | 0.02
+
+Nlocal: 4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9728 ave 9728 max 9728 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 524288 ave 524288 max 524288 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:21
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16
new file mode 100644
index 0000000000..6e6e8f6e94
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 4 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 4 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000361443 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7477245 0 0.50172614 10.443537
+ 10 1.5000176 -1.7475898 0 0.50188725 10.443798
+ 20 1.5000161 -1.7475262 0 0.50194874 10.443843
+ 30 1.4999486 -1.7474019 0 0.50197176 10.443413
+ 40 1.4997889 -1.7471525 0 0.50198161 10.442357
+ 50 1.4995945 -1.7468614 0 0.50198122 10.441061
+ 60 1.499609 -1.7468813 0 0.50198309 10.44116
+ 70 1.5004314 -1.7481179 0 0.50197962 10.446638
+ 80 1.5033149 -1.7524495 0 0.50197233 10.46585
+ 90 1.5108219 -1.7637095 0 0.50197005 10.515883
+ 100 1.529239 -1.7913105 0 0.501988 10.638649
+Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms
+
+Performance: 27571.239 tau/day, 63.822 timesteps/s
+99.8% CPU use with 16 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03
+Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65
+Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02
+Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06
+Other | | 0.001859 | | | 0.12
+
+Nlocal: 256 ave 256 max 256 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Nghost: 2816 ave 2816 max 2816 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+Neighs: 32768 ave 32768 max 32768 min
+Histogram: 16 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2
new file mode 100644
index 0000000000..72a53c48ff
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 1 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.0003438 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7477245 0 0.50172614 10.443537
+ 10 1.5000176 -1.7475898 0 0.50188725 10.443798
+ 20 1.5000161 -1.7475262 0 0.50194874 10.443843
+ 30 1.4999486 -1.7474019 0 0.50197176 10.443413
+ 40 1.4997889 -1.7471525 0 0.50198161 10.442357
+ 50 1.4995945 -1.7468614 0 0.50198122 10.441061
+ 60 1.499609 -1.7468813 0 0.50198309 10.44116
+ 70 1.5004314 -1.7481179 0 0.50197962 10.446638
+ 80 1.5033149 -1.7524495 0 0.50197233 10.46585
+ 90 1.5108219 -1.7637095 0 0.50197005 10.515883
+ 100 1.529239 -1.7913105 0 0.501988 10.638649
+Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms
+
+Performance: 4600.920 tau/day, 10.650 timesteps/s
+99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01
+Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21
+Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00
+Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06
+Other | | 0.002495 | | | 0.03
+
+Nlocal: 2048 ave 2048 max 2048 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 7168 ave 7168 max 7168 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 262144 ave 262144 max 262144 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:11
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4
new file mode 100644
index 0000000000..bf4494df8b
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 1 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000260592 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7477245 0 0.50172614 10.443537
+ 10 1.5000176 -1.7475898 0 0.50188725 10.443798
+ 20 1.5000161 -1.7475262 0 0.50194874 10.443843
+ 30 1.4999486 -1.7474019 0 0.50197176 10.443413
+ 40 1.4997889 -1.7471525 0 0.50198161 10.442357
+ 50 1.4995945 -1.7468614 0 0.50198122 10.441061
+ 60 1.499609 -1.7468813 0 0.50198309 10.44116
+ 70 1.5004314 -1.7481179 0 0.50197962 10.446638
+ 80 1.5033149 -1.7524495 0 0.50197233 10.46585
+ 90 1.5108219 -1.7637095 0 0.50197005 10.515883
+ 100 1.529239 -1.7913105 0 0.501988 10.638649
+Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms
+
+Performance: 8470.643 tau/day, 19.608 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01
+Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28
+Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01
+Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06
+Other | | 0.002036 | | | 0.04
+
+Nlocal: 1024 ave 1024 max 1024 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5120 ave 5120 max 5120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 131072 ave 131072 max 131072 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8
new file mode 100644
index 0000000000..b5e889dfc1
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8
@@ -0,0 +1,102 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+ orthogonal box = (0 0 0) to (1 1 1)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+replicate 8 8 8
+ orthogonal box = (0 0 0) to (8 8 8)
+ 2 by 2 by 2 MPI processor grid
+ 4096 atoms
+ Time spent = 0.000324488 secs
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 8 8 8
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -1.7477245 0 0.50172614 10.443537
+ 10 1.5000176 -1.7475898 0 0.50188725 10.443798
+ 20 1.5000161 -1.7475262 0 0.50194874 10.443843
+ 30 1.4999486 -1.7474019 0 0.50197176 10.443413
+ 40 1.4997889 -1.7471525 0 0.50198161 10.442357
+ 50 1.4995945 -1.7468614 0 0.50198122 10.441061
+ 60 1.499609 -1.7468813 0 0.50198309 10.44116
+ 70 1.5004314 -1.7481179 0 0.50197962 10.446638
+ 80 1.5033149 -1.7524495 0 0.50197233 10.46585
+ 90 1.5108219 -1.7637095 0 0.50197005 10.515883
+ 100 1.529239 -1.7913105 0 0.501988 10.638649
+Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms
+
+Performance: 14973.700 tau/day, 34.661 timesteps/s
+99.6% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02
+Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51
+Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01
+Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06
+Other | | 0.001645 | | | 0.06
+
+Nlocal: 512 ave 512 max 512 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Nghost: 3584 ave 3584 max 3584 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+Neighs: 65536 ave 65536 max 65536 min
+Histogram: 8 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 524288
+Ave neighs/atom = 128
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:03
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1
new file mode 100644
index 0000000000..b0a47e4f98
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1
@@ -0,0 +1,105 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777512 0 272.51604 0.17462195
+ 5 286.36222 -4.382053 0 424.73173 0.26918926
+ 6 481.42206 -4.3095567 0 717.1014 0.45274088
+ 7 488.59167 -3.8685194 0 728.2861 0.45956866
+ 8 497.85287 -3.0417966 0 742.99073 0.46838116
+ 9 499.61615 -3.419003 0 745.2558 0.46983345
+ 10 502.63684 -2.8360961 0 750.36521 0.47280809
+ 11 504.4846 -2.7628105 0 753.20736 0.47462793
+ 12 506.54485 -2.8460356 0 756.21142 0.47651441
+ 13 508.27211 -2.730935 0 758.91482 0.47813752
+ 14 510.57045 -2.6094877 0 762.48033 0.48031431
+ 15 513.14798 -2.7150827 0 766.23717 0.48275229
+ 16 515.78124 -2.3961811 0 770.50201 0.48526333
+ 17 515.70265 -2.2982683 0 770.48215 0.48526617
+ 18 515.7081 -2.1515983 0 770.63699 0.48530393
+ 19 515.74906 -2.0581436 0 770.79182 0.48530977
+ 20 515.70883 -1.8922577 0 770.89742 0.48527105
+Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 18547.165 tau/day, 42.933 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05
+Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08
+Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59
+Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03
+Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06
+Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12
+Other | | 0.0003715 | | | 0.08
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 247817 ave 247817 max 247817 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2
new file mode 100644
index 0000000000..1ffab0ca6a
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2
@@ -0,0 +1,105 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777512 0 272.51604 0.17462195
+ 5 286.36222 -4.382053 0 424.73173 0.26918926
+ 6 481.42206 -4.3095567 0 717.1014 0.45274088
+ 7 488.59167 -3.8685194 0 728.2861 0.45956866
+ 8 497.85287 -3.0417966 0 742.99073 0.46838116
+ 9 499.61615 -3.419003 0 745.2558 0.46983345
+ 10 502.63684 -2.8360961 0 750.36521 0.47280809
+ 11 504.4846 -2.7628105 0 753.20736 0.47462793
+ 12 506.54485 -2.8460356 0 756.21142 0.47651441
+ 13 508.27211 -2.730935 0 758.91482 0.47813752
+ 14 510.57045 -2.6094877 0 762.48033 0.48031431
+ 15 513.14798 -2.7150827 0 766.23717 0.48275229
+ 16 515.78124 -2.3961811 0 770.50201 0.48526333
+ 17 515.70265 -2.2982683 0 770.48215 0.48526617
+ 18 515.7081 -2.1515983 0 770.63699 0.48530393
+ 19 515.74906 -2.0581436 0 770.79182 0.48530977
+ 20 515.70883 -1.8922577 0 770.89742 0.48527105
+Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 30421.778 tau/day, 70.421 timesteps/s
+99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08
+Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19
+Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84
+Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58
+Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11
+Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10
+Other | | 0.0002506 | | | 0.09
+
+Nlocal: 500 ave 516 max 484 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 456.5 ave 475 max 438 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 123908 ave 172139 max 75678 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4
new file mode 100644
index 0000000000..1235c0a3cd
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4
@@ -0,0 +1,105 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777512 0 272.51604 0.17462195
+ 5 286.36222 -4.382053 0 424.73173 0.26918926
+ 6 481.42206 -4.3095567 0 717.1014 0.45274088
+ 7 488.59167 -3.8685194 0 728.2861 0.45956866
+ 8 497.85287 -3.0417966 0 742.99073 0.46838116
+ 9 499.61615 -3.419003 0 745.2558 0.46983345
+ 10 502.63684 -2.8360961 0 750.36521 0.47280809
+ 11 504.4846 -2.7628105 0 753.20736 0.47462793
+ 12 506.54485 -2.8460356 0 756.21142 0.47651441
+ 13 508.27211 -2.730935 0 758.91482 0.47813752
+ 14 510.57045 -2.6094877 0 762.48033 0.48031431
+ 15 513.14798 -2.7150827 0 766.23717 0.48275229
+ 16 515.78124 -2.3961811 0 770.50201 0.48526333
+ 17 515.70265 -2.2982683 0 770.48215 0.48526617
+ 18 515.7081 -2.1515983 0 770.63699 0.48530393
+ 19 515.74906 -2.0581436 0 770.79182 0.48530977
+ 20 515.70883 -1.8922577 0 770.89742 0.48527105
+Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 53553.228 tau/day, 123.966 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14
+Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19
+Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62
+Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60
+Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24
+Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10
+Other | | 0.0001805 | | | 0.11
+
+Nlocal: 250 ave 259 max 238 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 672.25 ave 683 max 663 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 61954.2 ave 97157 max 25016 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8
new file mode 100644
index 0000000000..e72ade73b5
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8
@@ -0,0 +1,105 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos direct 0.001
+
+timestep 0.005
+thermo 1
+run 20
+Setting up ScaFaCoS with solver direct ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777512 0 272.51604 0.17462195
+ 5 286.36222 -4.382053 0 424.73173 0.26918926
+ 6 481.42206 -4.3095567 0 717.1014 0.45274088
+ 7 488.59167 -3.8685194 0 728.2861 0.45956866
+ 8 497.85287 -3.0417966 0 742.99073 0.46838116
+ 9 499.61615 -3.419003 0 745.2558 0.46983345
+ 10 502.63684 -2.8360961 0 750.36521 0.47280809
+ 11 504.4846 -2.7628105 0 753.20736 0.47462793
+ 12 506.54485 -2.8460356 0 756.21142 0.47651441
+ 13 508.27211 -2.730935 0 758.91482 0.47813752
+ 14 510.57045 -2.6094877 0 762.48033 0.48031431
+ 15 513.14798 -2.7150827 0 766.23717 0.48275229
+ 16 515.78124 -2.3961811 0 770.50201 0.48526333
+ 17 515.70265 -2.2982683 0 770.48215 0.48526617
+ 18 515.7081 -2.1515983 0 770.63699 0.48530393
+ 19 515.74906 -2.0581436 0 770.79182 0.48530977
+ 20 515.70883 -1.8922577 0 770.89742 0.48527105
+Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 97743.448 tau/day, 226.258 timesteps/s
+99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27
+Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44
+Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15
+Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37
+Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50
+Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10
+Other | | 0.0001439 | | | 0.16
+
+Nlocal: 125 ave 133 max 113 min
+Histogram: 2 0 0 0 0 1 1 0 2 2
+Nghost: 773.625 ave 788 max 764 min
+Histogram: 1 1 2 1 1 0 0 0 1 1
+Neighs: 30977.1 ave 50690 max 10447 min
+Histogram: 1 1 1 0 1 1 0 0 2 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1
new file mode 100644
index 0000000000..4bef247e26
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1
@@ -0,0 +1,109 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.0015676581
+ 1 18.780412 -10.770009 0 17.372438 0.016719188
+ 2 65.294131 -11.084501 0 86.758754 0.06035827
+ 3 121.92555 -7.0612033 0 175.64423 0.1140457
+ 4 185.71165 -5.8781334 0 272.41077 0.17455524
+ 5 286.28339 -4.3800108 0 424.61565 0.26911306
+ 6 481.28097 -4.3052012 0 716.89433 0.45262045
+ 7 487.26022 -3.8672741 0 726.29216 0.45830216
+ 8 493.65478 -3.0242687 0 736.71742 0.46443761
+ 9 495.66203 -3.4336343 0 739.31592 0.46613014
+ 10 498.41831 -2.8837072 0 743.99613 0.46887706
+ 11 499.20944 -2.7724783 0 745.29287 0.46966875
+ 12 500.97345 -2.8281484 0 747.88057 0.47126462
+ 13 507.46412 -2.7752775 0 757.65971 0.47728761
+ 14 525.35729 -2.5749814 0 784.67292 0.49422171
+ 15 563.9578 -2.9982381 0 842.09253 0.53043696
+ 16 645.47602 -2.5519203 0 964.69389 0.60730795
+ 17 647.09276 -2.2568468 0 967.41166 0.60891914
+ 18 647.12596 -2.2791003 0 967.43915 0.60900309
+ 19 647.24862 -2.2495226 0 967.65253 0.60908339
+ 20 647.51175 -2.0239179 0 968.27244 0.60932598
+Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 10836.721 tau/day, 25.085 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03
+Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83
+Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95
+Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03
+Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05
+Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07
+Other | | 0.0003934 | | | 0.05
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 244342 ave 244342 max 244342 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2
new file mode 100644
index 0000000000..e8e614004d
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2
@@ -0,0 +1,109 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.0015676581
+ 1 18.780412 -10.770009 0 17.372438 0.016719188
+ 2 65.294131 -11.084501 0 86.758754 0.06035827
+ 3 121.92555 -7.0612033 0 175.64423 0.1140457
+ 4 185.71165 -5.8781334 0 272.41077 0.17455524
+ 5 286.28339 -4.3800108 0 424.61565 0.26911306
+ 6 481.28097 -4.3052012 0 716.89433 0.45262045
+ 7 487.26022 -3.8672741 0 726.29216 0.45830216
+ 8 493.65478 -3.0242687 0 736.71742 0.46443761
+ 9 495.66203 -3.4336343 0 739.31592 0.46613014
+ 10 498.41831 -2.8837072 0 743.99613 0.46887706
+ 11 499.20944 -2.7724783 0 745.29287 0.46966875
+ 12 500.97345 -2.8281484 0 747.88057 0.47126462
+ 13 507.46412 -2.7752775 0 757.65971 0.47728761
+ 14 525.35729 -2.5749814 0 784.67292 0.49422171
+ 15 563.9578 -2.9982381 0 842.09253 0.53043696
+ 16 645.47602 -2.5519203 0 964.69389 0.60730795
+ 17 647.09276 -2.2568468 0 967.41166 0.60891914
+ 18 647.12596 -2.2791003 0 967.43915 0.60900309
+ 19 647.24862 -2.2495226 0 967.65253 0.60908339
+ 20 647.51175 -2.0239179 0 968.27244 0.60932598
+Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 12321.981 tau/day, 28.523 timesteps/s
+99.7% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03
+Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00
+Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55
+Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27
+Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06
+Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05
+Other | | 0.0002786 | | | 0.04
+
+Nlocal: 500 ave 509 max 491 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 455.5 ave 467 max 444 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 122171 ave 171834 max 72508 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4
new file mode 100644
index 0000000000..e3f5bf44c9
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4
@@ -0,0 +1,109 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.0015676581
+ 1 18.780412 -10.770009 0 17.372438 0.016719188
+ 2 65.294131 -11.084501 0 86.758754 0.06035827
+ 3 121.92555 -7.0612033 0 175.64423 0.1140457
+ 4 185.71165 -5.8781334 0 272.41077 0.17455524
+ 5 286.28339 -4.3800108 0 424.61565 0.26911306
+ 6 481.28097 -4.3052012 0 716.89433 0.45262045
+ 7 487.26022 -3.8672741 0 726.29216 0.45830216
+ 8 493.65478 -3.0242687 0 736.71742 0.46443761
+ 9 495.66203 -3.4336343 0 739.31592 0.46613014
+ 10 498.41831 -2.8837072 0 743.99613 0.46887706
+ 11 499.20944 -2.7724783 0 745.29287 0.46966875
+ 12 500.97345 -2.8281484 0 747.88057 0.47126462
+ 13 507.46412 -2.7752775 0 757.65971 0.47728761
+ 14 525.35729 -2.5749814 0 784.67292 0.49422171
+ 15 563.9578 -2.9982381 0 842.09253 0.53043696
+ 16 645.47602 -2.5519203 0 964.69389 0.60730795
+ 17 647.09276 -2.2568468 0 967.41166 0.60891914
+ 18 647.12596 -2.2791003 0 967.43915 0.60900309
+ 19 647.24862 -2.2495226 0 967.65253 0.60908339
+ 20 647.51175 -2.0239179 0 968.27244 0.60932598
+Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 12955.555 tau/day, 29.990 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04
+Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38
+Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00
+Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43
+Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08
+Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03
+Other | | 0.0002366 | | | 0.04
+
+Nlocal: 250 ave 259 max 240 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 668.75 ave 679 max 657 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs: 61085.5 ave 95363 max 24964 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8
new file mode 100644
index 0000000000..22d1140813
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8
@@ -0,0 +1,109 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos fmm 0.001
+kspace_modify scafacos tolerance energy_rel
+kspace_modify scafacos fmm_tuning 1
+ScaFaCoS setting fmm inhomogen tuning ...
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver fmm ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417141 0 1.6235786 0.0015676581
+ 1 18.780412 -10.770009 0 17.372438 0.016719188
+ 2 65.294131 -11.084501 0 86.758754 0.06035827
+ 3 121.92555 -7.0612033 0 175.64423 0.1140457
+ 4 185.71165 -5.8781334 0 272.41077 0.17455524
+ 5 286.28339 -4.3800108 0 424.61565 0.26911306
+ 6 481.28097 -4.3052012 0 716.89433 0.45262045
+ 7 487.26022 -3.8672741 0 726.29216 0.45830216
+ 8 493.65478 -3.0242687 0 736.71742 0.46443761
+ 9 495.66203 -3.4336343 0 739.31592 0.46613014
+ 10 498.41831 -2.8837072 0 743.99613 0.46887706
+ 11 499.20944 -2.7724783 0 745.29287 0.46966875
+ 12 500.97345 -2.8281484 0 747.88057 0.47126462
+ 13 507.46412 -2.7752775 0 757.65971 0.47728761
+ 14 525.35729 -2.5749814 0 784.67292 0.49422171
+ 15 563.9578 -2.9982381 0 842.09253 0.53043696
+ 16 645.47602 -2.5519203 0 964.69389 0.60730795
+ 17 647.09276 -2.2568468 0 967.41166 0.60891914
+ 18 647.12596 -2.2791003 0 967.43915 0.60900309
+ 19 647.24862 -2.2495226 0 967.65253 0.60908339
+ 20 647.51175 -2.0239179 0 968.27244 0.60932598
+Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 15174.000 tau/day, 35.125 timesteps/s
+99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04
+Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66
+Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57
+Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55
+Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12
+Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02
+Other | | 0.0002268 | | | 0.04
+
+Nlocal: 125 ave 137 max 111 min
+Histogram: 1 1 0 0 0 2 2 1 0 1
+Nghost: 768.875 ave 788 max 761 min
+Histogram: 4 0 2 0 0 0 1 0 0 1
+Neighs: 30542.8 ave 48077 max 10011 min
+Histogram: 1 1 1 0 1 1 0 0 0 3
+
+Total # of neighbors = 244342
+Ave neighs/atom = 244.342
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1
new file mode 100644
index 0000000000..f8a85c6c6b
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1
@@ -0,0 +1,107 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777511 0 272.51603 0.17462194
+ 5 286.36221 -4.3820531 0 424.73172 0.26918925
+ 6 481.42203 -4.3095567 0 717.10136 0.45274086
+ 7 488.59165 -3.8685193 0 728.28607 0.45956865
+ 8 497.85288 -3.0417938 0 742.99075 0.46838117
+ 9 499.61619 -3.4190063 0 745.25585 0.46983349
+ 10 502.63691 -2.8360951 0 750.36531 0.47280815
+ 11 504.4847 -2.7628089 0 753.20751 0.47462802
+ 12 506.54494 -2.8460319 0 756.21157 0.4765145
+ 13 508.2722 -2.7309328 0 758.91497 0.47813761
+ 14 510.57053 -2.6094792 0 762.48045 0.48031438
+ 15 513.14804 -2.7150819 0 766.23726 0.48275234
+ 16 515.78127 -2.3961749 0 770.50206 0.48526336
+ 17 515.70267 -2.2982581 0 770.48219 0.48526619
+ 18 515.70813 -2.1516075 0 770.63702 0.48530395
+ 19 515.74908 -2.0581483 0 770.79185 0.48530979
+ 20 515.70881 -1.892235 0 770.89742 0.48527104
+Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms
+
+Performance: 8150.306 tau/day, 18.866 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02
+Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42
+Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43
+Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01
+Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03
+Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05
+Other | | 0.0003803 | | | 0.04
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 247817 ave 247817 max 247817 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:01
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2
new file mode 100644
index 0000000000..bd7e7fee1f
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2
@@ -0,0 +1,107 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777511 0 272.51603 0.17462194
+ 5 286.36221 -4.3820531 0 424.73172 0.26918925
+ 6 481.42203 -4.3095567 0 717.10136 0.45274086
+ 7 488.59165 -3.8685193 0 728.28607 0.45956865
+ 8 497.85288 -3.0417938 0 742.99075 0.46838117
+ 9 499.61619 -3.4190063 0 745.25585 0.46983349
+ 10 502.63691 -2.8360951 0 750.36531 0.47280815
+ 11 504.4847 -2.7628089 0 753.20751 0.47462802
+ 12 506.54494 -2.8460319 0 756.21157 0.4765145
+ 13 508.2722 -2.7309328 0 758.91497 0.47813761
+ 14 510.57053 -2.6094792 0 762.48045 0.48031438
+ 15 513.14804 -2.7150819 0 766.23726 0.48275234
+ 16 515.78127 -2.3961749 0 770.50206 0.48526336
+ 17 515.70267 -2.2982581 0 770.48219 0.48526619
+ 18 515.70813 -2.1516075 0 770.63702 0.48530395
+ 19 515.74908 -2.0581483 0 770.79185 0.48530979
+ 20 515.70881 -1.892235 0 770.89742 0.48527104
+Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms
+
+Performance: 12320.557 tau/day, 28.520 timesteps/s
+99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03
+Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95
+Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64
+Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24
+Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06
+Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04
+Other | | 0.000288 | | | 0.04
+
+Nlocal: 500 ave 516 max 484 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 456.5 ave 475 max 438 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs: 123908 ave 172139 max 75678 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4
new file mode 100644
index 0000000000..8a7e591f9a
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4
@@ -0,0 +1,107 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777511 0 272.51603 0.17462194
+ 5 286.36221 -4.3820531 0 424.73172 0.26918925
+ 6 481.42203 -4.3095567 0 717.10136 0.45274086
+ 7 488.59165 -3.8685193 0 728.28607 0.45956865
+ 8 497.85288 -3.0417938 0 742.99075 0.46838117
+ 9 499.61619 -3.4190063 0 745.25585 0.46983349
+ 10 502.63691 -2.8360951 0 750.36531 0.47280815
+ 11 504.4847 -2.7628089 0 753.20751 0.47462802
+ 12 506.54494 -2.8460319 0 756.21157 0.4765145
+ 13 508.2722 -2.7309328 0 758.91497 0.47813761
+ 14 510.57053 -2.6094792 0 762.48045 0.48031438
+ 15 513.14804 -2.7150819 0 766.23726 0.48275234
+ 16 515.78127 -2.3961749 0 770.50206 0.48526336
+ 17 515.70267 -2.2982581 0 770.48219 0.48526619
+ 18 515.70813 -2.1516075 0 770.63702 0.48530395
+ 19 515.74908 -2.0581483 0 770.79185 0.48530979
+ 20 515.70881 -1.892235 0 770.89742 0.48527104
+Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms
+
+Performance: 20210.785 tau/day, 46.784 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05
+Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85
+Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31
+Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60
+Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10
+Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04
+Other | | 0.0002093 | | | 0.05
+
+Nlocal: 250 ave 259 max 238 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Nghost: 672.25 ave 683 max 663 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 61954.2 ave 97157 max 25016 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8
new file mode 100644
index 0000000000..13922c09ac
--- /dev/null
+++ b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8
@@ -0,0 +1,107 @@
+LAMMPS (2 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.hammersley_shphere
+ orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5)
+ 2 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1000 atoms
+change_box all boundary f f f
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p2nfft 0.001
+kspace_modify scafacos tolerance potential
+
+timestep 0.005
+thermo 1
+
+run 20
+Setting up ScaFaCoS with solver p2nfft ...
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2
+ ghost atom cutoff = 2
+ binsize = 1, bins = 102 102 102
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair zero, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.5 -0.62417787 0 1.6235721 0.0015678854
+ 1 18.780041 -10.770002 0 17.371889 0.016718957
+ 2 65.289192 -11.084705 0 86.751149 0.060353634
+ 3 121.92987 -7.0625759 0 175.64933 0.11404974
+ 4 185.78164 -5.8777511 0 272.51603 0.17462194
+ 5 286.36221 -4.3820531 0 424.73172 0.26918925
+ 6 481.42203 -4.3095567 0 717.10136 0.45274086
+ 7 488.59165 -3.8685193 0 728.28607 0.45956865
+ 8 497.85288 -3.0417938 0 742.99075 0.46838117
+ 9 499.61619 -3.4190063 0 745.25585 0.46983349
+ 10 502.63691 -2.8360951 0 750.36531 0.47280815
+ 11 504.4847 -2.7628089 0 753.20751 0.47462802
+ 12 506.54494 -2.8460319 0 756.21157 0.4765145
+ 13 508.2722 -2.7309328 0 758.91497 0.47813761
+ 14 510.57053 -2.6094792 0 762.48045 0.48031438
+ 15 513.14804 -2.7150819 0 766.23726 0.48275234
+ 16 515.78127 -2.3961749 0 770.50206 0.48526336
+ 17 515.70267 -2.2982581 0 770.48219 0.48526619
+ 18 515.70813 -2.1516075 0 770.63702 0.48530395
+ 19 515.74908 -2.0581483 0 770.79185 0.48530979
+ 20 515.70881 -1.892235 0 770.89742 0.48527104
+Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms
+
+Performance: 35681.038 tau/day, 82.595 timesteps/s
+99.2% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10
+Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48
+Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81
+Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29
+Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20
+Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04
+Other | | 0.0001938 | | | 0.08
+
+Nlocal: 125 ave 133 max 113 min
+Histogram: 2 0 0 0 0 1 1 0 2 2
+Nghost: 773.625 ave 788 max 764 min
+Histogram: 1 1 2 1 1 0 0 0 1 1
+Neighs: 30977.1 ave 50690 max 10447 min
+Histogram: 1 1 1 0 1 1 0 0 2 1
+
+Total # of neighbors = 247817
+Ave neighs/atom = 247.817
+Neighbor list builds = 19
+Dangerous builds = 18
+Total wall time: 0:00:00
--
GitLab
From e08aaa7e397987c370a836723126aca66db05932 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 8 Aug 2018 15:03:47 -0600
Subject: [PATCH 083/332] added examples for P3M with ScaFaCoS
---
examples/USER/scafacos/in.scafacos.cw.p3m | 31 +++++++++++++++++++
examples/USER/scafacos/in.scafacos.p3m | 37 +++++++++++++++++++++++
2 files changed, 68 insertions(+)
create mode 100644 examples/USER/scafacos/in.scafacos.cw.p3m
create mode 100644 examples/USER/scafacos/in.scafacos.p3m
diff --git a/examples/USER/scafacos/in.scafacos.cw.p3m b/examples/USER/scafacos/in.scafacos.cw.p3m
new file mode 100644
index 0000000000..50ff1a64a8
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.cw.p3m
@@ -0,0 +1,31 @@
+
+units lj
+atom_style charge
+
+read_data data.cloud_wall
+
+velocity all set 0.0 0.0 0.0 mom no
+
+pair_style zero 1.0
+pair_coeff * *
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+kspace_style scafacos p3m 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+
+thermo_style custom step atoms cpu temp pe ke etotal ecoul press
+
+run_style verlet
+
+#dump simple all custom 1000 id x y z vx vy vz
+#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
+#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
+#dump_modify dmpvtk pad 7
+
+thermo 10
+run 100
diff --git a/examples/USER/scafacos/in.scafacos.p3m b/examples/USER/scafacos/in.scafacos.p3m
new file mode 100644
index 0000000000..874b1d151a
--- /dev/null
+++ b/examples/USER/scafacos/in.scafacos.p3m
@@ -0,0 +1,37 @@
+# Point dipoles in a 2d box
+
+units lj
+atom_style charge
+
+read_data data.NaCl
+
+replicate 8 8 8
+
+velocity all create 1.5 49893
+
+neighbor 1.0 bin
+neigh_modify delay 0
+
+fix 1 all nve
+
+# LAMMPS computes pairwise and long-range Coulombics
+
+#pair_style coul/long 3.0
+#pair_coeff * *
+#kspace_style pppm 1.0e-3
+
+# Scafacos computes entire long-range Coulombics
+# use dummy pair style to perform atom sorting
+
+pair_style zero 1.0
+pair_coeff * *
+
+#fix 2 all scafacos p3m tolerance field 0.001
+
+kspace_style scafacos p3m 0.001
+kspace_modify scafacos tolerance field
+
+timestep 0.005
+thermo 10
+
+run 100
--
GitLab
From 120fdbb9fc94dc049d94488a771b3c19e1f56208 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 10:53:22 -0600
Subject: [PATCH 084/332] Add data duplication to pair_eam_kokkos
---
src/KOKKOS/pair_eam_kokkos.cpp | 87 ++++++++++++++++++++++------------
src/KOKKOS/pair_eam_kokkos.h | 10 ++++
2 files changed, 66 insertions(+), 31 deletions(-)
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 1bfb8255dc..256cb8d55b 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -117,6 +117,19 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_rho);
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_rho);
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
// zero out density
@@ -228,6 +241,9 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
@@ -241,11 +257,15 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -503,8 +523,9 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
// rho = density at each atom
// loop over neighbors of my atoms
- // The rho array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > rho = v_rho;
+ // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto v_rho = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho);
+ auto a_rho = v_rho.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -538,13 +559,13 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
if (NEWTON_PAIR || j < nlocal) {
const int d_type2rhor_ij = d_type2rhor(itype,jtype);
- rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
- d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
+ a_rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
+ d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
}
}
}
- rho[i] += rhotmp;
+ a_rho[i] += rhotmp;
}
/* ---------------------------------------------------------------------- */
@@ -670,8 +691,9 @@ template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -778,18 +800,21 @@ void PairEAMKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &
const int EFLAG = eflag;
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (EFLAG) {
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
if (NEIGHFLAG!=FULL) {
- if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf;
- if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf;
+ if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf;
+ if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf;
} else {
- v_eatom[i] += epairhalf;
+ a_eatom[i] += epairhalf;
}
}
}
@@ -833,28 +858,28 @@ void PairEAMKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &
if (vflag_atom) {
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
} else {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
}
}
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index c821750da5..6523e3fe72 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -126,6 +126,16 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
--
GitLab
From d9fb37e25ea1586f3e069c712ec77db45d83fb1a Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:30:03 -0600
Subject: [PATCH 085/332] Add data duplication to pair_tersoff_kokkos and
variants
---
src/KOKKOS/pair_tersoff_kokkos.cpp | 79 +++++++++++++++++---------
src/KOKKOS/pair_tersoff_kokkos.h | 8 +++
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 79 +++++++++++++++++---------
src/KOKKOS/pair_tersoff_mod_kokkos.h | 8 +++
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 79 +++++++++++++++++---------
src/KOKKOS/pair_tersoff_zbl_kokkos.h | 8 +++
6 files changed, 180 insertions(+), 81 deletions(-)
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index cb4def2d37..7b21bf5793 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -200,6 +200,17 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
EV_FLOAT ev;
@@ -243,6 +254,9 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all += ev;
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev_all.evdwl;
if (vflag_global) {
virial[0] += ev_all.v[0];
@@ -254,11 +268,15 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -304,8 +322,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (i >= nlocal) return;
@@ -1117,14 +1137,18 @@ void PairTersoffKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const i
{
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
- v_eatom[i] += epairhalf;
- if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf;
+ a_eatom[i] += epairhalf;
+ if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf;
}
if (VFLAG) {
@@ -1154,20 +1178,20 @@ void PairTersoffKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const i
}
if (vflag_atom) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
}
@@ -1181,9 +1205,10 @@ KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
+ // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT v[6];
@@ -1204,13 +1229,13 @@ void PairTersoffKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const i
}
if (vflag_atom) {
- v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2];
- v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5];
+ a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
+ a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2];
- v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5];
- v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2];
- v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5];
+ a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2];
+ a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5];
+ a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2];
+ a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5];
}
}
diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h
index 2dac2c5991..f73d4fe2d8 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
@@ -202,6 +202,14 @@ class PairTersoffKokkos : public PairTersoff {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
typedef Kokkos::DualView<F_FLOAT**[7],Kokkos::LayoutRight,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7;
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 0d150f83e4..2fe4361503 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -200,6 +200,17 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
EV_FLOAT ev;
@@ -243,6 +254,9 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all += ev;
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev_all.evdwl;
if (vflag_global) {
virial[0] += ev_all.v[0];
@@ -254,11 +268,15 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -304,8 +322,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (i >= nlocal) return;
@@ -1120,14 +1140,18 @@ void PairTersoffMODKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
{
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
- v_eatom[i] += epairhalf;
- if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf;
+ a_eatom[i] += epairhalf;
+ if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf;
}
if (VFLAG) {
@@ -1157,20 +1181,20 @@ void PairTersoffMODKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
}
if (vflag_atom) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
}
@@ -1184,9 +1208,10 @@ KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
+ // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT v[6];
@@ -1207,13 +1232,13 @@ void PairTersoffMODKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, cons
}
if (vflag_atom) {
- v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2];
- v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5];
+ a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
+ a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2];
- v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5];
- v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2];
- v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5];
+ a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2];
+ a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5];
+ a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2];
+ a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5];
}
}
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h
index dd5efb50f1..d7c94ffc93 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h
@@ -202,6 +202,14 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
typedef Kokkos::DualView<F_FLOAT**[7],Kokkos::LayoutRight,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7;
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 2fb9675db6..2892947f66 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -214,6 +214,17 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
EV_FLOAT ev;
@@ -257,6 +268,9 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all += ev;
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev_all.evdwl;
if (vflag_global) {
virial[0] += ev_all.v[0];
@@ -268,11 +282,15 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -318,8 +336,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
if (i >= nlocal) return;
@@ -1214,14 +1234,18 @@ void PairTersoffZBLKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
{
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
- v_eatom[i] += epairhalf;
- if (NEIGHFLAG != FULL) v_eatom[j] += epairhalf;
+ a_eatom[i] += epairhalf;
+ if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf;
}
if (VFLAG) {
@@ -1251,20 +1275,20 @@ void PairTersoffZBLKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
}
if (vflag_atom) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
}
@@ -1278,9 +1302,10 @@ KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
+ // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT v[6];
@@ -1301,13 +1326,13 @@ void PairTersoffZBLKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, cons
}
if (vflag_atom) {
- v_vatom(i,0) += v[0]; v_vatom(i,1) += v[1]; v_vatom(i,2) += v[2];
- v_vatom(i,3) += v[3]; v_vatom(i,4) += v[4]; v_vatom(i,5) += v[5];
+ a_vatom(i,0) += v[0]; a_vatom(i,1) += v[1]; a_vatom(i,2) += v[2];
+ a_vatom(i,3) += v[3]; a_vatom(i,4) += v[4]; a_vatom(i,5) += v[5];
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += v[0]; v_vatom(j,1) += v[1]; v_vatom(j,2) += v[2];
- v_vatom(j,3) += v[3]; v_vatom(j,4) += v[4]; v_vatom(j,5) += v[5];
- v_vatom(k,0) += v[0]; v_vatom(k,1) += v[1]; v_vatom(k,2) += v[2];
- v_vatom(k,3) += v[3]; v_vatom(k,4) += v[4]; v_vatom(k,5) += v[5];
+ a_vatom(j,0) += v[0]; a_vatom(j,1) += v[1]; a_vatom(j,2) += v[2];
+ a_vatom(j,3) += v[3]; a_vatom(j,4) += v[4]; a_vatom(j,5) += v[5];
+ a_vatom(k,0) += v[0]; a_vatom(k,1) += v[1]; a_vatom(k,2) += v[2];
+ a_vatom(k,3) += v[3]; a_vatom(k,4) += v[4]; a_vatom(k,5) += v[5];
}
}
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
index 45982bd420..3af4e0d8eb 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
@@ -207,6 +207,14 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
typedef Kokkos::DualView<F_FLOAT**[7],Kokkos::LayoutRight,DeviceType> tdual_ffloat_2d_n7;
typedef typename tdual_ffloat_2d_n7::t_dev_const_randomread t_ffloat_2d_n7_randomread;
typedef typename tdual_ffloat_2d_n7::t_host t_host_ffloat_2d_n7;
--
GitLab
From faa21a059196067e0b9adc3486a14ac4e2295dbc Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:30:17 -0600
Subject: [PATCH 086/332] Add data duplication to pair_sw_kokkos
---
src/KOKKOS/pair_sw_kokkos.cpp | 92 ++++++++++++++++++++++-------------
src/KOKKOS/pair_sw_kokkos.h | 8 +++
2 files changed, 66 insertions(+), 34 deletions(-)
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index 8f4903c767..22da4f7858 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -115,6 +115,17 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
EV_FLOAT ev;
@@ -160,6 +171,9 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
ev_all += ev;
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev_all.evdwl;
if (vflag_global) {
virial[0] += ev_all.v[0];
@@ -171,11 +185,15 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -222,9 +240,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
F_FLOAT evdwl = 0.0;
@@ -777,17 +796,19 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
{
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for half/thread neighbor list
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
- v_eatom[i] += epairhalf;
+ a_eatom[i] += epairhalf;
if (NEIGHFLAG != FULL)
- v_eatom[j] += epairhalf;
+ a_eatom[j] += epairhalf;
}
if (VFLAG) {
@@ -817,20 +838,20 @@ void PairSWKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j
}
if (vflag_atom) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
}
@@ -853,17 +874,20 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
const int VFLAG = vflag_either;
-// The eatom and vatom arrays are atomic for half/thread neighbor list
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (eflag_atom) {
epairthird = THIRD * (evdwl + ecoul);
- v_eatom[i] += epairthird;
+ a_eatom[i] += epairthird;
if (NEIGHFLAG != FULL) {
- v_eatom[j] += epairthird;
- v_eatom[k] += epairthird;
+ a_eatom[j] += epairthird;
+ a_eatom[k] += epairthird;
}
}
@@ -885,18 +909,18 @@ void PairSWKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &
}
if (vflag_atom) {
- v_vatom(i,0) += THIRD*v[0]; v_vatom(i,1) += THIRD*v[1];
- v_vatom(i,2) += THIRD*v[2]; v_vatom(i,3) += THIRD*v[3];
- v_vatom(i,4) += THIRD*v[4]; v_vatom(i,5) += THIRD*v[5];
+ a_vatom(i,0) += THIRD*v[0]; a_vatom(i,1) += THIRD*v[1];
+ a_vatom(i,2) += THIRD*v[2]; a_vatom(i,3) += THIRD*v[3];
+ a_vatom(i,4) += THIRD*v[4]; a_vatom(i,5) += THIRD*v[5];
if (NEIGHFLAG != FULL) {
- v_vatom(j,0) += THIRD*v[0]; v_vatom(j,1) += THIRD*v[1];
- v_vatom(j,2) += THIRD*v[2]; v_vatom(j,3) += THIRD*v[3];
- v_vatom(j,4) += THIRD*v[4]; v_vatom(j,5) += THIRD*v[5];
+ a_vatom(j,0) += THIRD*v[0]; a_vatom(j,1) += THIRD*v[1];
+ a_vatom(j,2) += THIRD*v[2]; a_vatom(j,3) += THIRD*v[3];
+ a_vatom(j,4) += THIRD*v[4]; a_vatom(j,5) += THIRD*v[5];
- v_vatom(k,0) += THIRD*v[0]; v_vatom(k,1) += THIRD*v[1];
- v_vatom(k,2) += THIRD*v[2]; v_vatom(k,3) += THIRD*v[3];
- v_vatom(k,4) += THIRD*v[4]; v_vatom(k,5) += THIRD*v[5];
+ a_vatom(k,0) += THIRD*v[0]; a_vatom(k,1) += THIRD*v[1];
+ a_vatom(k,2) += THIRD*v[2]; a_vatom(k,3) += THIRD*v[3];
+ a_vatom(k,4) += THIRD*v[4]; a_vatom(k,5) += THIRD*v[5];
}
}
}
diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h
index eb59d5bc3c..1a3f0b862f 100644
--- a/src/KOKKOS/pair_sw_kokkos.h
+++ b/src/KOKKOS/pair_sw_kokkos.h
@@ -134,6 +134,14 @@ class PairSWKokkos : public PairSW {
typename AT::t_efloat_1d d_eatom;
typename AT::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
typename AT::t_int_1d_randomread d_type2frho;
typename AT::t_int_2d_randomread d_type2rhor;
typename AT::t_int_2d_randomread d_type2z2r;
--
GitLab
From ebc0abbb8d877c1c5fe370e721a132597b8aad21 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:30:37 -0600
Subject: [PATCH 087/332] Add data duplication to pair_eam_kokkos variants
---
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 86 ++++++++++++++++++----------
src/KOKKOS/pair_eam_alloy_kokkos.h | 10 ++++
src/KOKKOS/pair_eam_fs_kokkos.cpp | 85 +++++++++++++++++----------
src/KOKKOS/pair_eam_fs_kokkos.h | 10 ++++
src/KOKKOS/pair_eam_kokkos.cpp | 5 +-
5 files changed, 137 insertions(+), 59 deletions(-)
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index f21ea2335d..7c6510f311 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -38,6 +38,7 @@ using namespace LAMMPS_NS;
// Cannot use virtual inheritance on the GPU, so must duplicate code
+
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@@ -122,6 +123,19 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_rho);
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_rho);
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
// zero out density
@@ -233,6 +247,9 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
@@ -244,11 +261,15 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -503,8 +524,10 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelA<NEIGHFLAG
// rho = density at each atom
// loop over neighbors of my atoms
- // The rho array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > rho = v_rho;
+ // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_rho = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho);
+ auto a_rho = v_rho.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -672,8 +695,10 @@ template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -780,18 +805,22 @@ void PairEAMAlloyKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const
const int EFLAG = eflag;
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (EFLAG) {
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
if (NEIGHFLAG!=FULL) {
- if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf;
- if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf;
+ if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf;
+ if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf;
} else {
- v_eatom[i] += epairhalf;
+ a_eatom[i] += epairhalf;
}
}
}
@@ -835,28 +864,28 @@ void PairEAMAlloyKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const
if (vflag_atom) {
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
} else {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
}
}
@@ -1165,4 +1194,3 @@ template class PairEAMAlloyKokkos<LMPDeviceType>;
template class PairEAMAlloyKokkos<LMPHostType>;
#endif
}
-
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index 5848399672..9c6b1342ea 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -129,6 +129,16 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 627b56b84a..e0e87ecfc5 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -122,6 +122,19 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_rho);
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_eatom);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_rho = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_rho);
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_eatom);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
copymode = 1;
// zero out density
@@ -233,6 +246,9 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
@@ -246,11 +262,15 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_eatom, dup_eatom);
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -503,8 +523,10 @@ void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelA<NEIGHFLAG,NEWTO
// rho = density at each atom
// loop over neighbors of my atoms
- // The rho array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > rho = v_rho;
+ // The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_rho = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho);
+ auto a_rho = v_rho.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -672,8 +694,10 @@ template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
@@ -780,18 +804,22 @@ void PairEAMFSKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int
const int EFLAG = eflag;
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
+ auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
if (EFLAG) {
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
if (NEIGHFLAG!=FULL) {
- if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf;
- if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf;
+ if (NEWTON_PAIR || i < nlocal) a_eatom[i] += epairhalf;
+ if (NEWTON_PAIR || j < nlocal) a_eatom[j] += epairhalf;
} else {
- v_eatom[i] += epairhalf;
+ a_eatom[i] += epairhalf;
}
}
}
@@ -835,28 +863,28 @@ void PairEAMFSKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int
if (vflag_atom) {
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
} else {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
}
}
}
@@ -1174,4 +1202,3 @@ template class PairEAMFSKokkos<LMPDeviceType>;
template class PairEAMFSKokkos<LMPHostType>;
#endif
}
-
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index ce0b572ea2..432a486276 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -129,6 +129,16 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 256cb8d55b..f6271a5a04 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -1,3 +1,4 @@
+/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
@@ -34,7 +35,6 @@
using namespace LAMMPS_NS;
-
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@@ -524,6 +524,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
// loop over neighbors of my atoms
// The rho array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_rho = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_rho),decltype(ndup_rho)>::get(dup_rho,ndup_rho);
auto a_rho = v_rho.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -692,6 +693,7 @@ KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
// The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -801,6 +803,7 @@ void PairEAMKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &
const int VFLAG = vflag_either;
// The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
--
GitLab
From 12ecc45b6a9d315f7e9bd0a9d4e4f3b42d07c812 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:30:58 -0600
Subject: [PATCH 088/332] Add data duplication to pair_snap_kokkos
---
src/KOKKOS/pair_snap_kokkos.h | 6 ++++
src/KOKKOS/pair_snap_kokkos_impl.h | 52 +++++++++++++++++++++---------
2 files changed, 42 insertions(+), 16 deletions(-)
diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h
index 5c68284219..b2019879ed 100644
--- a/src/KOKKOS/pair_snap_kokkos.h
+++ b/src/KOKKOS/pair_snap_kokkos.h
@@ -129,6 +129,12 @@ inline double dist2(double* x,double* y);
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
+ int need_dup;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
+ Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
+
friend void pair_virial_fdotr_compute<PairSNAPKokkos>(PairSNAPKokkos*);
};
diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h
index a024e5cbd1..013a8f1ba9 100644
--- a/src/KOKKOS/pair_snap_kokkos_impl.h
+++ b/src/KOKKOS/pair_snap_kokkos_impl.h
@@ -170,6 +170,15 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
+ need_dup = lmp->kokkos->need_dup<DeviceType>();
+ if (need_dup) {
+ dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);
+ dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(d_vatom);
+ } else {
+ ndup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(f);
+ ndup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterNonDuplicated>(d_vatom);
+ }
+
/*
for (int i = 0; i < nlocal; i++) {
typename t_neigh_list::t_neighs neighs_i = neigh_list.get_neighs(i);
@@ -232,6 +241,9 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//if (step%10==0)
// printf(" %e %e %e %e %e (%e %e): %e\n",t1,t2,t3,t4,t5,t6,t7,t1+t2+t3+t4+t5);
+ if (need_dup)
+ Kokkos::Experimental::contribute(f, dup_f);
+
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
@@ -244,12 +256,15 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
+
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_vatom, dup_vatom);
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
@@ -349,8 +364,11 @@ template<class DeviceType>
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAP<NEIGHFLAG,EVFLAG> >::member_type& team, EV_FLOAT& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
+ auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const int ii = team.league_rank();
const int i = d_ilist[ii];
@@ -591,8 +609,10 @@ void PairSNAPKokkos<DeviceType>::v_tally_xyz(EV_FLOAT &ev, const int &i, const i
const F_FLOAT &fx, const F_FLOAT &fy, const F_FLOAT &fz,
const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const
{
- // The vatom array is atomic for Half/Thread neighbor style
- Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
+ // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
+ auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
+ auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
const E_FLOAT v0 = delx*fx;
const E_FLOAT v1 = dely*fy;
@@ -611,18 +631,18 @@ void PairSNAPKokkos<DeviceType>::v_tally_xyz(EV_FLOAT &ev, const int &i, const i
}
if (vflag_atom) {
- v_vatom(i,0) += 0.5*v0;
- v_vatom(i,1) += 0.5*v1;
- v_vatom(i,2) += 0.5*v2;
- v_vatom(i,3) += 0.5*v3;
- v_vatom(i,4) += 0.5*v4;
- v_vatom(i,5) += 0.5*v5;
- v_vatom(j,0) += 0.5*v0;
- v_vatom(j,1) += 0.5*v1;
- v_vatom(j,2) += 0.5*v2;
- v_vatom(j,3) += 0.5*v3;
- v_vatom(j,4) += 0.5*v4;
- v_vatom(j,5) += 0.5*v5;
+ a_vatom(i,0) += 0.5*v0;
+ a_vatom(i,1) += 0.5*v1;
+ a_vatom(i,2) += 0.5*v2;
+ a_vatom(i,3) += 0.5*v3;
+ a_vatom(i,4) += 0.5*v4;
+ a_vatom(i,5) += 0.5*v5;
+ a_vatom(j,0) += 0.5*v0;
+ a_vatom(j,1) += 0.5*v1;
+ a_vatom(j,2) += 0.5*v2;
+ a_vatom(j,3) += 0.5*v3;
+ a_vatom(j,4) += 0.5*v4;
+ a_vatom(j,5) += 0.5*v5;
}
}
--
GitLab
From 9f058f19bc5664f53fd9e0547d3699590dac7d17 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:49:02 -0600
Subject: [PATCH 089/332] Deallocate duplicated memory
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 7 ++++---
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 8 ++++++++
src/KOKKOS/pair_eam_fs_kokkos.cpp | 8 ++++++++
src/KOKKOS/pair_eam_kokkos.cpp | 8 ++++++++
src/KOKKOS/pair_reaxc_kokkos.cpp | 4 ++--
src/KOKKOS/pair_snap_kokkos_impl.h | 7 +++++++
src/KOKKOS/pair_sw_kokkos.cpp | 7 +++++++
src/KOKKOS/pair_tersoff_kokkos.cpp | 7 +++++++
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 7 +++++++
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 7 +++++++
10 files changed, 65 insertions(+), 5 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index bc9c935576..c2ad719a47 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -260,9 +260,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
// 2nd cg solve over b_t, t
cg_solve2();
- if (need_dup)
- dup_o = decltype(dup_o)(); // free duplicated memory
-
// calculate_Q();
calculate_q();
k_s_hist.template modify<DeviceType>();
@@ -272,6 +269,10 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
if (!allocated_flag)
allocated_flag = 1;
+
+ // free duplicated memory
+ if (need_dup)
+ dup_o = decltype(dup_o)();
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 7c6510f311..2684ede376 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -277,6 +277,14 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_rho = decltype(dup_rho)();
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index e0e87ecfc5..d46b81b9ae 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -276,6 +276,14 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_rho = decltype(dup_rho)();
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index f6271a5a04..5e3c06294b 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -271,6 +271,14 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_rho = decltype(dup_rho)();
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 4db6235ca6..6cf9b3979a 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -1063,6 +1063,8 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (fixspecies_flag)
FindBondSpecies();
+ copymode = 0;
+
// free duplicated memory
if (need_dup) {
dup_f = decltype(dup_f)();
@@ -1075,8 +1077,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
dup_eatom = decltype(dup_eatom)();
dup_vatom = decltype(dup_vatom)();
}
-
- copymode = 0;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h
index 013a8f1ba9..c452042cfe 100644
--- a/src/KOKKOS/pair_snap_kokkos_impl.h
+++ b/src/KOKKOS/pair_snap_kokkos_impl.h
@@ -270,7 +270,14 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
atomKK->modified(execution_space,F_MASK);
+
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index 22da4f7858..5452d2293f 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -201,6 +201,13 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 7b21bf5793..c3e1494d0b 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -284,6 +284,13 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 2fe4361503..61493794ba 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -284,6 +284,13 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 2892947f66..f51da2afde 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -298,6 +298,13 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
+
+ // free duplicated memory
+ if (need_dup) {
+ dup_f = decltype(dup_f)();
+ dup_eatom = decltype(dup_eatom)();
+ dup_vatom = decltype(dup_vatom)();
+ }
}
/* ---------------------------------------------------------------------- */
--
GitLab
From eb4d5864937a6b0eb6634b04996f8fed1940d556 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 12:53:27 -0600
Subject: [PATCH 090/332] Remove duplicate if test in fix_qeq_reax_kokkos
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 12 ++++--------
1 file changed, 4 insertions(+), 8 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index c2ad719a47..578afd2077 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -496,8 +496,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse13_functor);
}
if (need_dup)
- if (need_dup)
- Kokkos::Experimental::contribute(d_o, dup_o);
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec1> (inum, teamsize), *this);
}
@@ -555,8 +554,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
Kokkos::parallel_for(inum,sparse23_functor);
}
if (need_dup)
- if (need_dup)
- Kokkos::Experimental::contribute(d_o, dup_o);
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
@@ -635,8 +633,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse33_functor);
}
if (need_dup)
- if (need_dup)
- Kokkos::Experimental::contribute(d_o, dup_o);
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec3> (inum, teamsize), *this);
}
@@ -694,8 +691,7 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
Kokkos::parallel_for(inum,sparse23_functor);
}
if (need_dup)
- if (need_dup)
- Kokkos::Experimental::contribute(d_o, dup_o);
+ Kokkos::Experimental::contribute(d_o, dup_o);
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
--
GitLab
From 6f1986a8f149dc4873d1c86fa1f031995983fc77 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 13:10:02 -0600
Subject: [PATCH 091/332] Small tweaks to Kokkos EAM
---
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 1 -
src/KOKKOS/pair_eam_alloy_kokkos.h | 5 ++---
src/KOKKOS/pair_eam_fs_kokkos.cpp | 1 -
src/KOKKOS/pair_eam_fs_kokkos.h | 5 ++---
src/KOKKOS/pair_eam_kokkos.cpp | 1 -
src/KOKKOS/pair_eam_kokkos.h | 5 ++---
6 files changed, 6 insertions(+), 12 deletions(-)
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 2684ede376..d20e71fe4c 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -110,7 +110,6 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
- v_rho = k_rho.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
tag = atomKK->k_tag.view<DeviceType>();
nlocal = atom->nlocal;
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index 9c6b1342ea..6593ccae73 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -130,11 +130,11 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
int need_dup;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
@@ -142,7 +142,6 @@ class PairEAMAlloyKokkos : public PairEAM, public KokkosBase {
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
- typename AT::t_ffloat_1d v_rho;
typename AT::t_ffloat_1d d_fp;
HAT::t_ffloat_1d h_rho;
HAT::t_ffloat_1d h_fp;
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index d46b81b9ae..8f5571bf29 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -109,7 +109,6 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
- v_rho = k_rho.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
tag = atomKK->k_tag.view<DeviceType>();
nlocal = atom->nlocal;
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index 432a486276..f75605ff6d 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -130,11 +130,11 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
int need_dup;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
@@ -142,7 +142,6 @@ class PairEAMFSKokkos : public PairEAM, public KokkosBase {
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
- typename AT::t_ffloat_1d v_rho;
typename AT::t_ffloat_1d d_fp;
HAT::t_ffloat_1d h_rho;
HAT::t_ffloat_1d h_fp;
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 5e3c06294b..1a49e1357c 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -104,7 +104,6 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
- v_rho = k_rho.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
tag = atomKK->k_tag.view<DeviceType>();
nlocal = atom->nlocal;
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 6523e3fe72..4040eba858 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -127,11 +127,11 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
int need_dup;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterDuplicated> dup_vatom;
- Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
+ Kokkos::Experimental::ScatterView<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_rho;
Kokkos::Experimental::ScatterView<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_f;
Kokkos::Experimental::ScatterView<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_eatom;
Kokkos::Experimental::ScatterView<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::Experimental::ScatterSum,Kokkos::Experimental::ScatterNonDuplicated> ndup_vatom;
@@ -139,7 +139,6 @@ class PairEAMKokkos : public PairEAM, public KokkosBase {
DAT::tdual_ffloat_1d k_rho;
DAT::tdual_ffloat_1d k_fp;
typename AT::t_ffloat_1d d_rho;
- typename AT::t_ffloat_1d v_rho;
typename AT::t_ffloat_1d d_fp;
HAT::t_ffloat_1d h_rho;
HAT::t_ffloat_1d h_fp;
--
GitLab
From 8f665a5a0f35a3022655a530161f95ed285b8e50 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 13:46:03 -0600
Subject: [PATCH 092/332] Update Kokkos docs for data duplication
---
doc/src/Speed_kokkos.txt | 21 +++++++++++++++++++++
src/KOKKOS/kokkos.cpp | 4 +++-
2 files changed, 24 insertions(+), 1 deletion(-)
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 597ed73e53..5846781e66 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -178,6 +178,11 @@ this manner no modification to the input script is
needed. Alternatively, one can run with the KOKKOS package by editing
the input script as described below.
+NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e.
+Makefile.kokkos_mpi_only) will give better performance than the OpenMP
+backend (i.e. Makefile.kokkos_omp) because some of the overhead to make
+the code thread-safe is removed.
+
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
pairwise and bonded interactions. However, when running on CPUs, it
@@ -194,6 +199,22 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
If the "newton"_newton.html command is used in the input
script, it can also override the Newton flag defaults.
+For half neighbor lists and OpenMP, the KOKKOS package uses data
+duplication (i.e. thread-private arrays) by default to avoid
+thread-level write conflicts in the force arrays (and other data
+structures as necessary). Data duplication is typically fastest for
+small numbers of threads (i.e. 8 or less) but does increase memory
+footprint and is not scalable to large numbers of threads. An
+alternative to data duplication is to use thread-level atomics, which
+don't require duplication. The use of atomics can be forced by compiling
+with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
+Kokkos-enabled pair_styles support data duplication. Alternatively, full
+neighbor lists avoid the need for duplication or atomics but require
+more compute operations per atom. When using the Kokkos Serial backend
+or the OpenMP backend with a single thread, no duplication or atomics is
+used. For CUDA and half neighbor lists, the KOKKOS package always uses
+atomics.
+
[Core and Thread Affinity:]
When using multi-threading, it is important for performance to bind
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index e8bc610de6..9973b5a688 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -168,7 +168,9 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
#ifndef KOKKOS_HAVE_SERIAL
if (num_threads == 1)
- error->warning(FLERR,"Using Kokkos Serial backend (i.e. Makefile.kokkos_mpi_only) performs better with 1 thread");
+ error->warning(FLERR,"When using a single thread, the Kokkos Serial backend "
+ "(i.e. Makefile.kokkos_mpi_only) gives better performance "
+ "than the OpenMP backend");
#endif
Kokkos::InitArguments args;
--
GitLab
From 165fa01a97816c7430f2f2f1283036d92408e926 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Fri, 10 Aug 2018 14:23:51 -0600
Subject: [PATCH 093/332] Cleanup
---
doc/src/Speed_kokkos.txt | 2 +-
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 1 -
src/KOKKOS/pair_eam_kokkos.cpp | 1 -
src/KOKKOS/pair_reaxc_kokkos.cpp | 79 ++++++++++------------------
4 files changed, 29 insertions(+), 54 deletions(-)
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 5846781e66..dc5dbd6049 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -211,7 +211,7 @@ with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all
Kokkos-enabled pair_styles support data duplication. Alternatively, full
neighbor lists avoid the need for duplication or atomics but require
more compute operations per atom. When using the Kokkos Serial backend
-or the OpenMP backend with a single thread, no duplication or atomics is
+or the OpenMP backend with a single thread, no duplication or atomics are
used. For CUDA and half neighbor lists, the KOKKOS package always uses
atomics.
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index d20e71fe4c..fc19da1c8a 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -38,7 +38,6 @@ using namespace LAMMPS_NS;
// Cannot use virtual inheritance on the GPU, so must duplicate code
-
/* ---------------------------------------------------------------------- */
template<class DeviceType>
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 1a49e1357c..a1431334b4 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -1,4 +1,3 @@
-/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 6cf9b3979a..46ecddfd83 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -73,14 +73,6 @@ PairReaxCKokkos<DeviceType>::PairReaxCKokkos(LAMMPS *lmp) : PairReaxC(lmp)
k_error_flag = DAT::tdual_int_scalar("pair:error_flag");
k_nbuf_local = DAT::tdual_int_scalar("pair:nbuf_local");
-
- static double t1 = 0.0;
- static double t2 = 0.0;
- static double t3 = 0.0;
- static double t4 = 0.0;
- static double t5 = 0.0;
- static double t6 = 0.0;
- static double t7 = 0.0;
}
/* ---------------------------------------------------------------------- */
@@ -678,8 +670,6 @@ void PairReaxCKokkos<DeviceType>::LR_vdW_Coulomb( int i, int j, double r_ij, LR_
template<class DeviceType>
void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
- Kokkos::Timer timer;
-
copymode = 1;
bocnt = hbcnt = 0;
@@ -828,7 +818,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// zero
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxZero>(0,nmax),*this);
-
if (neighflag == HALF)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
@@ -1115,8 +1104,8 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -1276,8 +1265,8 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- // The f array is atomic for Half/Thread neighbor style
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
+ // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -1660,10 +1649,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf<NEIGHFLAG>,
if (d_resize_bo() || d_resize_hb())
return;
- //Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_dDeltap_self = d_dDeltap_self;
auto v_dDeltap_self = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_dDeltap_self),decltype(ndup_dDeltap_self)>::get(dup_dDeltap_self,ndup_dDeltap_self);
auto a_dDeltap_self = v_dDeltap_self.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_total_bo = d_total_bo;
+
auto v_total_bo = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_total_bo),decltype(ndup_total_bo)>::get(dup_total_bo,ndup_total_bo);
auto a_total_bo = v_total_bo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -2356,7 +2344,6 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -2509,12 +2496,10 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
- //auto a_Cdbo = dup_Cdbo.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+
auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -2758,10 +2743,10 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
// Forces
- d_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- d_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- d_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
- d_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ a_Cdbo(i,j_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ a_Cdbo(j,i_index) += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ a_Cdbo(i,k_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ a_Cdbo(k,i_index) += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
CdDelta_i += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
CdDelta_j += CEcoa4;
@@ -2776,7 +2761,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeAngular<NEIGHFLAG,EV
temp = temp_bo_jt * temp_bo_jt * temp_bo_jt;
pBOjt7 = temp * temp * temp_bo_jt;
- d_Cdbo(i,l_index) += (CEval6 * pBOjt7);
+ a_Cdbo(i,l_index) += (CEval6 * pBOjt7);
d_Cdbopi(i,l_index) += CEval5;
d_Cdbopi2(i,l_index) += CEval5;
}
@@ -2823,10 +2808,9 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+
auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
Kokkos::View<F_FLOAT**, typename DAT::t_ffloat_2d_dl::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_Cdbo = d_Cdbo;
@@ -3131,9 +3115,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTorsion<NEIGHFLAG,EV
CdDelta_i += CEtors3;
CdDelta_j += CEtors3;
- d_Cdbo(i,k_index) += CEtors4 + CEconj1;
- d_Cdbo(i,j_index) += CEtors5 + CEconj2;
- d_Cdbo(j,l_index) += CEtors6 + CEconj3; // trouble
+ a_Cdbo(i,k_index) += CEtors4 + CEconj1;
+ a_Cdbo(i,j_index) += CEtors5 + CEconj2;
+ a_Cdbo(j,l_index) += CEtors6 + CEconj3; // trouble
// dcos_theta_ijk
const F_FLOAT coeff74 = CEtors7 + CEconj4;
@@ -3200,7 +3184,6 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeHydrogen<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3387,9 +3370,9 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxUpdateBond<NEIGHFLAG>, cons
}
if (flag) {
- d_Cdbo(j,k_index) += Cdbo_i;
- d_Cdbopi(j,k_index) += Cdbopi_i;
- d_Cdbopi2(j,k_index) += Cdbopi2_i;
+ a_Cdbo(j,k_index) += Cdbo_i;
+ a_Cdbopi(j,k_index) += Cdbopi_i;
+ a_Cdbopi2(j,k_index) += Cdbopi2_i;
}
}
}
@@ -3401,14 +3384,12 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond1<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //Kokkos::View<F_FLOAT*, typename DAT::t_ffloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_CdDelta = d_CdDelta;
+
auto v_CdDelta = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_CdDelta),decltype(ndup_CdDelta)>::get(dup_CdDelta,ndup_CdDelta);
auto a_CdDelta = v_CdDelta.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
-
F_FLOAT delij[3];
F_FLOAT p_be1, p_be2, De_s, De_p, De_pp, pow_BOs_be2, exp_be12, CEbo, ebond;
@@ -3544,7 +3525,6 @@ template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeBond2<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT_REAX& ev) const {
- //Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
auto v_f = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f);
auto a_f = v_f.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3758,11 +3738,11 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
{
const int VFLAG = vflag_either;
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+
auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3827,10 +3807,10 @@ void PairReaxCKokkos<DeviceType>::e_tally(EV_FLOAT_REAX &ev, const int &i, const
const F_FLOAT &epair) const
{
- // The eatom array is atomic for Half/Thread neighbor style
+ // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
if (eflag_atom) {
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3848,8 +3828,7 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::e_tally_single(EV_FLOAT_REAX &ev, const int &i,
const F_FLOAT &epair) const
{
- // The eatom array is atomic for Half/Thread neighbor style
- //Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_eatom = d_eatom;
+ // The eatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
auto v_eatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_eatom),decltype(ndup_eatom)>::get(dup_eatom,ndup_eatom);
auto a_eatom = v_eatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3884,7 +3863,6 @@ void PairReaxCKokkos<DeviceType>::v_tally(EV_FLOAT_REAX &ev, const int &i,
}
if (vflag_atom) {
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3902,8 +3880,7 @@ void PairReaxCKokkos<DeviceType>::v_tally3(EV_FLOAT_REAX &ev, const int &i, cons
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
- // The eatom and vatom arrays are atomic for Half/Thread neighbor style
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
+ // The eatom and vatom arrays are duplicated for OpenMP, atomic for CUDA, and neither for Serial
auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
@@ -3945,7 +3922,8 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
const int &l, F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *dril, F_FLOAT *drjl, F_FLOAT *drkl) const
{
- // The vatom array is atomic for Half/Thread neighbor style
+ // The vatom array is duplicated for OpenMP, atomic for CUDA, and neither for Serial
+
F_FLOAT v[6];
v[0] = dril[0]*fi[0] + drjl[0]*fj[0] + drkl[0]*fk[0];
@@ -3965,7 +3943,6 @@ void PairReaxCKokkos<DeviceType>::v_tally4(EV_FLOAT_REAX &ev, const int &i, cons
}
if (vflag_atom) {
- //Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_vatom = d_vatom;
auto v_vatom = ScatterViewHelper<NeedDup<NEIGHFLAG,DeviceType>::value,decltype(dup_vatom),decltype(ndup_vatom)>::get(dup_vatom,ndup_vatom);
auto a_vatom = v_vatom.template access<AtomicDup<NEIGHFLAG,DeviceType>::value>();
--
GitLab
From 781ddc07c738f0055ed85c12981309c0d68c7bd2 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 13 Aug 2018 15:29:28 -0600
Subject: [PATCH 094/332] update to CSlib website link
---
doc/src/Section_howto.txt | 4 ++--
doc/src/server_mc.txt | 6 +++---
doc/src/server_md.txt | 6 +++---
lib/message/README | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 3a38ccedcb..1bcab52cd1 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -2994,8 +2994,8 @@ below. The MESSAGE package also wraps a client/server library called
CSlib which enables two codes to exchange messages in different ways,
either via files, a socket, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. It has its own
-"website"_http://cslib.sandia.gov (as of Aug 2018) with documentation
-and test programs.
+"website"_http://cslib.sandia.gov with documentation and test
+programs.
NOTE: For client/server coupling to work between LAMMPS and another
code, the other code also has to use the CSlib. This can sometimes be
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index 44335efc95..94545c8732 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -55,9 +55,9 @@ The format and content of the exchanged messages are explained here in
a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
-pages for more details on the actual library syntax (as of Aug 2018).
-The "cs" object in this pseudo code is an instance of the CSlib that
-both the client and server codes store.
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is an instance of the CSlib that both the client
+and server codes store.
See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 422b207bed..66534c1ad6 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -58,9 +58,9 @@ The format and content of the exchanged messages are explained here in
a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
-pages for more details on the actual library syntax (as of Aug 2018).
-The "cs" object in this pseudo code is an instance of the CSlib that
-both the client and server codes store.
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is an instance of the CSlib that both the client
+and server codes store.
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
files for details on how LAMMPS uses these messages. See the
diff --git a/lib/message/README b/lib/message/README
index 71e46a8286..c93ae81104 100644
--- a/lib/message/README
+++ b/lib/message/README
@@ -4,8 +4,8 @@ in a LAMMPS input script.
The CSlib libary is included in the LAMMPS distribution. A fuller
version including documentation and test programs is available at
-http:cslib.sandia.gov (by Aug 2018) and was developed by Steve
-Plimpton at Sandia National Laboratories.
+http:cslib.sandia.gov and was developed by Steve Plimpton at Sandia
+National Laboratories.
You can type "make lib-message" from the src directory to see help on
how to build this library via make commands, or you can do the same
--
GitLab
From e0fc050bf40563d69c1b1fa71e9c204ed02c618b Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Mon, 20 Aug 2018 15:12:05 -0400
Subject: [PATCH 095/332] Changes to linux makefile.
---
lib/gpu/Makefile.linux | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
index ed5b6092d3..be103d7f89 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -8,7 +8,7 @@
EXTRAMAKE = Makefile.lammps.standard
ifeq ($(CUDA_HOME),)
-CUDA_HOME = /usr/local/cuda
+CUDA_HOME = /opt/cuda
endif
NVCC = nvcc
@@ -19,7 +19,7 @@ CUDA_ARCH = -arch=sm_21
#CUDA_ARCH = -arch=sm_13
# older CUDA
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
-CUDA_ARCH = -arch=sm_35
+CUDA_ARCH = -arch=sm_61
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
--
GitLab
From 937d4707dc69f069d70c5d4cef1644bd521bc711 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 20 Aug 2018 15:03:21 -0600
Subject: [PATCH 096/332] proposed SJP changes for 2nd cutoff_triple
---
doc/src/pair_atm.txt | 17 ++++++++++++-----
src/MANYBODY/pair_atm.cpp | 24 ++++++++++++++++++++++--
src/MANYBODY/pair_atm.h | 3 ++-
3 files changed, 36 insertions(+), 8 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index 2e961a1356..c2718973ad 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -10,16 +10,20 @@ pair_style atm command :h3
[Syntax:]
-pair_style atm cutoff :pre
+SJP: add an arg
-cutoff = global cutoff for 3-body interactions (distance units) :ul
+pair_style atm cutoff cutoff_triple :pre
+
+cutoff = cutoff for each pair in 3-body interaction (distance units)
+cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) :ul
[Examples:]
-pair_style atm 2.5
+SJP: is 1.5 a good value?
+pair_style atm 2.5 1.5
pair_coeff * * * 0.072 :pre
-pair_style hybrid/overlay lj/cut 6.5 atm 2.5
+pair_style hybrid/overlay lj/cut 6.5 atm 2.5 1.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 1 1 atm 1 0.064
pair_coeff 1 1 atm 2 0.080
@@ -50,7 +54,10 @@ potential using the "pair_style hybrid/overlay"_pair_hybrid.html
command as in the example above.
The potential for a triplet of atom is calculated only if all 3
-distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
+SJP: In addition, the product of the 3 distances r12*r23*r31 <
+cutoff_triple^3 is required, which limits the contribution of the
+potential to ???
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 9afa36b3c0..e960398ab3 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -92,6 +92,10 @@ void PairATM::compute(int eflag, int vflag)
int *type = atom->type;
double cutoff_squared = cut_global*cut_global;
+ // SJP: new cutoff
+ double triple = cut_triple*cut_triple*cut_triple;
+ double cutoff_triple_sixth = triple*triple;
+
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@@ -138,6 +142,10 @@ void PairATM::compute(int eflag, int vflag)
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
if (rik2 > cutoff_squared) continue;
+ // SJP: add this line?
+
+ if (rij2*rjk2*rik2 > cutoff_triple_sixth) continue;
+
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
@@ -192,9 +200,14 @@ void PairATM::allocate()
void PairATM::settings(int narg, char **arg)
{
- if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+ // SJP: change to 2 args, require triple <= global
+
+ if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
+ cut_triple = force->numeric(FLERR,arg[1]);
+
+ if (cut_triple > cut_global) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
@@ -311,6 +324,8 @@ void PairATM::read_restart(FILE *fp)
void PairATM::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
+ // SJP: 2nd arg
+ fwrite(&cut_triple,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
@@ -319,9 +334,14 @@ void PairATM::write_restart_settings(FILE *fp)
void PairATM::read_restart_settings(FILE *fp)
{
+ // SJP: 2nd arg
int me = comm->me;
- if (me == 0) fread(&cut_global,sizeof(double),1,fp);
+ if (me == 0) {
+ fread(&cut_global,sizeof(double),1,fp);
+ fread(&cut_triple,sizeof(double),1,fp);
+ }
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index 60d22348c3..cc868df832 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -39,7 +39,8 @@ class PairATM : public Pair {
void read_restart_settings(FILE *);
protected:
- double cut_global, cutoff_squared;
+ // SJP: add 2nd cutoff
+ double cut_global,cut_triple;
double ***nu;
void allocate();
--
GitLab
From d66d696dff4f6bacbd9254da0fe00887a9629f3e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 20 Aug 2018 22:34:32 -0400
Subject: [PATCH 097/332] minor tweak
---
doc/src/Speed_gpu.txt | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index 3ae4639dc2..4a075516ce 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -48,12 +48,11 @@ hardware. :l
To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA CUDA software on your system:
-Check if you have an NVIDIA GPU: cat
-/proc/driver/nvidia/gpus/0/information Go to
-http://www.nvidia.com/object/cuda_get.html Install a driver and
-toolkit appropriate for your system (SDK is not necessary) Run
-lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
-below) to list supported devices and properties :ul
+Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
+Go to http://www.nvidia.com/object/cuda_get.html :l
+Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
+Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
+list supported devices and properties :ule,l
[Building LAMMPS with the GPU package:]
--
GitLab
From 95d462e5d3dc456cce8ab14198d1a0010e7d1527 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 21 Aug 2018 02:28:53 -0600
Subject: [PATCH 098/332] bond/react: better template validity check
now always throws error if a bond type changes, but both of of the involved atoms are too close to edge of template
---
doc/src/fix_bond_react.txt | 8 +++----
src/USER-MISC/fix_bond_react.cpp | 40 ++++++++++++++++++++++++++++++--
2 files changed, 42 insertions(+), 6 deletions(-)
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 7317dd26bb..327088cb99 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
[Default:]
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
:line
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index c72a1b027b..d529848e39 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
hang_catch++;
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
- if (hang_catch > atom->nlocal*3) {
- error->all(FLERR,"Excessive iteration of superimpose algorithm");
+ if (hang_catch > atom->nlocal*30) {
+ error->one(FLERR,"Excessive iteration of superimpose algorithm");
}
}
}
@@ -1554,6 +1554,42 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+ // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+ // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (landlocked_atoms[i][myrxn] == 0) {
+ int twomol_atomi = i+1;
+ for (int j = 0; j < twomol->num_bond[i]; j++) {
+ int twomol_atomj = twomol->bond_atom[i][j];
+ if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
+ int onemol_atomi = equivalences[i][1][myrxn];
+ int onemol_batom;
+ for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+ if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+ printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ if (newton_bond) {
+ int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+ for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+ if (onemol_batom == equivalences[i][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+ printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
for (int i = 0; i < twomol->natoms; i++) {
--
GitLab
From 2b5618dc404c6ffa27bce91758986523a3acf86e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 21 Aug 2018 06:50:30 -0400
Subject: [PATCH 099/332] Updates for Speed_gpu.txt doc page
This corrects some inaccurate statements about required hardware and briefly discusses some OpenCL related basics. also a typo is fixed
---
doc/src/Speed_gpu.txt | 43 +++++++++++++++++++++++++++++--------------
1 file changed, 29 insertions(+), 14 deletions(-)
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index 4a075516ce..acef5bf6c1 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
GPU package :h3
-The GPU package was developed by Mike Brown at ORNL and his
-collaborators, particularly Trung Nguyen (ORNL). It provides GPU
-versions of many pair styles, including the 3-body Stillinger-Weber
-pair style, and for "kspace_style pppm"_kspace_style.html for
-long-range Coulombics. It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+"kspace_style pppm"_kspace_style.html for long-range Coulombics.
+It has the following general features:
It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
e.g. within a node of a parallel machine. :ulb,l
-Atom-based data (e.g. coordinates, forces) moves back-and-forth
+Atom-based data (e.g. coordinates, forces) are moved back-and-forth
between the CPU(s) and GPU every timestep. :l
Neighbor lists can be built on the CPU or on the GPU :l
@@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l
-Asynchronous force computations can be performed simultaneously on the
-CPU(s) and GPU. :l
+Force computations of different style (pair vs. bond/angle/dihedral/improper)
+can be performed concurrently on the GPU and CPU(s), respectively. :l
It allows for GPU computations to be performed in single or double
precision, or in mixed-mode precision, where pairwise forces are
@@ -39,14 +39,15 @@ force vectors. :l
LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
-same functionality can eventually be supported on a variety of GPU
-hardware. :l
+same functionality is supported on a variety of hardware. :l
:ule
[Required hardware/software:]
-To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA CUDA software on your system:
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
Go to http://www.nvidia.com/object/cuda_get.html :l
@@ -54,6 +55,17 @@ Install a driver and toolkit appropriate for your system (SDK is not necessary)
Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
list supported devices and properties :ule,l
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
+Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
+installed. There can be multiple of them for the same or different hardware
+(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
+as 'platforms'. The GPU library will select the [first] suitable platform,
+but this can be overridded using the device option of the "package"_package.html
+command. run lammps/lib/gpu/ocl_get_devices to get a list of available
+platforms and devices with a suitable ICD available.
+
[Building LAMMPS with the GPU package:]
See the "Build extras"_Build_extras.html#gpu doc page for
@@ -119,7 +131,10 @@ GPUs/node to use, as well as other options.
The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
-precision used on the GPU (double, single, mixed).
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the GPU package on various
@@ -145,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
performance. Neighbor lists can be built on the GPU or CPU. Force
calculations can be dynamically balanced across the CPU cores and
GPUs. GPU-specific settings can be made which can be optimized
-for different hardware. See the "packakge"_package.html command
+for different hardware. See the "package"_package.html command
doc page for details. :l
As described by the "package gpu"_package.html command, GPU
--
GitLab
From fd788e5bbd4eb69ad5663012481c0d1402dffc0a Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 21 Aug 2018 09:25:06 -0600
Subject: [PATCH 100/332] cmake/README.md: add BUILD_EXE option
---
cmake/README.md | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/cmake/README.md b/cmake/README.md
index 85375cd2aa..21e728c1f0 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_EXE</code></td>
+ <td>control whether to build LAMMPS executable</td>
+ <td>
+ <dl>
+ <dt><code>on</code> (default)</dt>
+ <dt><code>off</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>BUILD_SHARED_LIBS</code></td>
<td>control whether to build LAMMPS as a shared-library</td>
--
GitLab
From fc7d9ff558482730137755ce86cfd26af1b37f77 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 21 Aug 2018 11:12:21 -0600
Subject: [PATCH 101/332] apply PBC to coords passed to scafacos
---
src/USER-SCAFACOS/scafacos.cpp | 50 ++++++++++++++++++++++------------
src/USER-SCAFACOS/scafacos.h | 4 +--
2 files changed, 34 insertions(+), 20 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 5832f5b052..23d51b07b8 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -101,8 +101,8 @@ void Scafacos::init()
if (logfile && me == 0) fprintf(logfile,
"Setting up ScaFaCoS with solver %s ...\n",method);
- if (!atom->q_flag) error->all(FLERR,
- "Kspace style requires atom attribute q");
+ if (!atom->q_flag)
+ error->all(FLERR,"Kspace style requires atom attribute q");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
@@ -166,15 +166,12 @@ void Scafacos::init()
// more useful here, since the parameters should be tuned now
if (me == 0) fcs_print_parameters(fcs);
}
+
initialized = 1;
}
/* ---------------------------------------------------------------------- */
-void Scafacos::setup() {}
-
-/* ---------------------------------------------------------------------- */
-
void Scafacos::compute(int eflag, int vflag)
{
double **x = atom->x;
@@ -209,20 +206,14 @@ void Scafacos::compute(int eflag, int vflag)
check_result(result);
}
- // grow epot & efield if necessary
-
- if (nlocal == 0 && maxatom == 0) {
- memory->destroy(epot);
- memory->destroy(efield);
- maxatom = 1;
- memory->create(epot,maxatom,"scafacos:epot");
- memory->create(efield,maxatom,3,"scafacos:efield");
- }
+ // grow xpbc, epot, efield if necessary
- if (nlocal > maxatom) {
+ if (nlocal > maxatom || maxatom == 0) {
+ memory->destroy(xpbc);
memory->destroy(epot);
memory->destroy(efield);
maxatom = atom->nmax;
+ memory->create(xpbc,3*maxatom,"scafacos:xpbc");
memory->create(epot,maxatom,"scafacos:epot");
memory->create(efield,maxatom,3,"scafacos:efield");
}
@@ -231,12 +222,27 @@ void Scafacos::compute(int eflag, int vflag)
{
fcs_set_compute_virial(fcs,1);
if (strcmp(method,"p3m") == 0)
- error->all(FLERR,"ScaFaCoS p3m does not support the computation of virial");
+ error->all(FLERR,"ScaFaCoS p3m does not support computation of virial");
+ }
+
+ // pack coords into xpbc and apply PBC
+
+ double **x = atom->x;
+ memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
+
+ int j = 0;
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
}
- result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
+ // invoke ScaFaCoS solver
+
+ result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot);
check_result(result);
+ // extract virial
+
if (vflag_global)
{
fcs_get_virial(fcs,virial_int);
@@ -272,6 +278,14 @@ void Scafacos::compute(int eflag, int vflag)
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
}
+/* ----------------------------------------------------------------------
+ pack local coords into xpbc, enforcing PBC
+------------------------------------------------------------------------- */
+
+void Scafacos::pack_coords()
+{
+}
+
/* ---------------------------------------------------------------------- */
int Scafacos::modify_param(int narg, char **arg)
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index 8f7c46dc6b..bf07b3b45a 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -30,7 +30,7 @@ class Scafacos : public KSpace {
Scafacos(class LAMMPS *, int, char **);
~Scafacos();
void init();
- void setup();
+ void setup() {}
void compute(int, int);
int modify_param(int, char **);
double memory_usage();
@@ -40,7 +40,7 @@ class Scafacos : public KSpace {
char *method;
double tolerance;
- double *epot,**efield;
+ double *xpbc,*epot,**efield;
int tolerance_type;
int initialized,maxatom;
--
GitLab
From 4b0382cadd10132f55e98fda4a5e7f710d5dbdf6 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 21 Aug 2018 14:45:01 -0400
Subject: [PATCH 102/332] Fixes issue #1069
---
python/lammps.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/python/lammps.py b/python/lammps.py
index 2f4ffb642e..598e4c506f 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -173,6 +173,9 @@ class lammps(object):
self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
else:
+ if lammps.has_mpi4py:
+ from mpi4py import MPI
+ self.comm = MPI.COMM_WORLD
self.opened = 1
if cmdargs:
cmdargs.insert(0,"lammps.py")
@@ -862,6 +865,10 @@ class PyLammps(object):
def run(self, *args, **kwargs):
output = self.__getattr__('run')(*args, **kwargs)
+
+ if(lammps.has_mpi4py):
+ output = self.lmp.comm.bcast(output, root=0)
+
self.runs += get_thermo_data(output)
return output
--
GitLab
From 3573970e4a168c409d3cef2a6c6c3008504c6043 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 21 Aug 2018 17:04:52 -0600
Subject: [PATCH 103/332] fixed double definition, removed virial check for p3m
and removed unused function definition Scafacos::pack...
---
src/USER-SCAFACOS/scafacos.cpp | 29 ++++++++++-------------------
1 file changed, 10 insertions(+), 19 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 23d51b07b8..d68d3db323 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -198,13 +198,6 @@ void Scafacos::compute(int eflag, int vflag)
vflag_global = 0;
}
- // if simulation box has changed, call fcs_tune()
-
- if (box_has_changed()) {
- setup_handle();
- result = fcs_tune(fcs,nlocal,&x[0][0],q);
- check_result(result);
- }
// grow xpbc, epot, efield if necessary
@@ -221,13 +214,11 @@ void Scafacos::compute(int eflag, int vflag)
if (vflag_global)
{
fcs_set_compute_virial(fcs,1);
- if (strcmp(method,"p3m") == 0)
- error->all(FLERR,"ScaFaCoS p3m does not support computation of virial");
+ //if (strcmp(method,"p3m") == 0)
+ // error->all(FLERR,"ScaFaCoS p3m does not support computation of virial");
}
// pack coords into xpbc and apply PBC
-
- double **x = atom->x;
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
int j = 0;
@@ -236,6 +227,14 @@ void Scafacos::compute(int eflag, int vflag)
j += 3;
}
+ // if simulation box has changed, call fcs_tune()
+
+ if (box_has_changed()) {
+ setup_handle();
+ result = fcs_tune(fcs,nlocal,xpbc,q);
+ check_result(result);
+ }
+
// invoke ScaFaCoS solver
result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot);
@@ -278,14 +277,6 @@ void Scafacos::compute(int eflag, int vflag)
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
}
-/* ----------------------------------------------------------------------
- pack local coords into xpbc, enforcing PBC
-------------------------------------------------------------------------- */
-
-void Scafacos::pack_coords()
-{
-}
-
/* ---------------------------------------------------------------------- */
int Scafacos::modify_param(int narg, char **arg)
--
GitLab
From c23534019c5077ef208c3a36b439095e5376f5c6 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 21 Aug 2018 17:28:42 -0600
Subject: [PATCH 104/332] fixed typo in example file name
---
.../{data.hammersley_shphere => data.hammersley_sphere} | 6 +++---
examples/USER/scafacos/in.scafacos.hsph.direct | 2 +-
examples/USER/scafacos/in.scafacos.hsph.fmm | 2 +-
examples/USER/scafacos/in.scafacos.hsph.p2nfft | 2 +-
4 files changed, 6 insertions(+), 6 deletions(-)
rename examples/USER/scafacos/{data.hammersley_shphere => data.hammersley_sphere} (99%)
diff --git a/examples/USER/scafacos/data.hammersley_shphere b/examples/USER/scafacos/data.hammersley_sphere
similarity index 99%
rename from examples/USER/scafacos/data.hammersley_shphere
rename to examples/USER/scafacos/data.hammersley_sphere
index e0d067adfb..0d238ebf8f 100644
--- a/examples/USER/scafacos/data.hammersley_shphere
+++ b/examples/USER/scafacos/data.hammersley_sphere
@@ -4,9 +4,9 @@ LAMMPS Description
1 atom types
--50.5 51.5 xlo xhi
--50.5 51.5 ylo yhi
--50.5 51.5 zlo zhi
+-51.5 51.5 xlo xhi
+-51.5 51.5 ylo yhi
+-51.5 51.5 zlo zhi
Masses
diff --git a/examples/USER/scafacos/in.scafacos.hsph.direct b/examples/USER/scafacos/in.scafacos.hsph.direct
index 60448880ec..3688b5157c 100644
--- a/examples/USER/scafacos/in.scafacos.hsph.direct
+++ b/examples/USER/scafacos/in.scafacos.hsph.direct
@@ -3,7 +3,7 @@
units lj
atom_style charge
-read_data data.hammersley_shphere
+read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
diff --git a/examples/USER/scafacos/in.scafacos.hsph.fmm b/examples/USER/scafacos/in.scafacos.hsph.fmm
index 515809dbde..48a60a4b8b 100644
--- a/examples/USER/scafacos/in.scafacos.hsph.fmm
+++ b/examples/USER/scafacos/in.scafacos.hsph.fmm
@@ -3,7 +3,7 @@
units lj
atom_style charge
-read_data data.hammersley_shphere
+read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
diff --git a/examples/USER/scafacos/in.scafacos.hsph.p2nfft b/examples/USER/scafacos/in.scafacos.hsph.p2nfft
index d690a29e49..a91f8f91c7 100644
--- a/examples/USER/scafacos/in.scafacos.hsph.p2nfft
+++ b/examples/USER/scafacos/in.scafacos.hsph.p2nfft
@@ -3,7 +3,7 @@
units lj
atom_style charge
-read_data data.hammersley_shphere
+read_data data.hammersley_sphere
change_box all boundary f f f
velocity all create 1.5 49893
--
GitLab
From bfd711ad12e2a6fd56aba5ff69de7efc8d025fcc Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Tue, 21 Aug 2018 17:29:38 -0600
Subject: [PATCH 105/332] fixed missing initialization of xpbc as well as
deallocation in constructor
---
src/USER-SCAFACOS/scafacos.cpp | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index d68d3db323..f3e8ce64f7 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -74,6 +74,7 @@ Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
initialized = 0;
maxatom = 0;
+ xpbc = NULL;
epot = NULL;
efield = NULL;
}
@@ -84,6 +85,7 @@ Scafacos::~Scafacos()
{
delete [] method;
+ memory->destroy(xpbc);
memory->destroy(epot);
memory->destroy(efield);
@@ -221,10 +223,12 @@ void Scafacos::compute(int eflag, int vflag)
// pack coords into xpbc and apply PBC
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
- int j = 0;
+ //int j = 0;
for (int i = 0; i < nlocal; i++) {
- domain->remap(&xpbc[j]);
- j += 3;
+ if (domain->xperiodic) domain->remap(&xpbc[3*i]);
+ if (domain->yperiodic) domain->remap(&xpbc[3*i+1]);
+ if (domain->zperiodic) domain->remap(&xpbc[3*i+2]);
+ //j += 3;
}
// if simulation box has changed, call fcs_tune()
--
GitLab
From fd0b041e0e06091085afc4a9236abd44ff043eb8 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 21 Aug 2018 21:10:34 -0600
Subject: [PATCH 106/332] remove debugging comments
---
src/USER-MISC/fix_bond_react.cpp | 2 --
1 file changed, 2 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index d529848e39..d71a31f566 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1568,7 +1568,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
- printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
error->one(FLERR,"Bond type affected by reaction too close to template edge");
}
}
@@ -1579,7 +1578,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
if (onemol_batom == equivalences[i][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
- printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
error->one(FLERR,"Bond type affected by reaction too close to template edge");
}
}
--
GitLab
From 2baa0b34521f43d401930cffbb1abda1042b51d1 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Wed, 22 Aug 2018 03:32:17 -0600
Subject: [PATCH 107/332] nasty little bug
---
src/USER-MISC/fix_bond_react.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index d71a31f566..5ce1f11475 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -2101,7 +2101,7 @@ void FixBondReact::update_everything()
nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
}
- for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+ for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
}
special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];
--
GitLab
From 87afaa44fdef4992d900864ee7519935287ef812 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 09:41:12 -0400
Subject: [PATCH 108/332] add notes on compiling LAMMPS for windows
---
doc/src/Build.txt | 4 +-
doc/src/Build_windows.txt | 83 +++++++++++++++++++++++++++++++++++++++
doc/src/lammps.book | 1 +
3 files changed, 87 insertions(+), 1 deletion(-)
create mode 100644 doc/src/Build_windows.txt
diff --git a/doc/src/Build.txt b/doc/src/Build.txt
index 1046171de1..df30af36f5 100644
--- a/doc/src/Build.txt
+++ b/doc/src/Build.txt
@@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
Build_settings
Build_package
Build_extras
+ Build_windows
END_RST -->
@@ -39,7 +40,8 @@ END_RST -->
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html :all(b)
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html :all(b)
If you have problems building LAMMPS, it is often due to software
issues on your local machine. If you can, find a local expert to
diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt
new file mode 100644
index 0000000000..4d4efb398f
--- /dev/null
+++ b/doc/src/Build_windows.txt
@@ -0,0 +1,83 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#general
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross
+
+:line
+
+General remarks :h4,link(general)
+
+LAMMPS is developed and tested primarily on Linux machines. The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers). If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler. In case of problems, you are recommended to
+contact somebody with experience in using cygwin. If you come across
+portability problems requiring changes to the LAMMPS source code, or
+figure out corrections yourself, please report them on the lammps-users
+mailing list, or file them as an issue or pull request on the LAMMPS
+github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows. Please keep in mind, though, that this only
+applies to compiling. Whether the resulting binaries do work correctly
+is no tested. The LAMMPS developers rely on the feedback of the users
+of the precompiled LAMMPS packages for Windows to become aware of
+issues and then try to apply corrections, if possible.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index f1ff39d80b..47d05570be 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -25,6 +25,7 @@ Build_basics.html
Build_settings.html
Build_package.html
Build_extras.html
+Build_windows.html
Run_head.html
Run_basics.html
Run_options.html
--
GitLab
From c4bda59f9ac8ea225a86131cd1781bc41a10dbf6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 09:41:29 -0400
Subject: [PATCH 109/332] make the statement, that the group id is ignored more
visible
---
doc/src/compute_pair.txt | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index a2c25fcc8d..b309019e30 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -27,7 +27,9 @@ compute 1 all pair reax :pre
Define a computation that extracts additional values calculated by a
pair style, and makes them accessible for output or further processing
-by other commands. The group specified for this command is ignored.
+by other commands.
+
+NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
--
GitLab
From fc47b8c6ddd462794018230c31979c7be4d1f1d8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 09:51:29 -0400
Subject: [PATCH 110/332] some more tweaks and epxlanations for windows support
---
doc/src/Build_windows.txt | 40 ++++++++++++++++++++++++++-------------
1 file changed, 27 insertions(+), 13 deletions(-)
diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt
index 4d4efb398f..e847711705 100644
--- a/doc/src/Build_windows.txt
+++ b/doc/src/Build_windows.txt
@@ -9,14 +9,14 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Notes for building LAMMPS on Windows :h3
-"General remarks"_#general
+"General remarks"_#generic
"Running Linux on Windows"_#linux
"Using GNU GCC ported to Windows"_#gnu
"Using a cross-compiler"_#cross
:line
-General remarks :h4,link(general)
+General remarks :h4,link(generic)
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
@@ -53,12 +53,20 @@ are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. The CMake build system is untested
for this; you will have to request that makefiles are generated and
-manually set the compiler. In case of problems, you are recommended to
-contact somebody with experience in using cygwin. If you come across
-portability problems requiring changes to the LAMMPS source code, or
-figure out corrections yourself, please report them on the lammps-users
-mailing list, or file them as an issue or pull request on the LAMMPS
-github project.
+manually set the compiler.
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin. If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
Using a cross-compiler :h4,link(cross)
@@ -68,11 +76,17 @@ need to do the compilation on Windows, please consider using a Linux
to Windows cross-compiler. This is how currently the Windows binary
packages are created by the LAMMPS developers. Because of that, this is
probably the currently best tested and supported way to build LAMMPS
-executables for Windows. Please keep in mind, though, that this only
-applies to compiling. Whether the resulting binaries do work correctly
-is no tested. The LAMMPS developers rely on the feedback of the users
-of the precompiled LAMMPS packages for Windows to become aware of
-issues and then try to apply corrections, if possible.
+executables for Windows. There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers. We instead rely on the feedback of the users
+of these precompiled LAMMPS packages for Windows. We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
Native Visual C++ support :h4,link(native)
--
GitLab
From 9d4994b38328030935dcdb5a6e6e5585a2719e96 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 22 Aug 2018 10:08:56 -0400
Subject: [PATCH 111/332] Add missing bullet points
---
doc/src/Build_windows.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt
index e847711705..da257ccbc8 100644
--- a/doc/src/Build_windows.txt
+++ b/doc/src/Build_windows.txt
@@ -12,7 +12,7 @@ Notes for building LAMMPS on Windows :h3
"General remarks"_#generic
"Running Linux on Windows"_#linux
"Using GNU GCC ported to Windows"_#gnu
-"Using a cross-compiler"_#cross
+"Using a cross-compiler"_#cross :ul
:line
--
GitLab
From b47e49223377d4ff6779e712bae54bbddc3596cf Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 08:45:41 -0600
Subject: [PATCH 112/332] patch 22Aug18
---
doc/src/Manual.txt | 4 ++--
src/version.h | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index c5e5aff61b..ad3e66a4b2 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="16 Aug 2018 version">
+<META NAME="docnumber" CONTENT="22 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-16 Aug 2018 version :c,h2
+22 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/src/version.h b/src/version.h
index db73df1ad1..2192b25d91 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Aug 2018"
+#define LAMMPS_VERSION "22 Aug 2018"
--
GitLab
From f466c6407129641e9e9c29ab57f99f826a68cb53 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 09:21:54 -0600
Subject: [PATCH 113/332] enable merge to current GH master
---
doc/src/Packages_details.txt | 1552 +++++++---------------------------
1 file changed, 303 insertions(+), 1249 deletions(-)
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 4bbb235245..892774be38 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -17,100 +17,97 @@ library it requires. It also gives links to documentation, example
scripts, and pictures/movies (if available) that illustrate use of the
package.
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
+make). See the "Build package"_Build_package.html doc page for more
+info. A few packages may require additional steps; this is indicated
+in the descriptions below. The "Build extras"_Build_extras.html doc
+page gives those details.
+
NOTE: To see the complete list of commands a package adds to LAMMPS,
you can examine the files in its src directory, e.g. "ls
src/GRANULAR". Files with names that start with fix, compute, atom,
pair, bond, angle, etc correspond to commands with the same style name
as contained in the file name.
-"ASPHERE"_#ASPHERE,
-"BODY"_#BODY,
-"CLASS2"_#CLASS2,
-"COLLOID"_#COLLOID,
-"COMPRESS"_#COMPRESS,
-"CORESHELL"_#CORESHELL,
-"DIPOLE"_#DIPOLE,
-"GPU"_#GPU,
-"GRANULAR"_#GRANULAR,
-"KIM"_#KIM,
-"KOKKOS"_#KOKKOS,
-"KSPACE"_#KSPACE,
-"LATTE"_#LATTE,
-"MANYBODY"_#MANYBODY,
-"MC"_#MC,
-"MEAM"_#MEAM,
-"MISC"_#MISC,
-"MOLECULE"_#MOLECULE,
-"MPIIO"_#MPIIO,
-"MSCG"_#MSCG,
-"OPT"_#OPT,
-"PERI"_#PERI,
-"POEMS"_#POEMS,
-"PYTHON"_#PYTHON,
-"QEQ"_#QEQ,
-"REAX"_#REAX,
-"REPLICA"_#REPLICA,
-"RIGID"_#RIGID,
-"SHOCK"_#SHOCK,
-"SNAP"_#SNAP,
-"SPIN"_#SPIN,
-"SRD"_#SRD,
-"VORONOI"_#VORONOI :tb(c=6,ea=c)
-
-"USER-ATC"_#USER-ATC,
-"USER-AWPMD"_#USER-AWPMD,
-"USER-BOCS"_#USER-BOCS,
-"USER-CGDNA"_#USER-CGDNA,
-"USER-CGSDK"_#USER-CGSDK,
-"USER-COLVARS"_#USER-COLVARS,
-"USER-DIFFRACTION"_#USER-DIFFRACTION,
-"USER-DPD"_#USER-DPD,
-"USER-DRUDE"_#USER-DRUDE,
-"USER-EFF"_#USER-EFF,
-"USER-FEP"_#USER-FEP,
-"USER-H5MD"_#USER-H5MD,
-"USER-INTEL"_#USER-INTEL,
-"USER-LB"_#USER-LB,
-"USER-MANIFOLD"_#USER-MANIFOLD,
-"USER-MEAMC"_#USER-MEAMC,
-"USER-MESO"_#USER-MESO,
-"USER-MGPT"_#USER-MGPT,
-"USER-MISC"_#USER-MISC,
-"USER-MOFFF"_#USER-MOFFF,
-"USER-MOLFILE"_#USER-MOLFILE,
-"USER-NETCDF"_#USER-NETCDF,
-"USER-OMP"_#USER-OMP,
-"USER-PHONON"_#USER-PHONON,
-"USER-QMMM"_#USER-QMMM,
-"USER-QTB"_#USER-QTB,
-"USER-QUIP"_#USER-QUIP,
-"USER-REAXC"_#USER-REAXC,
-"USER-SCAFACOS"_#USER-SCAFACOS,
-"USER-SMD"_#USER-SMD,
-"USER-SMTBQ"_#USER-SMTBQ,
-"USER-SPH"_#USER-SPH,
-"USER-TALLY"_#USER-TALLY,
-"USER-UEF"_#USER-UEF,
-"USER-VTK"_#USER-VTK :tb(c=6,ea=c)
-
-:line
-:line
-
-ASPHERE package :link(ASPHERE),h4
+"ASPHERE"_#PKG-ASPHERE,
+"BODY"_#PKG-BODY,
+"CLASS2"_#PKG-CLASS2,
+"COLLOID"_#PKG-COLLOID,
+"COMPRESS"_#PKG-COMPRESS,
+"CORESHELL"_#PKG-CORESHELL,
+"DIPOLE"_#PKG-DIPOLE,
+"GPU"_#PKG-GPU,
+"GRANULAR"_#PKG-GRANULAR,
+"KIM"_#PKG-KIM,
+"KOKKOS"_#PKG-KOKKOS,
+"KSPACE"_#PKG-KSPACE,
+"LATTE"_#PKG-LATTE,
+"MANYBODY"_#PKG-MANYBODY,
+"MC"_#PKG-MC,
+"MEAM"_#PKG-MEAM,
+"MISC"_#PKG-MISC,
+"MOLECULE"_#PKG-MOLECULE,
+"MPIIO"_#PKG-MPIIO,
+"MSCG"_#PKG-MSCG,
+"OPT"_#PKG-OPT,
+"PERI"_#PKG-PERI,
+"POEMS"_#PKG-POEMS,
+"PYTHON"_#PKG-PYTHON,
+"QEQ"_#PKG-QEQ,
+"REAX"_#PKG-REAX,
+"REPLICA"_#PKG-REPLICA2,
+"RIGID"_#PKG-RIGID,
+"SHOCK"_#PKG-SHOCK,
+"SNAP"_#PKG-SNAP,
+"SPIN"_#PKG-SPIN,
+"SRD"_#PKG-SRD,
+"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
+
+"USER-ATC"_#PKG-USER-ATC,
+"USER-AWPMD"_#PKG-USER-AWPMD,
+"USER-BOCS"_#PKG-USER-BOCS,
+"USER-CGDNA"_#PKG-USER-CGDNA,
+"USER-CGSDK"_#PKG-USER-CGSDK,
+"USER-COLVARS"_#PKG-USER-COLVARS,
+"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
+"USER-DPD"_#PKG-USER-DPD,
+"USER-DRUDE"_#PKG-USER-DRUDE,
+"USER-EFF"_#PKG-USER-EFF,
+"USER-FEP"_#PKG-USER-FEP,
+"USER-H5MD"_#PKG-USER-H5MD,
+"USER-INTEL"_#PKG-USER-INTEL,
+"USER-LB"_#PKG-USER-LB,
+"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
+"USER-MEAMC"_#PKG-USER-MEAMC,
+"USER-MESO"_#PKG-USER-MESO,
+"USER-MGPT"_#PKG-USER-MGPT,
+"USER-MISC"_#PKG-USER-MISC,
+"USER-MOFFF"_#PKG-USER-MOFFF,
+"USER-MOLFILE"_#PKG-USER-MOLFILE,
+"USER-NETCDF"_#PKG-USER-NETCDF,
+"USER-OMP"_#PKG-USER-OMP,
+"USER-PHONON"_#PKG-USER-PHONON,
+"USER-QMMM"_#PKG-USER-QMMM,
+"USER-QTB"_#PKG-USER-QTB,
+"USER-QUIP"_#PKG-USER-QUIP,
+"USER-REAXC"_#PKG-USER-REAXC,
+"USER-SMD"_#PKG-USER-SMD,
+"USER-SMTBQ"_#PKG-USER-SMTBQ,
+"USER-SPH"_#PKG-USER-SPH,
+"USER-TALLY"_#PKG-USER-TALLY,
+"USER-UEF"_#PKG-USER-UEF,
+"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+
+:line
+
+ASPHERE package :link(PKG-ASPHERE),h4
[Contents:]
Computes, time-integration fixes, and pair styles for aspherical
particle models including ellipsoids, 2d lines, and 3d triangles.
-[Install or un-install:]
-
-make yes-asphere
-make machine :pre
-
-make no-asphere
-make machine :pre
-
[Supporting info:]
src/ASPHERE: filenames -> commands
@@ -126,7 +123,7 @@ http://lammps.sandia.gov/movies.html#tri :ul
:line
-BODY package :link(BODY),h4
+BODY package :link(PKG-BODY),h4
[Contents:]
@@ -135,14 +132,6 @@ time-integration fixes, pair styles, as well as the body styles
themselves. See the "Howto body"_Howto_body.html doc page for an
overview.
-[Install or un-install:]
-
-make yes-body
-make machine :pre
-
-make no-body
-make machine :pre
-
[Supporting info:]
src/BODY filenames -> commands
@@ -154,21 +143,13 @@ examples/body :ul
:line
-CLASS2 package :link(CLASS2),h4
+CLASS2 package :link(PKG-CLASS2),h4
[Contents:]
Bond, angle, dihedral, improper, and pair styles for the COMPASS
CLASS2 molecular force field.
-[Install or un-install:]
-
-make yes-class2
-make machine :pre
-
-make no-class2
-make machine :pre
-
[Supporting info:]
src/CLASS2: filenames -> commands
@@ -180,7 +161,7 @@ src/CLASS2: filenames -> commands
:line
-COLLOID package :link(COLLOID),h4
+COLLOID package :link(PKG-COLLOID),h4
[Contents:]
@@ -193,14 +174,6 @@ simplified approximation to Stokesian dynamics.
which were created by Amit Kumar and Michael Bybee from Jonathan
Higdon's group at UIUC.
-[Install or un-install:]
-
-make yes-colloid
-make machine :pre
-
-make no-colloid
-make machine :pre
-
[Supporting info:]
src/COLLOID: filenames -> commands
@@ -215,7 +188,7 @@ examples/srd :ul
:line
-COMPRESS package :link(COMPRESS),h4
+COMPRESS package :link(PKG-COMPRESS),h4
[Contents:]
@@ -227,19 +200,11 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that building with this package assumes you have the zlib
-compression library available on your system. The LAMMPS build uses
-the settings in the lib/compress/Makefile.lammps file in the
-compile/link process. You should only need to edit this file if the
-LAMMPS build fails on your system.
+[Install:]
-make yes-compress
-make machine :pre
-
-make no-compress
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -253,7 +218,7 @@ lib/compress/README
:line
-CORESHELL package :link(CORESHELL),h4
+CORESHELL package :link(PKG-CORESHELL),h4
[Contents:]
@@ -267,14 +232,6 @@ this package.
[Author:] Hendrik Heenen (Technical U of Munich).
-[Install or un-install:]
-
-make yes-coreshell
-make machine :pre
-
-make no-coreshell
-make machine :pre
-
[Supporting info:]
src/CORESHELL: filenames -> commands
@@ -288,21 +245,13 @@ examples/coreshell :ul
:line
-DIPOLE package :link(DIPOLE),h4
+DIPOLE package :link(PKG-DIPOLE),h4
[Contents:]
An atom style and several pair styles for point dipole models with
short-range or long-range interactions.
-[Install or un-install:]
-
-make yes-dipole
-make machine :pre
-
-make no-dipole
-make machine :pre
-
[Supporting info:]
src/DIPOLE: filenames -> commands
@@ -314,7 +263,7 @@ examples/dipole :ul
:line
-GPU package :link(GPU),h4
+GPU package :link(PKG-GPU),h4
[Contents:]
@@ -326,66 +275,17 @@ and only the CUDA versions are regularly tested. The "Speed
gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
-package, which has GPU-enabled styles.
+gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
+also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and CUDA files. You can
-do this manually if you prefer; follow the instructions in
-lib/gpu/README. Please note, that the GPU library uses MPI calls, so
-you have to make certain to use the same MPI library (or the STUBS
-library) settings as the main LAMMPS code. That same applies to the
--DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
-
-You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/gpu/Install.py script with the specified args:
-
-make lib-gpu # print help message
-make lib-gpu args="-b" # build GPU library with default Makefile.linux
-make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
-
-Note that this procedure through the '-m machine' flag starts with one of
-the existing Makefile.machine files in lib/gpu. For your convenience,
-machine makefiles for "mpi" and "serial" are provided, which have the
-same settings as the corresponding machine makefiles in the main LAMMPS
-source folder. In addition you can alter 4 important settings in that
-Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
-new Makefile, if desired:
-
-CUDA_HOME = where NVIDIA CUDA software is installed on your system
-CUDA_ARCH = what GPU hardware you have (see help message for details)
-CUDA_PRECISION = precision (double, mixed, single)
-EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
-
-If the library build is successful, at least 3 files should be created:
-lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
-The latter has settings that enable LAMMPS to link with CUDA libraries.
-If the settings in Makefile.lammps for your machine are not correct,
-the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
-be edited.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-gpu
-make machine :pre
-
-make no-gpu
-make machine :pre
-
-NOTE: If you re-build the GPU library in lib/gpu, you should always
-un-install the GPU package, then re-install it and re-build LAMMPS.
-This is because the compilation of files in the GPU package use the
-library settings from the lib/gpu/Makefile.machine used to build the
-GPU library.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -393,16 +293,16 @@ src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
-"Speed gpu"_Speed_gpu.html.html
-"Section 2.6 -sf gpu"_Section_start.html#start_6
-"Section 2.6 -pk gpu"_Section_start.html#start_6
+"Speed gpu"_Speed_gpu.html
+"Section 2.6 -sf gpu"_Run_options.html
+"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-GRANULAR package :link(GRANULAR),h4
+GRANULAR package :link(PKG-GRANULAR),h4
[Contents:]
@@ -410,14 +310,6 @@ Pair styles and fixes for finite-size granular particles, which
interact with each other and boundaries via frictional and dissipative
potentials.
-[Install or un-install:]
-
-make yes-granular
-make machine :pre
-
-make no-granular
-make machine :pre
-
[Supporting info:]
src/GRANULAR: filenames -> commands
@@ -437,7 +329,7 @@ http://lammps.sandia.gov/movies.html#granregion :ul
:line
-KIM package :link(KIM),h4
+KIM package :link(PKG-KIM),h4
[Contents:]
@@ -457,48 +349,11 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the KIM library and include the KIM models that you want to
-use. You can do this manually if you prefer; follow the instructions
-in lib/kim/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/kim/Install.py script with the specified args.
-
-make lib-kim # print help message
-make lib-kim args="-b " # (re-)install KIM API lib with only example models
-make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
-make lib-kim args="-b -a everything" # install KIM API lib with all models
-make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+[Install:]
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file. Also note that installing the KIM API
-library with all its models, may take around 30 min to build. Of
-course you only need to do that once.
-
-See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-kim
-make machine :pre
-
-make no-kim
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -510,7 +365,7 @@ examples/kim :ul
:line
-KOKKOS package :link(KOKKOS),h4
+KOKKOS package :link(PKG-KOKKOS),h4
[Contents:]
@@ -522,11 +377,16 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs, KNLs, and GPUs.
+switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
[Authors:] The KOKKOS package was created primarily by Christian Trott
and Stan Moore (Sandia), with contributions from other folks as well.
@@ -535,53 +395,11 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
-[Install or un-install:]
-
-For the KOKKOS package, you have 3 choices when building. You can
-build with either CPU or KNL or GPU support. Each choice requires
-additional settings in your Makefile.machine for the KOKKOS_DEVICES
-and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos*
-files for examples.
-
-For multicore CPUs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
-
-For Intel KNLs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL :pre
-
-For NVIDIA GPUs using CUDA:
-
-KOKKOS_DEVICES = Cuda
-KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre
-
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx. The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
-files.
-
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC = mpicxx :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (CPU or KNL or GPU). You need to build LAMMPS once for each
-hardware target, to produce a separate executable. Also note that we
-do not recommend building with other acceleration packages installed
-(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS.
-
-make yes-kokkos
-make machine :pre
+[Install:]
-make no-kokkos
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -590,16 +408,16 @@ src/KOKKOS/README
lib/kokkos/README
"Speed packages"_Speed_packages.html
"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Section_start.html#start_6
-"Section 2.6 -sf kk"_Section_start.html#start_6
-"Section 2.6 -pk kokkos"_Section_start.html#start_6
+"Section 2.6 -k on ..."_Run_options.html
+"Section 2.6 -sf kk"_Run_options.html
+"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-KSPACE package :link(KSPACE),h4
+KSPACE package :link(PKG-KSPACE),h4
[Contents:]
@@ -608,20 +426,14 @@ which compute the corresponding short-range pairwise Coulombic
interactions. These include Ewald, particle-particle particle-mesh
(PPPM), and multilevel summation method (MSM) solvers.
-[Install or un-install:]
+[Install:]
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a
-vendor-supplied FFT library. See step 6 of "Section
-2.2.2"_Section_start.html#start_2_2 of the manual for details on how
-to select different FFT options in your machine Makefile.
-
-make yes-kspace
-make machine :pre
-
-make no-kspace
-make machine :pre
+vendor-supplied FFT library. See the "Build
+settings"_Build_settings.html doc page for details on how to select
+different FFT options for your LAMPMS build.
[Supporting info:]
@@ -638,7 +450,7 @@ bench/in.rhodo :ul
:line
-LATTE package :link(LATTE),h4
+LATTE package :link(PKG-LATTE),h4
[Contents:]
@@ -656,36 +468,11 @@ description is given with the "fix latte"_fix_latte.html command.
itself is developed at Los Alamos National Laboratory by Marc
Cawkwell, Anders Niklasson, and Christian Negre.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the LATTE library. You can do this manually if you prefer;
-follow the instructions in lib/latte/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invokes the lib/latte/Install.py script with the specified
-args:
-
-make lib-latte # print help message
-make lib-latte args="-b" # download and build in lib/latte/LATTE-master
-make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran" # download and build in lib/latte and
- # copy Makefile.lammps.gfortran to Makefile.lammps
-:pre
+[Install:]
-Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink.o", are created in lib/latte to point into the LATTE home dir.
-When LAMMPS builds in src it will use these links. You should
-also check that the Makefile.lammps file you create is appropriate
-for the compiler you use on your system to build LATTE.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-latte
-make machine :pre
-
-make no-latte
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -698,21 +485,13 @@ examples/latte
:line
-MANYBODY package :link(MANYBODY),h4
+MANYBODY package :link(PKG-MANYBODY),h4
[Contents:]
A variety of manybody and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-[Install or un-install:]
-
-make yes-manybody
-make machine :pre
-
-make no-manybody
-make machine :pre
-
[Supporting info:]
src/MANYBODY: filenames -> commands
@@ -727,7 +506,7 @@ bench/in.eam :ul
:line
-MC package :link(MC),h4
+MC package :link(PKG-MC),h4
[Contents:]
@@ -736,14 +515,6 @@ attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
-[Install or un-install:]
-
-make yes-mc
-make machine :pre
-
-make no-mc
-make machine :pre
-
[Supporting info:]
src/MC: filenames -> commands
@@ -757,51 +528,26 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
:line
-MEAM package :link(MEAM),h4
+MEAM package :link(PKG-MEAM),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential.
-Please note that the MEAM package has been superseded by the
-"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
-of the MEAM package to C++. USER-MEAMC contains additional
-optimizations making it run faster than MEAM on most machines,
-while providing the identical features and USER interface.
+Please note that the use of the MEAM package is discouraged as
+it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
+which is a direct translation of the MEAM package to C++.
+USER-MEAMC contains additional optimizations making it run faster
+than MEAM on most machines, while providing the identical features
+and user interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-MEAM library in lib/meam. You can do this manually if you prefer;
-follow the instructions in lib/meam/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/meam/Install.py script with the specified args:
-
-make lib-meam # print help message
-make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
-
-The build should produce two files: lib/meam/libmeam.a and
-lib/meam/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (MEAM library). Typically the two compilers used for LAMMPS
-and the MEAM library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/meam/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-meam
-make machine :pre
-
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
@@ -817,7 +563,7 @@ examples/meam :ul
:line
-MISC package :link(MISC),h4
+MISC package :link(PKG-MISC),h4
[Contents:]
@@ -828,14 +574,6 @@ listing, "ls src/MISC", to see the list of commands.
NOTE: the MISC package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-[Install or un-install:]
-
-make yes-misc
-make machine :pre
-
-make no-misc
-make machine :pre
-
[Supporting info:]
src/MISC: filenames -> commands
@@ -852,7 +590,7 @@ http://lammps.sandia.gov/movies.html#evaporation :ul
:line
-MOLECULE package :link(MOLECULE),h4
+MOLECULE package :link(PKG-MOLECULE),h4
[Contents:]
@@ -861,14 +599,6 @@ that are used to model molecular systems with fixed covalent bonds.
The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
force fields, and a TIP4P water model.
-[Install or un-install:]
-
-make yes-molecule
-make machine :pre
-
-make no-molecule
-make machine :pre
-
[Supporting info:]
src/MOLECULE: filenames -> commands
@@ -889,7 +619,7 @@ bench/in.rhodo :ul
:line
-MPIIO package :link(MPIIO),h4
+MPIIO package :link(PKG-MPIIO),h4
[Contents:]
@@ -898,18 +628,6 @@ MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
-[Install or un-install:]
-
-Note that MPIIO is part of the standard message-passing interface
-(MPI) library, so you should not need any additional compiler or link
-settings, beyond what LAMMPS normally uses for MPI on your system.
-
-make yes-mpiio
-make machine :pre
-
-make no-mpiio
-make machine :pre
-
[Supporting info:]
src/MPIIO: filenames -> commands
@@ -920,7 +638,7 @@ src/MPIIO: filenames -> commands
:line
-MSCG package :link(mscg),h4
+MSCG package :link(PKG-mscg),h4
[Contents:]
@@ -937,39 +655,11 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the MS-CG library. Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler and that the GSL
-(GNU Scientific Library) headers and libraries are installed on your
-machine. See the lib/mscg/README and MSCG/Install files for more details.
-
-Assuming these libraries are in place, you can do the download and
-build of MS-CG manually if you prefer; follow the instructions in
-lib/mscg/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/mscg/Install.py script with the specified args:
-
-make lib-mscg # print help message
-make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make serial"
-make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make mpi"
-make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
-to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links.
-You should not need to edit the lib/mscg/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-mscg
-make machine :pre
-
-make no-mscg
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -980,7 +670,7 @@ examples/mscg :ul
:line
-OPT package :link(OPT),h4
+OPT package :link(PKG-OPT),h4
[Contents:]
@@ -990,40 +680,31 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
-"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
+switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
-[Install or un-install:]
-
-make yes-opt
-make machine :pre
-
-make no-opt
-make machine :pre
+[Install:]
-NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package when using Intel compilers. It should be added to
-the CCFLAGS line of your Makefile.machine. See Makefile.opt in
-src/MAKE/OPTIONS for an example.
-
-CCFLAGS: add -restrict for Intel compilers :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/OPT: filenames -> commands
"Speed packages"_Speed_packages.html
"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Section_start.html#start_6
+"Section 2.6 -sf opt"_Run_options.html
"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-PERI package :link(PERI),h4
+PERI package :link(PKG-PERI),h4
[Contents:]
@@ -1036,14 +717,6 @@ model.
Additional Peridynamics models were added by Rezwanur Rahman and John
Foster (UTSA).
-[Install or un-install:]
-
-make yes-peri
-make machine :pre
-
-make no-peri
-make machine :pre
-
[Supporting info:]
src/PERI: filenames -> commands
@@ -1059,7 +732,7 @@ http://lammps.sandia.gov/movies.html#peri :ul
:line
-POEMS package :link(POEMS),h4
+POEMS package :link(PKG-POEMS),h4
[Contents:]
@@ -1071,35 +744,11 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-POEMS library in lib/poems. You can do this manually if you prefer;
-follow the instructions in lib/poems/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/poems/Install.py script with the specified args:
-
-make lib-poems # print help message
-make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
-make lib-poems args="-m icc" # build with Intel icc compiler :pre
+[Install:]
-The build should produce two files: lib/poems/libpoems.a and
-lib/poems/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-POEMS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/poems/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-poems
-make machine :pre
-
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1111,7 +760,7 @@ examples/rigid :ul
:line
-PYTHON package :link(PYTHON),h4
+PYTHON package :link(PKG-PYTHON),h4
[Contents:]
@@ -1119,35 +768,30 @@ A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and all the "Python"_Python.html doc pages for
-other ways to use LAMMPS and Python together.
-
-[Install or un-install:]
-
-make yes-python
-make machine :pre
-
-make no-python
-make machine :pre
+LAMMPS in this manner and all the "Python"_Python_head.html doc pages
+for other ways to use LAMMPS and Python together.
NOTE: Building with the PYTHON package assumes you have a Python
shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
-lib/python/README for more details. Note that the build uses the
-lib/python/Makefile.lammps file in the compile/link process. You
-should only need to create a new Makefile.lammps.* file (and copy it
-to Makefile.lammps) if the LAMMPS build fails.
+lib/python/README for more details.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/PYTHON: filenames -> commands
-"Python call"_Python.html
+"Python call"_Python_head.html
lib/python/README
examples/python :ul
:line
-QEQ package :link(QEQ),h4
+QEQ package :link(PKG-QEQ),h4
[Contents:]
@@ -1155,14 +799,6 @@ Several fixes for performing charge equilibration (QEq) via different
algorithms. These can be used with pair styles that perform QEq as
part of their formulation.
-[Install or un-install:]
-
-make yes-qeq
-make machine :pre
-
-make no-qeq
-make machine :pre
-
[Supporting info:]
src/QEQ: filenames -> commands
@@ -1172,49 +808,27 @@ examples/streitz :ul
:line
-REAX package :link(REAX),h4
+REAX package :link(PKG-REAX),h4
[Contents:]
+NOTE: the use of the REAX package is discouraged, as it is no longer
+maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
+and possibly the KOKKOS enabled variant of that, which has a more robust
+memory management.
+
A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field. See the
-"USER-REAXC package"_#USER-REAXC for an alternate implementation in
-C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for
-monitoring molecules as bonds are created and destroyed.
+potential, which is a universal reactive force field. Also included is
+a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
+as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-REAX library in lib/reax. You can do this manually if you prefer;
-follow the instructions in lib/reax/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/reax/Install.py script with the specified args:
-
-make lib-reax # print help message
-make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library). Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-reax
-make machine :pre
+[Install:]
-make no-reax
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1226,7 +840,7 @@ examples/reax :ul
:line
-REPLICA package :link(REPLICA),h4
+REPLICA package :link(PKG-REPLICA2),h4
[Contents:]
@@ -1240,14 +854,6 @@ verlet/split algorithm for performing long-range Coulombics on one set
of processors, and the remainder of the force field calcalation on
another set.
-[Install or un-install:]
-
-make yes-replica
-make machine :pre
-
-make no-replica
-make machine :pre
-
[Supporting info:]
src/REPLICA: filenames -> commands
@@ -1263,7 +869,7 @@ examples/tad :ul
:line
-RIGID package :link(RIGID),h4
+RIGID package :link(PKG-RIGID),h4
[Contents:]
@@ -1272,16 +878,6 @@ particles. This includes SHAKE and RATTLE, as well as varous
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
-To install/build:
-
-make yes-rigid
-make machine :pre
-
-To un-install/re-build:
-
-make no-rigid
-make machine :pre
-
[Supporting info:]
src/RIGID: filenames -> commands
@@ -1297,21 +893,13 @@ http://lammps.sandia.gov/movies.html#star :ul
:line
-SHOCK package :link(SHOCK),h4
+SHOCK package :link(PKG-SHOCK),h4
[Contents:]
Fixes for running impact simulations where a shock-wave passes through
a material.
-[Install or un-install:]
-
-make yes-shock
-make machine :pre
-
-make no-shock
-make machine :pre
-
[Supporting info:]
src/SHOCK: filenames -> commands
@@ -1324,7 +912,7 @@ examples/msst :ul
:line
-SNAP package :link(SNAP),h4
+SNAP package :link(PKG-SNAP),h4
[Contents:]
@@ -1335,14 +923,6 @@ computes which analyze attributes of the potential.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-make yes-snap
-make machine :pre
-
-make no-snap
-make machine :pre
-
[Supporting info:]
src/SNAP: filenames -> commands
@@ -1354,7 +934,7 @@ examples/snap :ul
:line
-SPIN package :link(SPIN),h4
+SPIN package :link(PKG-SPIN),h4
[Contents:]
@@ -1363,18 +943,10 @@ the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
-[Install or un-install:]
-
-make yes-spin
-make machine :pre
-
-make no-spin
-make machine :pre
-
[Supporting info:]
src/SPIN: filenames -> commands
-"Howto spin"_Howto_spin.html
+"Howto spins"_Howto_spins.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
@@ -1386,7 +958,7 @@ examples/SPIN :ul
:line
-SRD package :link(SRD),h4
+SRD package :link(PKG-SRD),h4
[Contents:]
@@ -1394,16 +966,6 @@ A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
method for coarse-graining of a solvent, typically around large
colloidal particles.
-To install/build:
-
-make yes-srd
-make machine :pre
-
-To un-install/re-build:
-
-make no-srd
-make machine :pre
-
[Supporting info:]
src/SRD: filenames -> commands
@@ -1417,7 +979,7 @@ http://lammps.sandia.gov/movies.html#poly :ul
:line
-VORONOI package :link(VORONOI),h4
+VORONOI package :link(PKG-VORONOI),h4
[Contents:]
@@ -1435,33 +997,11 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the Voro++ library. You can do this manually if you prefer;
-follow the instructions in lib/voronoi/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/voronoi/Install.py script with the specified
-args:
-
-make lib-voronoi # print help message
-make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
-make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
-make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
-builds in src it will use these links. You should not need to edit
-the lib/voronoi/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-voronoi
-make machine :pre
+[Install:]
-make no-voronoi
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1471,10 +1011,9 @@ lib/voronoi/README
"compute voronoi/atom"_compute_voronoi_atom.html
examples/voronoi :ul
-:line
:line
-USER-ATC package :link(USER-ATC),h4
+USER-ATC package :link(PKG-USER-ATC),h4
[Contents:]
@@ -1485,46 +1024,11 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the ATC
-library in lib/atc. You can do this manually if you prefer; follow
-the instructions in lib/atc/README. You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/atc/Install.py script with the specified args:
-
-make lib-atc # print help message
-make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-atc args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/atc/libatc.a and
-lib/atc/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
-library. If necessary, you can edit/create a new
-lib/atc/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/atc/README these
-can either exist on your system, or you can use the files provided in
-lib/linalg. In the latter case you also need to build the library
-in lib/linalg with a command like these:
+[Install:]
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-atc
-make machine :pre
-
-make no-user-atc
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1536,7 +1040,7 @@ http://lammps.sandia.gov/pictures.html#atc :ul
:line
-USER-AWPMD package :link(USER-AWPMD),h4
+USER-AWPMD package :link(PKG-USER-AWPMD),h4
[Contents:]
@@ -1547,46 +1051,11 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-AWPMD library in lib/awpmd. You can do this manually if you prefer;
-follow the instructions in lib/awpmd/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/awpmd/Install.py script with the specified args:
+[Install:]
-make lib-awpmd # print help message
-make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/awpmd/libawpmd.a and
-lib/awpmd/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-AWPMD library. If necessary, you can edit/create a new
-lib/awpmd/Makefile.machine file for your system, which should define
-an EXTRAMAKE variable to specify a corresponding
-Makefile.lammps.machine file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/awpmd/README
-these can either exist on your system, or you can use the files
-provided in lib/linalg. In the latter case you also need to build the
-library in lib/linalg with a command like these:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-awpmd
-make machine :pre
-
-make no-user-awpmd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1597,7 +1066,7 @@ examples/USER/awpmd :ul
:line
-USER-BOCS package :link(USER-BOCS),h4
+USER-BOCS package :link(PKG-USER-BOCS),h4
[Contents:]
@@ -1609,15 +1078,8 @@ N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
-
-[Install or un-install:]
-
-make yes-user-bocs
-make machine :pre
-
-make no-user-bocs
-make machine :pre
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
[Supporting info:]
@@ -1634,7 +1096,7 @@ Example inputs are in the examples/USER/bocs folder.
:line
-USER-CGDNA package :link(USER-CGDNA),h4
+USER-CGDNA package :link(PKG-USER-CGDNA),h4
[Contents:]
@@ -1646,14 +1108,6 @@ stability.
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-[Install or un-install:]
-
-make yes-user-cgdna
-make machine :pre
-
-make no-user-cgdna
-make machine :pre
-
[Supporting info:]
src/USER-CGDNA: filenames -> commands
@@ -1666,7 +1120,7 @@ src/USER-CGDNA: filenames -> commands
:line
-USER-CGSDK package :link(USER-CGSDK),h4
+USER-CGSDK package :link(PKG-USER-CGSDK),h4
[Contents:]
@@ -1677,14 +1131,6 @@ acids.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-cgsdk
-make machine :pre
-
-make no-user-cgsdk
-make machine :pre
-
[Supporting info:]
src/USER-CGSDK: filenames -> commands
@@ -1696,7 +1142,7 @@ http://lammps.sandia.gov/pictures.html#cg :ul
:line
-USER-COLVARS package :link(USER-COLVARS),h4
+USER-COLVARS package :link(PKG-USER-COLVARS),h4
[Contents:]
@@ -1713,36 +1159,11 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-COLVARS library in lib/colvars. You can do this manually if you
-prefer; follow the instructions in lib/colvars/README. You can also
-do it in one step from the lammps/src dir, using a command like these,
-which simply invoke the lib/colvars/Install.py script with the
-specified args:
-
-make lib-colvars # print help message
-make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
-
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-colvars
-make machine :pre
-
-make no-user-colvars
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1755,7 +1176,7 @@ examples/USER/colvars :ul
:line
-USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
+USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
[Contents:]
@@ -1764,14 +1185,6 @@ intensities based on kinematic diffraction theory.
[Author:] Shawn Coleman while at the U Arkansas.
-[Install or un-install:]
-
-make yes-user-diffraction
-make machine :pre
-
-make no-user-diffraction
-make machine :pre
-
[Supporting info:]
src/USER-DIFFRACTION: filenames -> commands
@@ -1782,7 +1195,7 @@ examples/USER/diffraction :ul
:line
-USER-DPD package :link(USER-DPD),h4
+USER-DPD package :link(PKG-USER-DPD),h4
[Contents:]
@@ -1799,14 +1212,6 @@ algorithm.
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
Brennan (ARL).
-[Install or un-install:]
-
-make yes-user-dpd
-make machine :pre
-
-make no-user-dpd
-make machine :pre
-
[Supporting info:]
src/USER-DPD: filenames -> commands
@@ -1828,7 +1233,7 @@ examples/USER/dpd :ul
:line
-USER-DRUDE package :link(USER-DRUDE),h4
+USER-DRUDE package :link(PKG-USER-DRUDE),h4
[Contents:]
@@ -1841,14 +1246,6 @@ for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-[Install or un-install:]
-
-make yes-user-drude
-make machine :pre
-
-make no-user-drude
-make machine :pre
-
[Supporting info:]
src/USER-DRUDE: filenames -> commands
@@ -1866,7 +1263,7 @@ tools/drude :ul
:line
-USER-EFF package :link(USER-EFF),h4
+USER-EFF package :link(PKG-USER-EFF),h4
[Contents:]
@@ -1880,14 +1277,6 @@ tools/eff; see its README file.
[Author:] Andres Jaramillo-Botero (CalTech).
-[Install or un-install:]
-
-make yes-user-eff
-make machine :pre
-
-make no-user-eff
-make machine :pre
-
[Supporting info:]
src/USER-EFF: filenames -> commands
@@ -1907,7 +1296,7 @@ http://lammps.sandia.gov/movies.html#eff :ul
:line
-USER-FEP package :link(USER-FEP),h4
+USER-FEP package :link(PKG-USER-FEP),h4
[Contents:]
@@ -1919,14 +1308,6 @@ for using this package in tools/fep; see its README file.
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-[Install or un-install:]
-
-make yes-user-fep
-make machine :pre
-
-make no-user-fep
-make machine :pre
-
[Supporting info:]
src/USER-FEP: filenames -> commands
@@ -1940,7 +1321,7 @@ tools/fep :ul
:line
-USER-H5MD package :link(USER-H5MD),h4
+USER-H5MD package :link(PKG-USER-H5MD),h4
[Contents:]
@@ -1958,37 +1339,11 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
-[Install or un-install:]
+[Install:]
-Note that to follow these steps to compile and link to the CH5MD
-library, you need the standard HDF5 software package installed on your
-system, which should include the h5cc compiler and the HDF5 library.
-
-Before building LAMMPS with this package, you must first build the
-CH5MD library in lib/h5md. You can do this manually if you prefer;
-follow the instructions in lib/h5md/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/h5md/Install.py script with the specified args:
-
-make lib-h5md # print help message
-make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
-
-The build should produce two files: lib/h5md/libch5md.a and
-lib/h5md/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-system HDF5 library. If necessary, you can edit/create a new
-lib/h5md/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-h5md
-make machine :pre
-
-make no-user-h5md
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1999,7 +1354,7 @@ lib/h5md/README
:line
-USER-INTEL package :link(USER-INTEL),h4
+USER-INTEL package :link(PKG-USER-INTEL),h4
[Contents:]
@@ -2009,9 +1364,9 @@ All of them have an "intel" in their style name. The "Speed
intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs and KNLs.
+"-suffix intel" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
+which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
@@ -2020,49 +1375,13 @@ supported, performance will be suboptimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-
[Author:] Mike Brown (Intel).
-[Install or un-install:]
-
-For the USER-INTEL package, you have 2 choices when building. You can
-build with either CPU or KNL support. Each choice requires additional
-settings in your Makefile.machine for CCFLAGS and LINKFLAGS and
-optimized malloc libraries. See the
-src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl
-files for examples.
+[Install:]
-For CPUs:
-
-OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc -ltbbmalloc_proxy :pre
-
-For KNLs:
-
-OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (Intel CPUs or KNL). You need to build LAMMPS once for each
-hardware target, to produce a separate executable.
-
-You should also typically install the USER-OMP package, as it can be
-used in tandem with the USER-INTEL package to good effect, as
-explained on the "Speed intel"_Speed_intel.html doc page.
-
-make yes-user-intel yes-user-omp
-make machine :pre
-
-make no-user-intel no-user-omp
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2070,8 +1389,8 @@ src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Speed packages"_Speed_packages.html
"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Section_start.html#start_6
-"Section 2.6 -pk intel"_Section_start.html#start_6
+"Section 2.6 -sf intel"_Run_options.html
+"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
@@ -2079,7 +1398,7 @@ src/USER-INTEL/TEST
:line
-USER-LB package :link(USER-LB),h4
+USER-LB package :link(PKG-USER-LB),h4
[Contents:]
@@ -2089,14 +1408,6 @@ can be used to model MD particles influenced by hydrodynamic forces.
[Authors:] Frances Mackay and Colin Denniston (University of Western
Ontario).
-[Install or un-install:]
-
-make yes-user-lb
-make machine :pre
-
-make no-user-lb
-make machine :pre
-
[Supporting info:]
src/USER-LB: filenames -> commands
@@ -2108,7 +1419,7 @@ examples/USER/lb :ul
:line
-USER-MGPT package :link(USER-MGPT),h4
+USER-MGPT package :link(PKG-USER-MGPT),h4
[Contents:]
@@ -2123,14 +1434,6 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-[Install or un-install:]
-
-make yes-user-mgpt
-make machine :pre
-
-make no-user-mgpt
-make machine :pre
-
[Supporting info:]
src/USER-MGPT: filenames -> commands
@@ -2140,7 +1443,7 @@ examples/USER/mgpt :ul
:line
-USER-MISC package :link(USER-MISC),h4
+USER-MISC package :link(PKG-USER-MISC),h4
[Contents:]
@@ -2151,14 +1454,6 @@ dihedral, improper, or command style.
[Authors:] The author for each style in the package is listed in the
src/USER-MISC/README file.
-[Install or un-install:]
-
-make yes-user-misc
-make machine :pre
-
-make no-user-misc
-make machine :pre
-
[Supporting info:]
src/USER-MISC: filenames -> commands
@@ -2168,7 +1463,7 @@ examples/USER/misc :ul
:line
-USER-MANIFOLD package :link(USER-MANIFOLD),h4
+USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
[Contents:]
@@ -2179,16 +1474,9 @@ algorithm to formulate single-particle constraint functions
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
n = grad(g).
-[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
-Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
-
-[Install or un-install:]
-
-make yes-user-manifold
-make machine :pre
-
-make no-user-manifold
-make machine :pre
+[Author:] Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
[Supporting info:]
@@ -2203,7 +1491,7 @@ http://lammps.sandia.gov/movies.html#manifold :ul
:line
-USER-MEAMC package :link(USER-MEAMC),h4
+USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
@@ -2217,14 +1505,6 @@ multiple times.
based on the Fortran version of Greg Wagner (Northwestern U) while at
Sandia.
-[Install or un-install:]
-
-make yes-user-meamc
-make machine :pre
-
-make no-user-meamc
-make machine :pre
-
[Supporting info:]
src/USER-MEAMC: filenames -> commands
@@ -2234,7 +1514,7 @@ examples/meam :ul
:line
-USER-MESO package :link(USER-MESO),h4
+USER-MESO package :link(PKG-USER-MESO),h4
[Contents:]
@@ -2248,14 +1528,6 @@ algorithm.
[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-[Install or un-install:]
-
-make yes-user-meso
-make machine :pre
-
-make no-user-meso
-make machine :pre
-
[Supporting info:]
src/USER-MESO: filenames -> commands
@@ -2270,7 +1542,7 @@ http://lammps.sandia.gov/movies.html#mesodpd :ul
:line
-USER-MOFFF package :link(USER-MOFFF),h4
+USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
@@ -2288,14 +1560,6 @@ well as the "MOF+"_MOFplus website.
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
-[Install or un-install:]
-
-make yes-user-mofff
-make machine :pre
-
-make no-user-mofff
-make machine :pre
-
[Supporting info:]
src/USER-MOFFF: filenames -> commands
@@ -2308,7 +1572,7 @@ examples/USER/mofff :ul
:line
-USER-MOLFILE package :link(USER-MOLFILE),h4
+USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
@@ -2336,20 +1600,11 @@ at
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that the lib/molfile/Makefile.lammps file has a setting for a
-dynamic loading library libdl.a that should is typically present on
-all systems, which is required for LAMMPS to link with this package.
-If the setting is not valid for your system, you will need to edit the
-Makefile.lammps file. See lib/molfile/README and
-lib/molfile/Makefile.lammps for details.
+[Install:]
-make yes-user-molfile
-make machine :pre
-
-make no-user-molfile
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2360,7 +1615,7 @@ lib/molfile/README
:line
-USER-NETCDF package :link(USER-NETCDF),h4
+USER-NETCDF package :link(PKG-USER-NETCDF),h4
[Contents:]
@@ -2384,20 +1639,11 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-[Install or un-install:]
-
-Note that to follow these steps, you need the standard NetCDF software
-package installed on your system. The lib/netcdf/Makefile.lammps file
-has settings for NetCDF include and library files that LAMMPS needs to
-compile and linkk with this package. If the settings are not valid
-for your system, you will need to edit the Makefile.lammps file. See
-lib/netcdf/README for details.
+[Install:]
-make yes-user-netcdf
-make machine :pre
-
-make no-user-netcdf
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2408,7 +1654,7 @@ lib/netcdf/README
:line
-USER-OMP package :link(USER-OMP),h4
+USER-OMP package :link(PKG-USER-OMP),h4
[Contents:]
@@ -2418,10 +1664,9 @@ via OpenMP directives. All of them have an "omp" in their style name.
The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
-"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
-CPUs.
+or "-suffix omp" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
+packages, which have styles optimized for CPUs.
[Author:] Axel Kohlmeyer (Temple U).
@@ -2438,16 +1683,11 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
-[Install or un-install:]
-
-make yes-user-omp
-make machine :pre
+[Install:]
-make no-user-omp
-make machine :pre
-
-CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
-LINKFLAGS: add -fopenmp :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2455,15 +1695,15 @@ src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Speed packages"_Speed_packages.html
"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Section_start.html#start_6
-"Section 2.6 -pk omp"_Section_start.html#start_6
+"Section 2.6 -sf omp"_Run_options.html
+"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
-USER-PHONON package :link(USER-PHONON),h4
+USER-PHONON package :link(PKG-USER-PHONON),h4
[Contents:]
@@ -2473,14 +1713,6 @@ relations, directly from molecular dynamics simulations.
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
-[Install or un-install:]
-
-make yes-user-phonon
-make machine :pre
-
-make no-user-phonon
-make machine :pre
-
[Supporting info:]
src/USER-PHONON: filenames -> commands
@@ -2490,7 +1722,7 @@ examples/USER/phonon :ul
:line
-USER-QMMM package :link(USER-QMMM),h4
+USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
@@ -2511,42 +1743,11 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-QMMM library in lib/qmmm. You can do this manually if you prefer;
-follow the first two steps explained in lib/qmmm/README. You can
-also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/qmmm/Install.py script with the
-specified args:
-
-make lib-qmmm # print help message
-make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
-make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
-make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
+[Install:]
-The build should produce two files: lib/qmmm/libqmmm.a and
-lib/qmmm/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-QMMM library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/qmmm/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-qmmm
-make machine :pre
-
-make no-user-qmmm
-make machine :pre
-
-NOTE: The LAMMPS executable these steps produce is not yet functional
-for a QM/MM simulation. You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quantum ESPRESSO
-together. These are steps 3 and 4 described in the lib/qmmm/README
-file.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2559,7 +1760,7 @@ lib/qmmm/example-mc/README :ul
:line
-USER-QTB package :link(USER-QTB),h4
+USER-QTB package :link(PKG-USER-QTB),h4
[Contents:]
@@ -2574,14 +1775,6 @@ simulation.
[Author:] Yuan Shen (Stanford U).
-[Install or un-install:]
-
-make yes-user-qtb
-make machine :pre
-
-make no-user-qtb
-make machine :pre
-
[Supporting info:]
src/USER-QTB: filenames -> commands
@@ -2592,7 +1785,7 @@ examples/USER/qtb :ul
:line
-USER-QUIP package :link(USER-QUIP),h4
+USER-QUIP package :link(PKG-USER-QUIP),h4
[Contents:]
@@ -2608,26 +1801,11 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
-[Install or un-install:]
-
-Note that to follow these steps to compile and link to the QUIP
-library, you must first download and build QUIP on your systems. It
-can be obtained from GitHub. See step 1 and step 1.1 in the
-lib/quip/README file for details on how to do this. Note that it
-requires setting two environment variables, QUIP_ROOT and QUIP_ARCH,
-which will be accessed by the lib/quip/Makefile.lammps file which is
-used when you compile and link LAMMPS with this package. You should
-only need to edit this file if the LAMMPS build can not use its
-settings to successfully build on your system.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-quip
-make machine :pre
-
-make no-user-quip
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2638,26 +1816,18 @@ examples/USER/quip :ul
:line
-USER-REAXC package :link(USER-REAXC),h4
+USER-REAXC package :link(PKG-USER-REAXC),h4
[Contents:]
A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF
+contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
is universal reactive force field. See the src/USER-REAXC/README file
for more info on differences between the two packages. Also two fixes
for monitoring molecules as bonds are created and destroyed.
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-[Install or un-install:]
-
-make yes-user-reaxc
-make machine :pre
-
-make no-user-reaxc
-make machine :pre
-
[Supporting info:]
src/USER-REAXC: filenames -> commands
@@ -2669,66 +1839,14 @@ examples/reax :ul
:line
-USER-SCAFACOS package :link(USER-SCAFACOS),h4
-
-[Contents:]
-
-A KSpace style which wraps the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de.
-
-To use this package you must have the ScaFaCoS library available on
-your system. It is available for download at "http://scafacos.de" or
-can be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
-
-[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
-
-ScaFaCoS was developed by a consortium of German research facilities
-with a BMBF (German Ministry of Science and Education) funded project
-in 2009-2012. Participants of the consortium were the Universities of
-Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
-Forschungszentrum Juelich.
-
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the ScaFaCoS library. You can do this manually if you prefer;
-follow the instructions in lib/scafacos/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/scafacos/Install.py script with the specified
-args:
-
-make lib-scafacos # print help message
-make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
-make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-scafacos
-make machine :pre
-
-make no-user-scafacos
-make machine :pre
-
-[Supporting info:]
-
-src/USER-SCAFACOS: filenames -> commands
-src/USER-SCAFACOS/README
-"kspace_style scafacos"_kspace_style.html
-"kspace_modify"_kspace_modify.html
-examples/USER/scafacos :ul
-
-:line
-
-USER-SMD package :link(USER-SMD),h4
+USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]
An atom style, fixes, computes, and several pair styles which
implements smoothed Mach dynamics (SMD) for solids, which is a model
related to smoothed particle hydrodynamics (SPH) for liquids (see the
-"USER-SPH package"_#USER-SPH).
+"USER-SPH package"_#PKG-USER-SPH).
This package solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control. It can specify
@@ -2742,31 +1860,11 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download the
-Eigen library. Eigen is a template library, so you do not need to
-build it, just download it. You can do this manually if you prefer;
-follow the instructions in lib/smd/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/smd/Install.py script with the specified args:
-
-make lib-smd # print help message
-make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
-
-Note that a symbolic (soft) link named "includelink" is created in
-lib/smd to point to the Eigen dir. When LAMMPS builds it will use
-this link. You should not need to edit the lib/smd/Makefile.lammps file.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-smd
-make machine :pre
-
-make no-user-smd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2778,7 +1876,7 @@ http://lammps.sandia.gov/movies.html#smd :ul
:line
-USER-SMTBQ package :link(USER-SMTBQ),h4
+USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
[Contents:]
@@ -2789,14 +1887,6 @@ ionocovalent bonds in oxides.
[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
Tetot (LAAS-CNRS, France).
-[Install or un-install:]
-
-make yes-user-smtbq
-make machine :pre
-
-make no-user-smtbq
-make machine :pre
-
[Supporting info:]
src/USER-SMTBQ: filenames -> commands
@@ -2806,13 +1896,13 @@ examples/USER/smtbq :ul
:line
-USER-SPH package :link(USER-SPH),h4
+USER-SPH package :link(PKG-USER-SPH),h4
[Contents:]
An atom style, fixes, computes, and several pair styles which
implements smoothed particle hydrodynamics (SPH) for liquids. See the
-related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics
+related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
(SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states,
@@ -2828,14 +1918,6 @@ property/atom"_compute_property_atom.html command.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-make yes-user-sph
-make machine :pre
-
-make no-user-sph
-make machine :pre
-
[Supporting info:]
src/USER-SPH: filenames -> commands
@@ -2846,7 +1928,7 @@ http://lammps.sandia.gov/movies.html#sph :ul
:line
-USER-TALLY package :link(USER-TALLY),h4
+USER-TALLY package :link(PKG-USER-TALLY),h4
[Contents:]
@@ -2856,14 +1938,6 @@ stress, etc) about individual interactions.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-tally
-make machine :pre
-
-make no-user-tally
-make machine :pre
-
[Supporting info:]
src/USER-TALLY: filenames -> commands
@@ -2873,7 +1947,7 @@ examples/USER/tally :ul
:line
-USER-UEF package :link(USER-UEF),h4
+USER-UEF package :link(PKG-USER-UEF),h4
[Contents:]
@@ -2883,14 +1957,6 @@ supporting compute styles and an output option.
[Author:] David Nicholson (MIT).
-[Install or un-install:]
-
-make yes-user-uef
-make machine :pre
-
-make no-user-uef
-make machine :pre
-
[Supporting info:]
src/USER-UEF: filenames -> commands
@@ -2904,7 +1970,7 @@ examples/uef :ul
:line
-USER-VTK package :link(USER-VTK),h4
+USER-VTK package :link(PKG-USER-VTK),h4
[Contents:]
@@ -2920,23 +1986,11 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-[Install or un-install:]
-
-The lib/vtk/Makefile.lammps file has settings for accessing VTK files
-and its library, which are required for LAMMPS to build and link with
-this package. If the settings are not valid for your system, check if
-one of the other lib/vtk/Makefile.lammps.* files is compatible and
-copy it to Makefile.lammps. If none of the provided files work, you
-will need to edit the Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-vtk
-make machine :pre
+[Install:]
-make no-user-vtk
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
--
GitLab
From a9fb8636adc555486d4ed3080d2a5766436539d5 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 09:52:44 -0600
Subject: [PATCH 114/332] doc page updates and changed domain->remap() call
---
doc/src/Build_extras.txt | 40 ++++++++++++++++++++++++++++++++++
doc/src/Build_package.txt | 1 +
doc/src/Packages_details.txt | 36 ++++++++++++++++++++++++++++++
doc/src/Packages_user.txt | 1 +
doc/src/kspace_style.txt | 4 ++--
src/USER-SCAFACOS/scafacos.cpp | 12 +++++++++-
6 files changed, 91 insertions(+), 3 deletions(-)
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 5c33a0a4d4..2fc0785227 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -47,6 +47,7 @@ This is the list of packages that may require additional steps.
"USER-OMP"_#user-omp,
"USER-QMMM"_#user-qmmm,
"USER-QUIP"_#user-quip,
+"USER-SCAFACOS"_#user-scafacos,
"USER-SMD"_#user-smd,
"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
@@ -894,6 +895,45 @@ successfully build on your system.
:line
+USER-SCAFACOS package :h4,link(user-scafacos)
+
+To build with this package, you must download and build the "ScaFaCoS
+Coulomb solver library"_scafacos_home
+
+:link(scafacos_home,http://www.scafacos.de)
+
+[CMake build]:
+
+-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
+-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location)
+-D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded
+and built inside the CMake build directory. If the ScaFaCoS library
+is already on your system (in a location CMake cannot find it),
+SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
+file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR
+is the directory the ScaFaCoS include file is in.
+
+[Traditional make]:
+
+You can download and build the ScaFaCoS library manually if you
+prefer; follow the instructions in lib/scafacos/README. You can also
+do it in one step from the lammps/src dir, using a command like these,
+which simply invoke the lib/scafacos/Install.py script with the
+specified args:
+
+make lib-scafacos # print help message
+make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
+make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS
+builds in src it will use these links. You should not need to edit
+the lib/scafacos/Makefile.lammps file.
+
+:line
+
USER-SMD package :h4,link(user-smd)
To build with this package, you must download the Eigen3 library.
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 4f71e9eb18..fab987ea0d 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -58,6 +58,7 @@ packages:
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
+"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 892774be38..c4c9043908 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -92,6 +92,7 @@ as contained in the file name.
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
+"USER-SCAFACOS"_#USER-SCAFACOS,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@@ -1839,6 +1840,41 @@ examples/reax :ul
:line
+USER-SCAFACOS package :link(USER-SCAFACOS),h4
+
+[Contents:]
+
+A KSpace style which wraps the "ScaFaCoS Coulomb solver
+library"_http://www.scafacos.de to compute long-range Coulombic
+interactions.
+
+To use this package you must have the ScaFaCoS library available on
+your system.
+
+[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
+
+ScaFaCoS itself was developed by a consortium of German research
+facilities with a BMBF (German Ministry of Science and Education)
+funded project in 2009-2012. Participants of the consortium were the
+Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
+the Forschungszentrum Juelich.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-scafacos on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-SCAFACOS: filenames -> commands
+src/USER-SCAFACOS/README
+"kspace_style scafacos"_kspace_style.html
+"kspace_modify"_kspace_modify.html
+examples/USER/scafacos :ul
+
+:line
+
USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index c1a52fd0d0..5ed5c6f6d3 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -66,6 +66,7 @@ Package, Description, Doc page, Example, Library
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
+"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index deb8d8ab51..ddf4e15703 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -252,7 +252,7 @@ These are the ScaFaCoS methods currently available from LAMMPS:
{p2nfft} = FFT-based Coulomb solver
{ewald} = Ewald summation
{direct} = direct O(N^2) summation
-{p3m} = PPPM
+{p3m} = PPPM :ul
We plan to support additional ScaFaCoS solvers from LAMMPS in the
future. For an overview of the included solvers, refer to
@@ -268,7 +268,7 @@ energy or the total Columic energy. To select from these options, see
the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
The "kspace_modify scafacos"_kspace_modify.html command also explains
-all the ScaFaCoS options currently exposed to LAMMPS.
+other ScaFaCoS options currently exposed to LAMMPS.
:line
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index f3e8ce64f7..d047853b55 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -199,7 +199,6 @@ void Scafacos::compute(int eflag, int vflag)
eflag_atom = 0;
vflag_global = 0;
}
-
// grow xpbc, epot, efield if necessary
@@ -223,6 +222,8 @@ void Scafacos::compute(int eflag, int vflag)
// pack coords into xpbc and apply PBC
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
+ // RENE: remove this section (see RENE below)
+
//int j = 0;
for (int i = 0; i < nlocal; i++) {
if (domain->xperiodic) domain->remap(&xpbc[3*i]);
@@ -231,6 +232,15 @@ void Scafacos::compute(int eflag, int vflag)
//j += 3;
}
+ // RENE: I think the call to domain->remap needs to be this way
+ // b/c the remap() method checks for PBC and does all 3 dims at once
+
+ int j = 0;
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
+ }
+
// if simulation box has changed, call fcs_tune()
if (box_has_changed()) {
--
GitLab
From cb8482b0e6e9ac007ca79eb96a38dd86f5ce4673 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 10:22:51 -0600
Subject: [PATCH 115/332] another doc change
---
doc/src/Commands_kspace.txt | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt
index a126344505..d56b7fa767 100644
--- a/doc/src/Commands_kspace.txt
+++ b/doc/src/Commands_kspace.txt
@@ -33,4 +33,5 @@ OPT.
"pppm/disp (i)"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
+"pppm/tip4p (o)"_kspace_style.html,
+"scafacos"_kspace_style.html :tb(c=4,ea=c)
--
GitLab
From c4b55385e20ebb84aa13f0d5e8dbe4703e11efd4 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 10:40:39 -0600
Subject: [PATCH 116/332] doc updates
---
doc/src/server_mc.txt | 39 +++++++++++++++++++--------------------
doc/src/server_md.txt | 41 ++++++++++++++++++++---------------------
lib/message/README | 4 ++--
3 files changed, 41 insertions(+), 43 deletions(-)
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index 94545c8732..fba969d9ce 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -56,8 +56,7 @@ a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
pages for more details on the actual library syntax. The "cs" object
-in this pseudo code is an instance of the CSlib that both the client
-and server codes store.
+in this pseudo code is a pointer to an instance of the CSlib.
See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
@@ -67,35 +66,35 @@ Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
[Client sends one of these kinds of message]:
-cs.send(NATOMS,0) # msgID = 1 with no fields :pre
+cs->send(NATOMS,0) # msgID = 1 with no fields :pre
-cs.send(EINIT,0) # msgID = 2 with no fields :pre
+cs->send(EINIT,0) # msgID = 2 with no fields :pre
-cs.send(DISPLACE,2) # msgID = 3 with 2 fields
-cs.pack(1,1,ID) # 1st field = ID of atom to displace
-cs.pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
+cs->send(DISPLACE,2) # msgID = 3 with 2 fields
+cs->pack(1,1,ID) # 1st field = ID of atom to displace
+cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
-cs.send(ACCEPT,1) # msgID = 4 with 1 field
-cs.pack(1,1,flag) # 1st field = accept/reject flag :pre
+cs->send(ACCEPT,1) # msgID = 4 with 1 field
+cs->pack(1,1,flag) # 1st field = accept/reject flag :pre
-cs.send(RUN,1) # msgID = 5 with 1 field
-cs.pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
+cs->send(RUN,1) # msgID = 5 with 1 field
+cs->pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
[Server replies]:
-cs.send(NATOMS,1) # msgID = 1 with 1 field
-cs.pack(1,1,Natoms) # 1st field = number of atoms :pre
+cs->send(NATOMS,1) # msgID = 1 with 1 field
+cs->pack(1,1,Natoms) # 1st field = number of atoms :pre
-cs.send(EINIT,2) # msgID = 2 with 2 fields
-cs.pack(1,1,poteng) # 1st field = potential energy of system
-cs.pack(2,3*Natoms,x) # 2nd field = 3N coords of Natoms :pre
+cs->send(EINIT,2) # msgID = 2 with 2 fields
+cs->pack(1,1,poteng) # 1st field = potential energy of system
+cs->pack(2,3*Natoms,x) # 2nd field = 3N coords of Natoms :pre
-cs.send(DISPLACE,1) # msgID = 3 with 1 field
-cs.pack(1,1,poteng) # 1st field = new potential energy of system :pre
+cs->send(DISPLACE,1) # msgID = 3 with 1 field
+cs->pack(1,1,poteng) # 1st field = new potential energy of system :pre
-cs.send(ACCEPT,0) # msgID = 4 with no fields
+cs->send(ACCEPT,0) # msgID = 4 with no fields
-cs.send(RUN,0) # msgID = 5 with no fields
+cs->send(RUN,0) # msgID = 5 with no fields
:line
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 66534c1ad6..8c5d83bfb8 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -59,8 +59,7 @@ a conceptual sense. Python-style pseudo code for the library calls to
the CSlib is shown, which performs the actual message exchange between
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
pages for more details on the actual library syntax. The "cs" object
-in this pseudo code is an instance of the CSlib that both the client
-and server codes store.
+in this pseudo code is a pointer to an instance of the CSlib.
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
files for details on how LAMMPS uses these messages. See the
@@ -78,34 +77,34 @@ enum{FORCES=1,ENERGY,VIRIAL}; :pre
# required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
# optional fields: others in 2nd enum above :pre
-cs.send(SETUP,nfields) # msgID with nfields :pre
+cs->send(SETUP,nfields) # msgID with nfields :pre
-cs.pack_string(UNITS,units) # units = "lj", "real", "metal", etc
-cs.pack_int(NATOMS,natoms) # total numer of atoms
-cs.pack_int(NTYPES,ntypes) # number of atom types
-cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
-cs.pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
-cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
-cs.pack(TYPES,natoms,type) # vector of per-atom types
-cs.pack(COORDS,3*natoms,x) # vector of 3N atom coords
-cs.pack(CHARGE,natoms,q) # vector of per-atom charge :pre
+cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
+cs->pack_int(NATOMS,natoms) # total numer of atoms
+cs->pack_int(NTYPES,ntypes) # number of atom types
+cs->pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
+cs->pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
+cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
+cs->pack(TYPES,natoms,type) # vector of per-atom types
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
# required fields: COORDS
# optional fields: BOXLO, BOXHI, BOXTILT :pre
-cs.send(STEP,nfields) # msgID with nfields :pre
+cs->send(STEP,nfields) # msgID with nfields :pre
-cs.pack_int(NATOMS,natoms) # total numer of atoms
-cs.pack_int(NTYPES,ntypes) # number of atom types
-cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
-cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :pre
+cs->pack_int(NATOMS,natoms) # total numer of atoms
+cs->pack_int(NTYPES,ntypes) # number of atom types
+cs->pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
+cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :pre
[Server replies to either kind of message]:
-cs.send(msgID,3) # msgID = 1 with 3 fields
-cs.pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
-cs.pack(ENERGY,1,poteng) # total potential energy of system
-cs.pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
+cs->send(msgID,3) # msgID = 1 with 3 fields
+cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
+cs->pack(ENERGY,1,poteng) # total potential energy of system
+cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
:line
diff --git a/lib/message/README b/lib/message/README
index c93ae81104..dafb94e9ef 100644
--- a/lib/message/README
+++ b/lib/message/README
@@ -4,7 +4,7 @@ in a LAMMPS input script.
The CSlib libary is included in the LAMMPS distribution. A fuller
version including documentation and test programs is available at
-http:cslib.sandia.gov and was developed by Steve Plimpton at Sandia
+http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia
National Laboratories.
You can type "make lib-message" from the src directory to see help on
@@ -16,7 +16,7 @@ The CSlib can be optionally built with support for sockets using
the open-source ZeroMQ (ZMQ) library. If it is not installed
on your system, it is easy to download and install.
-Go to this website: http://zeromq.org
+Go to the ZMQ website for details: http://zeromq.org
-----------------
--
GitLab
From 4e13ce1d257f8b8d76131b6a8155f36e80688ecf Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 11:21:14 -0600
Subject: [PATCH 117/332] add back in MESSAGE package info in CMakeLists.txt
---
cmake/CMakeLists.txt | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 460d177c92..44ea64b1cd 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -478,6 +478,32 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
+if(PKG_MESSAGE)
+ option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+ add_library(cslib STATIC ${cslib_SOURCES})
+
+ if(BUILD_MPI)
+ target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ else()
+ target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ endif()
+
+ if(MESSAGE_ZMQ)
+ target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+ find_package(ZMQ REQUIRED)
+ target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+ target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+ else()
+ target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+ target_include_directories(cslib PRIVATE ${LAMMPS_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ endif()
+
+ list(APPEND LAMMPS_LINK_LIBS cslib)
+ include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()
+
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
--
GitLab
From 03b880a31c2306489ae9e2afda511429db0ebb5e Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 11:42:41 -0600
Subject: [PATCH 118/332] more doc page updates
---
doc/src/Build_extras.txt | 10 +++++++---
doc/src/Howto_client_server.txt | 2 +-
doc/src/fix_client_md.txt | 22 +++++++++++-----------
doc/src/message.txt | 29 ++++++++++++++++-------------
doc/src/server.txt | 16 ++++++++--------
doc/src/server_mc.txt | 20 ++++++++++++--------
doc/src/server_md.txt | 16 ++++++++--------
examples/message/README | 7 ++++---
8 files changed, 67 insertions(+), 55 deletions(-)
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 6ed54c0334..9f640aee78 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -380,9 +380,13 @@ file.
MESSAGE package :h4,link(message)
+This package can optionally include support for messaging via sockets,
+using the open-source "ZeroMQ library"_http://zeromq.org, which must
+be installed on your system.
+
[CMake build]:
-No additional settings are needed besides "-D PKG_MESSAGE=yes".
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
[Traditional make]:
@@ -398,8 +402,8 @@ make lib-message args="-s" # build as serial lib with no ZMQ support
The build should produce two files: lib/message/cslib/src/libmessage.a
and lib/message/Makefile.lammps. The latter is copied from an
-existing Makefile.lammps.* and has settings to link with the
-open-source ZMQ library if requested in the build.
+existing Makefile.lammps.* and has settings to link with the ZeroMQ
+library if requested in the build.
:line
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index 73d67bbffb..ce9bbc0763 100644
--- a/doc/src/Howto_client_server.txt
+++ b/doc/src/Howto_client_server.txt
@@ -40,7 +40,7 @@ package"_Packages_details.html#PKG-MESSAGE which implements several
commands that enable LAMMPS to act as a client or server, as discussed
below. The MESSAGE package also wraps a client/server library called
CSlib which enables two codes to exchange messages in different ways,
-either via files, a socket, or MPI. The CSlib is provided with LAMMPS
+either via files, sockets, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. The CSlib has its own
"website"_http://cslib.sandia.gov with documentation and test
programs.
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
index 53cd7c36c2..1712e1615e 100644
--- a/doc/src/fix_client_md.txt
+++ b/doc/src/fix_client_md.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,11 +25,11 @@ This fix style enables LAMMPS to run as a "client" code and
communicate each timestep with a separate "server" code to perform an
MD simulation together.
-"This section"_Section_howto.html#howto_29 gives an overview of
-client/server coupling of LAMMPS with another code where one code is
-the "client" and sends request messages to a "server" code. The
-server responds to each request with a reply message. This enables
-the two codes to work in tandem to perform a simulation.
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
When using this fix, LAMMPS (as the client code) passes the current
coordinates of all particles to the server code each timestep, which
@@ -80,9 +80,9 @@ virial as part of "thermodynamic output"_thermo_style.html. The
default is {virial yes}
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-potential energy discussed above. The scalar value calculated by this
-fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MESSAGE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
diff --git a/doc/src/message.txt b/doc/src/message.txt
index bbea48f0f1..6c84f3135c 100644
--- a/doc/src/message.txt
+++ b/doc/src/message.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Command_all.html)
:line
@@ -44,11 +44,11 @@ message server md mpi/two tmp.couple :pre
Establish a messaging protocol between LAMMPS and another code for the
purpose of client/server coupling.
-"This section"_Section_howto.html#howto_29 gives an overview of
-client/server coupling of LAMMPS with another code where one code is
-the "client" and sends request messages to a "server" code. The
-server responds to each request with a reply message. This enables
-the two codes to work in tandem to perform a simulation.
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
:line
@@ -82,9 +82,12 @@ The filename can include a path. Both codes must be able to access
the path/file in a common filesystem.
For mode {zmq}, the 2 codes communicate via a socket on the server
-code's machine. The client specifies an IP address (IPv4 format) or
-the DNS name of the machine the server code is running on, followed by
-a 4-digit port ID for the socket, separated by a colon. E.g.
+code's machine. Support for socket messaging is provided by the
+open-source "ZeroMQ library"_http://zeromq.org, which must be
+installed on your system. The client specifies an IP address (IPv4
+format) or the DNS name of the machine the server code is running on,
+followed by a 4-digit port ID for the socket, separated by a colon.
+E.g.
localhost:5555 # client and server running on same machine
192.168.1.1:5555 # server is 192.168.1.1
@@ -106,8 +109,8 @@ mpirun -np 2 lmp_mpi -mpi 2 -in in.client -log log.client : -np 4 othercode args
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpi 2 -in in.server # LAMMPS is server :pre
Note the use of the "-mpi P" command-line argument with LAMMPS. See
-the "command-line args"_Section_start.html#start_6 doc page for
-further explanation.
+the "command-line args"_Run_options.html doc page for further
+explanation.
For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
be 2 separate mpirun commands. The specified {filename} argument is a
@@ -149,8 +152,8 @@ fix client or server command.
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/server.txt b/doc/src/server.txt
index ba6daa7fcf..86fb68d012 100644
--- a/doc/src/server.txt
+++ b/doc/src/server.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -26,11 +26,11 @@ message back to the client. The specified {protocol} determines the
format and content of messages LAMMPS expects to receive and how it
responds.
-"This section"_Section_howto.html#howto_29 gives an overview of
-client/server coupling of LAMMPS with another code where one code is
-the "client" and sends request messages to a "server" code. The
-server responds to each request with a reply message. This enables
-the two codes to work in tandem to perform a simulation.
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@@ -57,8 +57,8 @@ mc"_server_mc.html doc page for details on the protocol.
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index fba969d9ce..3c658187da 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,11 +25,11 @@ expect messages from a separate "client" code that match the {mc}
protocol for format and content explained below. For each message
LAMMPS receives it will send a message back to the client.
-"This section"_Section_howto.html#howto_29 gives an overview of
-client/server coupling of LAMMPS with another code where one code is
-the "client" and sends request messages to a "server" code. The
-server responds to each request with a reply message. This enables
-the two codes to work in tandem to perform a simulation.
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@@ -101,8 +101,12 @@ cs->send(RUN,0) # msgID = 5 with no fields
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
[Related commands:]
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 8c5d83bfb8..4fe605f7a5 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -25,11 +25,11 @@ expect messages from a separate "client" code that match the {md}
protocol for format and content explained below. For each message
LAMMPS receives it will send a message back to the client.
-"This section"_Section_howto.html#howto_29 gives an overview of
-client/server coupling of LAMMPS with another code where one code is
-the "client" and sends request messages to a "server" code. The
-server responds to each request with a reply message. This enables
-the two codes to work in tandem to perform a simulation.
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@@ -111,8 +111,8 @@ cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/examples/message/README b/examples/message/README
index 63055177a4..617a4249a5 100644
--- a/examples/message/README
+++ b/examples/message/README
@@ -11,9 +11,10 @@ LAMMPS as the server, e.g. a quantum code computing quantum forces, so
that ab initio MD could be performed. See an example of the latter in
examples/COUPLE/lammps_vasp.
-See the MESSAGE package (doc/Section_messages.html#MESSAGE)
-and Section_howto.html#howto10 for more details on how
-client/server coupling works in LAMMPS.
+See the doc pages for the "MESSAGE package"
+(Package_details.html#PKG-MESSAGE) and "Howto client/server"
+(Howto_client_server.html) for more details on how client/server
+coupling works in LAMMPS.
--------------
--
GitLab
From fd56124a94288635c942ac33a8c4aacd60231d74 Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 22 Aug 2018 14:17:21 -0600
Subject: [PATCH 119/332] corrected remap call and logic for check if correct
solver / tolerance combinations are set
---
src/USER-SCAFACOS/scafacos.cpp | 27 ++++++++-------------------
1 file changed, 8 insertions(+), 19 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index d047853b55..7c2dd0b68d 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -222,25 +222,14 @@ void Scafacos::compute(int eflag, int vflag)
// pack coords into xpbc and apply PBC
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
- // RENE: remove this section (see RENE below)
-
- //int j = 0;
- for (int i = 0; i < nlocal; i++) {
- if (domain->xperiodic) domain->remap(&xpbc[3*i]);
- if (domain->yperiodic) domain->remap(&xpbc[3*i+1]);
- if (domain->zperiodic) domain->remap(&xpbc[3*i+2]);
- //j += 3;
- }
-
- // RENE: I think the call to domain->remap needs to be this way
- // b/c the remap() method checks for PBC and does all 3 dims at once
int j = 0;
- for (int i = 0; i < nlocal; i++) {
- domain->remap(&xpbc[j]);
- j += 3;
+ if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
+ }
}
-
// if simulation box has changed, call fcs_tune()
if (box_has_changed()) {
@@ -328,20 +317,20 @@ int Scafacos::modify_param(int narg, char **arg)
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL
)
- ) &&
+ ) ||
(
strcmp(method,"p2nfft") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL
)
- ) &&
+ ) ||
(
strcmp(method,"p3m") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_FIELD
)
- ) &&
+ ) ||
(
strcmp(method,"ewald") == 0 &&
(
--
GitLab
From 8930a88e99d4c812f2eb78403b3ec37c9f7c8cba Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 22 Aug 2018 15:12:52 -0600
Subject: [PATCH 120/332] enrich the AIMD interface
---
src/MESSAGE/fix_client_md.cpp | 97 ++++++++++++++++----------
src/MESSAGE/fix_client_md.h | 6 +-
src/MESSAGE/server_md.cpp | 125 +++++++++++++++++++---------------
3 files changed, 134 insertions(+), 94 deletions(-)
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 9ca6df4edc..9c270ac2c9 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -28,8 +28,9 @@ using namespace LAMMPS_NS;
using namespace CSLIB_NS;
using namespace FixConst;
+enum{REAL,METAL}
enum{SETUP=1,STEP};
-enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
/* ---------------------------------------------------------------------- */
@@ -44,14 +45,32 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
if (sizeof(tagint) != 4)
error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else error->all(FLERR,"Units must be real or metal for fix client/md");
+
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
virial_flag = 1;
thermo_virial = 1;
+ if (domain->dimension == 2)
+ box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0;
+
maxatom = 0;
xpbc = NULL;
+
+ // unit conversion factors
+
+ double inv_nprocs = 1.0 / comm->nprocs;
+
+ fconvert = econvert = vconvert = 1.0;
+ if (units == REAL) {
+ fconvert = 1.0;
+ econvert = 1.0;
+ vconvert = 1.0;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -101,34 +120,28 @@ void FixClientMD::setup(int vflag)
{
CSlib *cs = (CSlib *) lmp->cslib;
- // required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
// optional fields: others in enum above
- int nfields = 6;
- if (domain->dimension == 2) nfields++;
- if (domain->triclinic) nfields++;
+ int nfields = 8;
if (atom->q_flag) nfields++;
cs->send(SETUP,nfields);
+ cs->pack_int(DIM,domain->dimension);
+ cs->pack(PERIODICITY,1,3,domain->periodicity);
+
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
+
cs->pack_int(NATOMS,atom->natoms);
cs->pack_int(NTYPES,atom->ntypes);
- cs->pack(BOXLO,4,3,domain->boxlo);
- cs->pack(BOXHI,4,3,domain->boxhi);
+
cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
pack_coords();
cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
- if (domain->dimension == 2) cs->pack_int(DIM,domain->dimension);
- if (domain->triclinic) {
- double boxtilt[3];
- boxtilt[0] = domain->xy;
- if (domain->dimension == 3) {
- boxtilt[1] = domain->xz;
- boxtilt[2] = domain->yz;
- } else boxtilt[1] = boxtilt[2] = 0.0;
- cs->pack(BOXTILT,4,3,boxtilt);
- }
if (atom->q_flag)
cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
@@ -156,7 +169,7 @@ void FixClientMD::post_force(int vflag)
else evflag = 0;
// required fields: COORDS
- // optional fields: BOXLO, BOXHI, BOXTILT
+ // optional fields: ORIGIN, BOX
// send coords
@@ -164,7 +177,6 @@ void FixClientMD::post_force(int vflag)
int nfields = 1;
if (domain->box_change) nfields += 2;
- if (domain->box_change && domain->triclinic) nfields++;;
cs->send(STEP,nfields);
@@ -172,17 +184,9 @@ void FixClientMD::post_force(int vflag)
cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
if (domain->box_change) {
- cs->pack(BOXLO,4,3,domain->boxlo);
- cs->pack(BOXHI,4,3,domain->boxhi);
- if (domain->triclinic) {
- double boxtilt[3];
- boxtilt[0] = domain->xy;
- if (domain->dimension == 3) {
- boxtilt[1] = domain->xz;
- boxtilt[2] = domain->yz;
- } else boxtilt[1] = boxtilt[2] = 0.0;
- cs->pack(BOXTILT,4,3,boxtilt);
- }
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
}
// recv forces, energy, virial
@@ -230,6 +234,26 @@ void FixClientMD::pack_coords()
}
}
+/* ----------------------------------------------------------------------
+ pack box info into box = 3 edge vectors of simulation box
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_box()
+{
+ double *boxlo = domain->boxlo;
+ double *boxhi = domain->boxhi;
+
+ box[0][0] = boxhi[0] - boxlo[0];
+ box[0][1] = 0.0;
+ box[0][2] = 0.0;
+ box[1][0] = domain->xy;
+ box[1][1] = boxhi[1] - boxlo[1];
+ box[1][2] = 0.0;
+ box[2][0] = domain->xz;
+ box[2][1] = domain->yz;
+ box[2][2] = boxhi[2] - boxlo[2];
+}
+
/* ----------------------------------------------------------------------
receive message from server with forces, energy, virial
------------------------------------------------------------------------- */
@@ -254,18 +278,17 @@ void FixClientMD::receive_fev(int vflag)
m = atom->map(id);
if (m < 0 || m >= nlocal) j += 3;
else {
- f[m][0] += forces[j++];
- f[m][1] += forces[j++];
- f[m][2] += forces[j++];
+ f[m][0] += fconvert * forces[j++];
+ f[m][1] += fconvert * forces[j++];
+ f[m][2] += fconvert * forces[j++];
}
}
- eng = cs->unpack_double(ENERGY);
-
+ eng = econvert * cs->unpack_double(ENERGY);
+
if (vflag) {
double *v = (double *) cs->unpack(VIRIAL);
- double invnprocs = 1.0 / comm->nprocs;
for (int i = 0; i < 6; i++)
- virial[i] = invnprocs*v[i];
+ virial[i] = inv_nprocs * vconvert * v[i];
}
}
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
index 8e4ec0c6de..b6561bce41 100644
--- a/src/MESSAGE/fix_client_md.h
+++ b/src/MESSAGE/fix_client_md.h
@@ -38,10 +38,14 @@ class FixClientMD : public Fix {
private:
void *cslib;
- int maxatom;
+ int maxatom,units;
+ double box[3][3];
double eng;
double *xpbc;
+ double inv_nprocs;
+ double fconvert,econvert,vconvert;
+
void pack_coords();
void receive_fev(int );
};
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index 9783383553..af93c3b4b0 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -33,8 +33,9 @@
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
+enum{REAL,METAL}
enum{SETUP=1,STEP};
-enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
// NOTE: features that could be added to this interface
@@ -54,9 +55,13 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
if (domain->box_exist == 0)
error->all(FLERR,"Server command before simulation box is defined");
- if (!atom->map_style) error->all(FLERR,"Server md mode requires atom map");
- if (atom->tag_enable == 0) error->all(FLERR,"Server md mode requires atom IDs");
+ if (!atom->map_style) error->all(FLERR,"Server md requires atom map");
+ if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs");
if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
+
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else error->all(FLERR,"Units must be real or metal for server md");
}
/* ---------------------------------------------------------------------- */
@@ -90,24 +95,31 @@ void ServerMD::loop()
if (msgID == SETUP) {
+ int dim = 0;
+ int *periodicity = NULL;
int natoms = -1;
int ntypes = -1;
- double *boxlo = NULL;
- double *boxhi = NULL;
- double *boxtilt = NULL;
+ double *origin = NULL;
+ double *box = NULL;
int *types = NULL;
double *coords = NULL;
double *charge = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
- if (fieldID[ifield] == UNITS) {
- char *units = cs->unpack_string(UNITS);
- if (strcmp(units,update->unit_style) != 0)
- error->all(FLERR,"Server md units mis-match with client");
- } else if (fieldID[ifield] == DIM) {
- int dim = cs->unpack_int(DIM);
- if (dim != domain->dimension)
+ if (fieldID[ifield] == DIM) {
+ dim = cs->unpack_int(DIM);
+ if (dim != domain->dimension)
error->all(FLERR,"Server md dimension mis-match with client");
+ } else if (fieldID[ifield] == PERIODICITY) {
+ periodicity = (int *) cs->unpack(PERIODICITY);
+ if (periodicity[0] != domain->periodicity[0] ||
+ periodicity[1] != domain->periodicity[1]
+ periodicity[2] != domain->periodicity[2])
+ error->all(FLERR,"Server md periodicity mis-match with client");
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
} else if (fieldID[ifield] == NATOMS) {
natoms = cs->unpack_int(NATOMS);
if (3*natoms > INT_MAX)
@@ -116,12 +128,6 @@ void ServerMD::loop()
ntypes = cs->unpack_int(NTYPES);
if (ntypes != atom->ntypes)
error->all(FLERR,"Server md ntypes mis-match with client");
- } else if (fieldID[ifield] == BOXLO) {
- boxlo = (double *) cs->unpack(BOXLO);
- } else if (fieldID[ifield] == BOXHI) {
- boxhi = (double *) cs->unpack(BOXHI);
- } else if (fieldID[ifield] == BOXTILT) {
- boxtilt = (double *) cs->unpack(BOXTILT);
} else if (fieldID[ifield] == TYPES) {
types = (int *) cs->unpack(TYPES);
} else if (fieldID[ifield] == COORDS) {
@@ -131,7 +137,8 @@ void ServerMD::loop()
} else error->all(FLERR,"Server md setup field unknown");
}
- if (natoms < 0 || ntypes < 0 || !boxlo || !boxhi || !types || !coords)
+ if (dim == 0 || !periodicity || !origin || !box ||
+ natoms < 0 || ntypes < 0 || !types || !coords)
error->all(FLERR,"Required server md setup field not received");
if (charge && atom->q_flag == 0)
@@ -139,8 +146,12 @@ void ServerMD::loop()
// reset box, global and local
// reset proc decomposition
+
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
- box_change(boxlo,boxhi,boxtilt);
+ box_change(origin,box);
domain->set_initial_box();
domain->set_global_box();
@@ -166,7 +177,7 @@ void ServerMD::loop()
int ntotal;
MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
if (ntotal != natoms)
- error->all(FLERR,"Server md atom cound does not match client");
+ error->all(FLERR,"Server md atom count does not match client");
atom->map_init();
atom->map_set();
@@ -190,29 +201,34 @@ void ServerMD::loop()
} else if (msgID == STEP) {
- double *boxlo = NULL;
- double *boxhi = NULL;
- double *boxtilt = NULL;
double *coords = NULL;
+ double *origin = NULL;
+ double *box = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
- if (fieldID[ifield] == BOXLO) {
- boxlo = (double *) cs->unpack(BOXLO);
- } else if (fieldID[ifield] == BOXHI) {
- boxhi = (double *) cs->unpack(BOXHI);
- } else if (fieldID[ifield] == BOXTILT) {
- boxtilt = (double *) cs->unpack(BOXTILT);
- } else if (fieldID[ifield] == COORDS) {
+ if (fieldID[ifield] == COORDS) {
coords = (double *) cs->unpack(COORDS);
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
} else error->all(FLERR,"Server md step field unknown");
}
if (!coords)
error->all(FLERR,"Required server md step field not received");
- // change box size/shape, only if both box lo/hi received
+ // change box size/shape, only if origin and box received
+ // reset global/local box like FixDeform at end_of_step()
- if (boxlo && boxhi) box_change(boxlo,boxhi,boxtilt);
+ if (origin && box) {
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
+ box_change(origin,box);
+ domain->set_global_box();
+ domain->set_local_box();
+ }
// assign received coords to owned atoms
// closest_image() insures xyz matches current server PBC
@@ -231,9 +247,11 @@ void ServerMD::loop()
}
}
- // if no need to reneighbor, just ghost comm
- // else setup_minimal(1) which includes reneigh
- // setup_minimal computes forces for 0 or 1
+ // if no need to reneighbor:
+ // ghost comm
+ // setup_minimal(0) which just computes forces
+ // else:
+ // setup_minimal(1) for pbc, reset_box, reneigh, forces
int nflag = neighbor->decide();
if (nflag == 0) {
@@ -278,26 +296,21 @@ void ServerMD::loop()
box change due to received message
------------------------------------------------------------------------- */
-void ServerMD::box_change(double *boxlo, double *boxhi, double *boxtilt)
+void ServerMD::box_change(double *origin, double *box)
{
- domain->boxlo[0] = boxlo[0];
- domain->boxhi[0] = boxhi[0];
- domain->boxlo[1] = boxlo[1];
- domain->boxhi[1] = boxhi[1];
- if (domain->dimension == 3) {
- domain->boxlo[2] = boxlo[2];
- domain->boxhi[2] = boxhi[2];
- }
-
- if (boxtilt) {
- if (!domain->triclinic)
- error->all(FLERR,"Server md not setup for triclinic box");
- domain->xy = boxtilt[0];
- if (domain->dimension == 3) {
- domain->xz = boxtilt[1];
- domain->yz = boxtilt[2];
- }
- }
+ domain->boxlo[0] = origin[0];
+ domain->boxlo[1] = origin[1];
+ domain->boxlo[2] = origin[2];
+
+ domain->boxhi[0] = origin[0] + box[0];
+ domain->boxhi[1] = origin[1] + box[4];
+ domain->boxhi[2] = origin[2] + box[8];
+
+ domain->xy = box[3];
+ domain->xz = box[6];
+ domain->yz = box[7];
+
+
}
/* ----------------------------------------------------------------------
--
GitLab
From a1098d5796e838540f7e1b2bf72777360024a668 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 18:45:32 -0400
Subject: [PATCH 121/332] fix broken and inconsistent links in the manual
---
doc/src/Commands_bond.txt | 2 +-
doc/src/Howto_spherical.txt | 2 +-
doc/src/Packages_details.txt | 8 ++++----
doc/src/Python_call.txt | 2 +-
doc/src/Speed_intel.txt | 2 +-
doc/src/Speed_packages.txt | 2 +-
6 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 48069d3120..0cf433d53a 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -95,7 +95,7 @@ OPT.
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.htm;,
+"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,
diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt
index 1e737df655..4dfe4e2f6c 100644
--- a/doc/src/Howto_spherical.txt
+++ b/doc/src/Howto_spherical.txt
@@ -159,7 +159,7 @@ ellipsoidal particles:
The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting. The "fix langevin"_fix_langevin
+calculation and thermostatting. The "fix langevin"_fix_langevin.html
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 892774be38..e4ca846cc3 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -297,7 +297,7 @@ lib/gpu/README
"Section 2.6 -sf gpu"_Run_options.html
"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
-"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
+"Commands all"_lc pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -412,7 +412,7 @@ lib/kokkos/README
"Section 2.6 -sf kk"_Run_options.html
"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -1392,7 +1392,7 @@ src/USER-INTEL/README
"Section 2.6 -sf intel"_Run_options.html
"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -1698,7 +1698,7 @@ src/USER-OMP/README
"Section 2.6 -sf omp"_Run_options.html
"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 029c8f831c..3854552188 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -59,7 +59,7 @@ and callbacks to LAMMPS.
The "fix python/invoke"_fix_python_invoke.html command can execute
Python code at selected timesteps during a simulation run.
-The "pair_style python"_pair_python command allows you to define
+The "pair_style python"_pair_python.html command allows you to define
pairwise potentials as python code which encodes a single pairwise
interaction. This is useful for rapid-developement and debugging of a
new potential.
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index ef876a7d42..3b25ade4d2 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
-grid numa"_processors.html" to the beginning of the input script for
+grid numa"_processors.html to the beginning of the input script for
better scalability.
When running on many nodes, performance might be better when using
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index 6c837885cd..4c87091e7e 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available for a particular
-style, find the style name in the "Commands_all"_Commands_all.html
+style, find the style name in the "Commands_all"_lc
style pages (fix,compute,pair,etc) and see what suffixes are listed
(g,i,k,o,t) with it. The doc pages for individual commands
(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list
--
GitLab
From 4074c4c67f6a15d85fefcfb19eb83c25d404c34d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:08:07 -0400
Subject: [PATCH 122/332] correct some more broken or outdated links
---
doc/src/Build_settings.txt | 4 ++--
doc/src/Packages_details.txt | 5 +++--
doc/src/Packages_user.txt | 2 +-
3 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt
index 773217e3a0..dfe2f900f3 100644
--- a/doc/src/Build_settings.txt
+++ b/doc/src/Build_settings.txt
@@ -80,8 +80,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run using the "kspace_style
-pppm"_kspace_style.html command. The "Run output"_doc page gives more
-details.
+pppm"_kspace_style.html command. The "Run output"_Run_output.html
+doc page gives more details.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index e4ca846cc3..c415a4058c 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1582,8 +1582,6 @@ molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation
tools.
-:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
-
To use this package you must have the desired VMD plugins available on
your system.
@@ -1635,6 +1633,7 @@ tools:
"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org)
+:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
:link(atomeye,http://www.libatoms.org)
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@@ -1998,3 +1997,5 @@ src/USER-VTK: filenames -> commands
src/USER-VTK/README
lib/vtk/README
"dump vtk"_dump_vtk.html :ul
+
+
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index c1a52fd0d0..7db2fa895c 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -58,7 +58,7 @@ Package, Description, Doc page, Example, Library
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
--
GitLab
From 2aa4770e0decd7f4bf2c739c095db8b5519b9c5a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:16:11 -0400
Subject: [PATCH 123/332] correct link in AtC html docs
---
doc/src/USER/atc/man_add_molecule.html | 2 +-
doc/src/USER/atc/man_add_species.html | 2 +-
doc/src/USER/atc/man_atom_element_map.html | 2 +-
doc/src/USER/atc/man_atom_weight.html | 2 +-
doc/src/USER/atc/man_atomic_charge.html | 2 +-
doc/src/USER/atc/man_boundary.html | 2 +-
doc/src/USER/atc/man_boundary_dynamics.html | 2 +-
doc/src/USER/atc/man_boundary_faceset.html | 2 +-
doc/src/USER/atc/man_boundary_integral.html | 2 +-
doc/src/USER/atc/man_consistent_fe_initialization.html | 2 +-
doc/src/USER/atc/man_contour_integral.html | 2 +-
doc/src/USER/atc/man_control.html | 2 +-
doc/src/USER/atc/man_control_momentum.html | 2 +-
doc/src/USER/atc/man_control_thermal.html | 2 +-
.../USER/atc/man_control_thermal_correction_max_iterations.html | 2 +-
doc/src/USER/atc/man_decomposition.html | 2 +-
doc/src/USER/atc/man_electron_integration.html | 2 +-
doc/src/USER/atc/man_equilibrium_start.html | 2 +-
doc/src/USER/atc/man_extrinsic_exchange.html | 2 +-
doc/src/USER/atc/man_fe_md_boundary.html | 2 +-
doc/src/USER/atc/man_fem_mesh.html | 2 +-
doc/src/USER/atc/man_filter_scale.html | 2 +-
doc/src/USER/atc/man_filter_type.html | 2 +-
doc/src/USER/atc/man_fix_atc.html | 2 +-
doc/src/USER/atc/man_fix_flux.html | 2 +-
doc/src/USER/atc/man_fix_nodes.html | 2 +-
doc/src/USER/atc/man_hardy_computes.html | 2 +-
doc/src/USER/atc/man_hardy_fields.html | 2 +-
doc/src/USER/atc/man_hardy_gradients.html | 2 +-
doc/src/USER/atc/man_hardy_kernel.html | 2 +-
doc/src/USER/atc/man_hardy_on_the_fly.html | 2 +-
doc/src/USER/atc/man_hardy_rates.html | 2 +-
doc/src/USER/atc/man_initial.html | 2 +-
doc/src/USER/atc/man_internal_atom_integrate.html | 2 +-
doc/src/USER/atc/man_internal_element_set.html | 2 +-
doc/src/USER/atc/man_internal_quadrature.html | 2 +-
doc/src/USER/atc/man_kernel_function.html | 2 +-
doc/src/USER/atc/man_localized_lambda.html | 2 +-
doc/src/USER/atc/man_lumped_lambda_solve.html | 2 +-
doc/src/USER/atc/man_mask_direction.html | 2 +-
doc/src/USER/atc/man_mass_matrix.html | 2 +-
doc/src/USER/atc/man_material.html | 2 +-
doc/src/USER/atc/man_mesh_add_to_nodeset.html | 2 +-
doc/src/USER/atc/man_mesh_create.html | 2 +-
doc/src/USER/atc/man_mesh_create_elementset.html | 2 +-
doc/src/USER/atc/man_mesh_create_faceset_box.html | 2 +-
doc/src/USER/atc/man_mesh_create_faceset_plane.html | 2 +-
doc/src/USER/atc/man_mesh_create_nodeset.html | 2 +-
doc/src/USER/atc/man_mesh_delete_elements.html | 2 +-
doc/src/USER/atc/man_mesh_nodeset_to_elementset.html | 2 +-
doc/src/USER/atc/man_mesh_output.html | 2 +-
doc/src/USER/atc/man_mesh_quadrature.html | 2 +-
doc/src/USER/atc/man_mesh_read.html | 2 +-
doc/src/USER/atc/man_mesh_write.html | 2 +-
doc/src/USER/atc/man_momentum_time_integration.html | 2 +-
doc/src/USER/atc/man_output.html | 2 +-
doc/src/USER/atc/man_output_elementset.html | 2 +-
doc/src/USER/atc/man_output_nodeset.html | 2 +-
doc/src/USER/atc/man_pair_interactions.html | 2 +-
doc/src/USER/atc/man_poisson_solver.html | 2 +-
doc/src/USER/atc/man_read_restart.html | 2 +-
doc/src/USER/atc/man_remove_molecule.html | 2 +-
doc/src/USER/atc/man_remove_source.html | 2 +-
doc/src/USER/atc/man_remove_species.html | 2 +-
doc/src/USER/atc/man_reset_atomic_reference_positions.html | 2 +-
doc/src/USER/atc/man_reset_time.html | 2 +-
doc/src/USER/atc/man_sample_frequency.html | 2 +-
doc/src/USER/atc/man_set.html | 2 +-
doc/src/USER/atc/man_source.html | 2 +-
doc/src/USER/atc/man_source_integration.html | 2 +-
doc/src/USER/atc/man_temperature_definition.html | 2 +-
doc/src/USER/atc/man_thermal_time_integration.html | 2 +-
doc/src/USER/atc/man_time_filter.html | 2 +-
doc/src/USER/atc/man_track_displacement.html | 2 +-
doc/src/USER/atc/man_unfix_flux.html | 2 +-
doc/src/USER/atc/man_unfix_nodes.html | 2 +-
doc/src/USER/atc/man_write_atom_weights.html | 2 +-
doc/src/USER/atc/man_write_restart.html | 2 +-
78 files changed, 78 insertions(+), 78 deletions(-)
diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html
index 8d9625e1bd..4e7810aa61 100644
--- a/doc/src/USER/atc/man_add_molecule.html
+++ b/doc/src/USER/atc/man_add_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html
index 9beded1b16..a990ab626f 100644
--- a/doc/src/USER/atc/man_add_species.html
+++ b/doc/src/USER/atc/man_add_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html
index 6725170928..a5707d280e 100644
--- a/doc/src/USER/atc/man_atom_element_map.html
+++ b/doc/src/USER/atc/man_atom_element_map.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html
index 28bc90fa01..350ab13b92 100644
--- a/doc/src/USER/atc/man_atom_weight.html
+++ b/doc/src/USER/atc/man_atom_weight.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html
index ef787f53ac..17e854a37f 100644
--- a/doc/src/USER/atc/man_atomic_charge.html
+++ b/doc/src/USER/atc/man_atomic_charge.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html
index 61596d3b31..8dcf328dd3 100644
--- a/doc/src/USER/atc/man_boundary.html
+++ b/doc/src/USER/atc/man_boundary.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html
index 40b82f3f61..335ff2d209 100644
--- a/doc/src/USER/atc/man_boundary_dynamics.html
+++ b/doc/src/USER/atc/man_boundary_dynamics.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html
index 7eb950f78e..6c2fb84940 100644
--- a/doc/src/USER/atc/man_boundary_faceset.html
+++ b/doc/src/USER/atc/man_boundary_faceset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html
index 0663dba176..c4b0d4865e 100644
--- a/doc/src/USER/atc/man_boundary_integral.html
+++ b/doc/src/USER/atc/man_boundary_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index a731b09116..baa306a1c8 100644
--- a/doc/src/USER/atc/man_consistent_fe_initialization.html
+++ b/doc/src/USER/atc/man_consistent_fe_initialization.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html
index 690f0fcc98..16f6d9abad 100644
--- a/doc/src/USER/atc/man_contour_integral.html
+++ b/doc/src/USER/atc/man_contour_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html
index 900952ba0b..e94a9a52ef 100644
--- a/doc/src/USER/atc/man_control.html
+++ b/doc/src/USER/atc/man_control.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html
index 8f4f486595..e3074eae8f 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html
index eab186f715..8d32f1c4f9 100644
--- a/doc/src/USER/atc/man_control_thermal.html
+++ b/doc/src/USER/atc/man_control_thermal.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
index a337a495e0..d28ec334f5 100644
--- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
+++ b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html
index d54a201034..98eedafa6c 100644
--- a/doc/src/USER/atc/man_decomposition.html
+++ b/doc/src/USER/atc/man_decomposition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html
index ab454c16d2..7cf40f6813 100644
--- a/doc/src/USER/atc/man_electron_integration.html
+++ b/doc/src/USER/atc/man_electron_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
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<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
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<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
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<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
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diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html
index 46487fdce7..821e50e4cf 100644
--- a/doc/src/USER/atc/man_mesh_quadrature.html
+++ b/doc/src/USER/atc/man_mesh_quadrature.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html
index e0571ccf88..315180e1db 100644
--- a/doc/src/USER/atc/man_mesh_read.html
+++ b/doc/src/USER/atc/man_mesh_read.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html
index 756cf49922..f709c02a84 100644
--- a/doc/src/USER/atc/man_mesh_write.html
+++ b/doc/src/USER/atc/man_mesh_write.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html
index 60fbfcd888..ee0505847c 100644
--- a/doc/src/USER/atc/man_momentum_time_integration.html
+++ b/doc/src/USER/atc/man_momentum_time_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html
index aec1d5d55a..d0a08fa0da 100644
--- a/doc/src/USER/atc/man_output.html
+++ b/doc/src/USER/atc/man_output.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html
index 54079027c5..18afe0aa97 100644
--- a/doc/src/USER/atc/man_output_elementset.html
+++ b/doc/src/USER/atc/man_output_elementset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html
index 2fc6e02681..7906c5fc52 100644
--- a/doc/src/USER/atc/man_output_nodeset.html
+++ b/doc/src/USER/atc/man_output_nodeset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html
index 2cb2cb6113..3ec2eecc60 100644
--- a/doc/src/USER/atc/man_pair_interactions.html
+++ b/doc/src/USER/atc/man_pair_interactions.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html
index b6fabbb27c..3e22a51f3e 100644
--- a/doc/src/USER/atc/man_poisson_solver.html
+++ b/doc/src/USER/atc/man_poisson_solver.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html
index 5fc21282f6..d13151a12e 100644
--- a/doc/src/USER/atc/man_read_restart.html
+++ b/doc/src/USER/atc/man_read_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html
index e6ad418de6..54e4e3419f 100644
--- a/doc/src/USER/atc/man_remove_molecule.html
+++ b/doc/src/USER/atc/man_remove_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html
index acea7a5607..c15e0ca46d 100644
--- a/doc/src/USER/atc/man_remove_source.html
+++ b/doc/src/USER/atc/man_remove_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html
index 561364518f..ee063ce57f 100644
--- a/doc/src/USER/atc/man_remove_species.html
+++ b/doc/src/USER/atc/man_remove_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
index 88e6748001..3c43861054 100644
--- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html
+++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html
index a6429bf6d6..9607848e1a 100644
--- a/doc/src/USER/atc/man_reset_time.html
+++ b/doc/src/USER/atc/man_reset_time.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html
index 4e48c4bb29..9a9a8e3a02 100644
--- a/doc/src/USER/atc/man_sample_frequency.html
+++ b/doc/src/USER/atc/man_sample_frequency.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html
index cf775c9b36..55ad8d952b 100644
--- a/doc/src/USER/atc/man_set.html
+++ b/doc/src/USER/atc/man_set.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html
index c7239f2c41..78fb1652eb 100644
--- a/doc/src/USER/atc/man_source.html
+++ b/doc/src/USER/atc/man_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html
index 3f43340af8..3b261b7810 100644
--- a/doc/src/USER/atc/man_source_integration.html
+++ b/doc/src/USER/atc/man_source_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html
index a07ba29cab..c317c06c00 100644
--- a/doc/src/USER/atc/man_temperature_definition.html
+++ b/doc/src/USER/atc/man_temperature_definition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html
index fe293138be..830591921e 100644
--- a/doc/src/USER/atc/man_thermal_time_integration.html
+++ b/doc/src/USER/atc/man_thermal_time_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html
index 732eaa3a36..5000fb079d 100644
--- a/doc/src/USER/atc/man_time_filter.html
+++ b/doc/src/USER/atc/man_time_filter.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html
index f5410816d7..2c7cf26150 100644
--- a/doc/src/USER/atc/man_track_displacement.html
+++ b/doc/src/USER/atc/man_track_displacement.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html
index 95e1f4be5a..551896431a 100644
--- a/doc/src/USER/atc/man_unfix_flux.html
+++ b/doc/src/USER/atc/man_unfix_flux.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html
index 78495c928a..4dfd9b3cfc 100644
--- a/doc/src/USER/atc/man_unfix_nodes.html
+++ b/doc/src/USER/atc/man_unfix_nodes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html
index 8a0e5b62a8..1722d74f67 100644
--- a/doc/src/USER/atc/man_write_atom_weights.html
+++ b/doc/src/USER/atc/man_write_atom_weights.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html
index 6dca57673b..74c6e2d289 100644
--- a/doc/src/USER/atc/man_write_restart.html
+++ b/doc/src/USER/atc/man_write_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
--
GitLab
From 357ffef09cbb4c01cfe88ac729e8d47ea2afdd70 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:16:36 -0400
Subject: [PATCH 124/332] fix some more broken links detected by ebook
conversion
---
doc/src/compute_coord_atom.txt | 2 +-
doc/src/compute_pressure_uef.txt | 4 ++--
doc/src/compute_temp_uef.txt | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index 66eecd195d..ddc4cc82d3 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -67,7 +67,7 @@ identify crystal-like atoms in a system, as discussed in "ten
Wolde"_#tenWolde1.
The ID of the previously specified "compute
-orientorder/atom"_compute_orientorder/atom command is specified as
+orientorder/atom"_compute_orientorder_atom.html command is specified as
{orientorderID}. The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
described in its documentation. Note that orientorder/atom compute
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index c4c0fc405f..72ed0ba5c4 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -27,8 +27,8 @@ compute 2 all pressure/uef my_temp_uef virial :pre
This command is used to compute the pressure tensor in
the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or
-"fix npt/uef"_fix_nh_uef.html" is used.
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html is used.
It is not necessary to use this command to compute the scalar
value of the pressure. A "compute pressure"_compute_pressure.html
may be used for that purpose.
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index 9a509da450..97e1d6e1ae 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -24,8 +24,8 @@ compute 2 sel temp/uef :pre
This command is used to compute the kinetic energy tensor in
the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or
-"fix npt/uef"_fix_nh_uef.html" is used.
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html is used.
It is not necessary to use this command to compute the scalar
value of the temperature. A "compute temp"_compute_temp.html
may be used for that purpose.
--
GitLab
From d5089858bdb9ae85f8ba388070765616430cda8f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:17:21 -0400
Subject: [PATCH 125/332] add support for the conversion of ePUB to MOBI
(compatible with Kindle)
---
doc/Makefile | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/doc/Makefile b/doc/Makefile
index 81f3623499..797095dfad 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
-.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
# ------------------------------------------
@@ -42,6 +42,7 @@ help:
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
+ @echo " mobi create MOBI format manual for e-book readers (e.g. Kindle)"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
@@ -106,6 +107,11 @@ epub: $(OBJECTS)
@rm -rf epub
@echo "Build finished. The ePUB manual file is created."
+mobi: epub
+ @rm -f LAMMPS.mobi
+ @ebook-convert LAMMPS.epub LAMMPS.mobi
+ @echo "Conversion finished. The MOBI manual file is created."
+
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \
--
GitLab
From 01fe3569041f5f8c19b9f46ebf4600e110bcfeae Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Wed, 22 Aug 2018 17:18:36 -0600
Subject: [PATCH 126/332] first version of scafacos.h without the inclusion of
the ScaFaCoS header
---
src/USER-SCAFACOS/scafacos.cpp | 83 +++++++++++++++++++---------------
src/USER-SCAFACOS/scafacos.h | 19 ++++----
2 files changed, 55 insertions(+), 47 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 7c2dd0b68d..92d0612947 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -90,7 +90,7 @@ Scafacos::~Scafacos()
memory->destroy(efield);
// clean up of the ScaFaCoS handle and internal arrays
- fcs_destroy(fcs);
+ fcs_destroy((FCS)fcs);
}
/* ---------------------------------------------------------------------- */
@@ -112,20 +112,24 @@ void Scafacos::init()
if (domain->triclinic)
error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
- if (atom->natoms > INT_MAX && sizeof(fcs_int) != 8)
+ if (atom->natoms > INT_MAX && sizeof(int) != 8)
error->all(FLERR,"Scafacos atom count exceeds 2B");
if (atom->molecular > 0)
error->all(FLERR,
"Cannot use Scafacos with molecular charged systems yet");
+ FCSResult result;
+
// one-time initialization of ScaFaCoS
qqrd2e = force->qqrd2e;
if (!initialized) {
- result = fcs_init(&fcs,method,world);
- check_result(result);
+ printf("DEBUG: %p\n",&fcs);
+ result = fcs_init((FCS*)&fcs,method,world);
+ check_result((void*)&result);
+ printf("DEBUG: %p\n",&fcs);
setup_handle();
@@ -136,8 +140,8 @@ void Scafacos::init()
strcmp(method,"p2nfft") == 0 ||
strcmp(method,"ewald") == 0)
{
- result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
- check_result(result);
+ result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance);
+ check_result((void*)&result);
}
double **x = atom->x;
@@ -147,9 +151,9 @@ void Scafacos::init()
if (strcmp(method,"fmm") == 0)
{
if (fmm_tuning_flag == 1)
- fcs_fmm_set_internal_tuning(fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
+ fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
else
- fcs_fmm_set_internal_tuning(fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
+ fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
}
// for the FMM at least one particle is required per process
@@ -158,15 +162,15 @@ void Scafacos::init()
int empty = (nlocal==0)?1:0;
MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
if (empty > 0)
- fcs_set_redistribute(fcs,1);
+ fcs_set_redistribute((FCS)fcs,1);
else
- fcs_set_redistribute(fcs,0);
+ fcs_set_redistribute((FCS)fcs,0);
}
- result = fcs_tune(fcs,nlocal,&x[0][0],q);
- check_result(result);
+ result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q);
+ check_result((void*)&result);
// more useful here, since the parameters should be tuned now
- if (me == 0) fcs_print_parameters(fcs);
+ if (me == 0) fcs_print_parameters((FCS)fcs);
}
initialized = 1;
@@ -181,6 +185,7 @@ void Scafacos::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
const double qscale = qqrd2e;
+ FCSResult result;
// for the FMM at least one particle is required per process
if (strcmp(method,"fmm"))
@@ -188,9 +193,9 @@ void Scafacos::compute(int eflag, int vflag)
int empty = (nlocal==0)?1:0;
MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
if (empty > 0)
- fcs_set_redistribute(fcs,1);
+ fcs_set_redistribute((FCS)fcs,1);
else
- fcs_set_redistribute(fcs,0);
+ fcs_set_redistribute((FCS)fcs,0);
}
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -214,7 +219,7 @@ void Scafacos::compute(int eflag, int vflag)
if (vflag_global)
{
- fcs_set_compute_virial(fcs,1);
+ fcs_set_compute_virial((FCS)fcs,1);
//if (strcmp(method,"p3m") == 0)
// error->all(FLERR,"ScaFaCoS p3m does not support computation of virial");
}
@@ -223,8 +228,8 @@ void Scafacos::compute(int eflag, int vflag)
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
- int j = 0;
if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){
+ int j = 0;
for (int i = 0; i < nlocal; i++) {
domain->remap(&xpbc[j]);
j += 3;
@@ -234,20 +239,20 @@ void Scafacos::compute(int eflag, int vflag)
if (box_has_changed()) {
setup_handle();
- result = fcs_tune(fcs,nlocal,xpbc,q);
- check_result(result);
+ result = fcs_tune((FCS)fcs,nlocal,xpbc,q);
+ check_result((void*)&result);
}
// invoke ScaFaCoS solver
- result = fcs_run(fcs,nlocal,xpbc,q,&efield[0][0],epot);
- check_result(result);
+ result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot);
+ check_result((void*)&result);
// extract virial
if (vflag_global)
{
- fcs_get_virial(fcs,virial_int);
+ fcs_get_virial((FCS)fcs,virial_int);
virial[0] = virial_int[0];
virial[1] = virial_int[1];
virial[2] = virial_int[2];
@@ -380,6 +385,8 @@ double Scafacos::memory_usage()
void Scafacos::setup_handle()
{
+ FCSResult result;
+
// store simulation box params
// setup periodicity
@@ -404,23 +411,23 @@ void Scafacos::setup_handle()
old_natoms = atom->natoms;
// store parameters to ScaFaCoS handle
- result = fcs_set_box_a(fcs,old_box_x);
- check_result(result);
+ result = fcs_set_box_a((FCS)fcs,old_box_x);
+ check_result((void*)&result);
- result = fcs_set_box_b(fcs,old_box_y);
- check_result(result);
+ result = fcs_set_box_b((FCS)fcs,old_box_y);
+ check_result((void*)&result);
- result = fcs_set_box_c(fcs,old_box_z);
- check_result(result);
+ result = fcs_set_box_c((FCS)fcs,old_box_z);
+ check_result((void*)&result);
- result = fcs_set_box_origin(fcs,old_origin);
- check_result(result);
+ result = fcs_set_box_origin((FCS)fcs,old_origin);
+ check_result((void*)&result);
- result = fcs_set_periodicity(fcs,old_periodicity);
- check_result(result);
+ result = fcs_set_periodicity((FCS)fcs,old_periodicity);
+ check_result((void*)&result);
- result = fcs_set_total_particles(fcs,old_natoms);
- check_result(result);
+ result = fcs_set_total_particles((FCS)fcs,old_natoms);
+ check_result((void*)&result);
// allow ScaFaCoS to calculate the near field computations for now
// TODO: allow the delegation of the near field computations
@@ -428,8 +435,8 @@ void Scafacos::setup_handle()
// (near_field_flag = 1 -> enables the internal near field calcs
// 0 -> disables the internal near field calcs
int near_field_flag = 1;
- result = fcs_set_near_field_flag(fcs,near_field_flag);
- check_result(result);
+ result = fcs_set_near_field_flag((FCS)fcs,near_field_flag);
+ check_result((void*)&result);
}
/* ----------------------------------------------------------------------
@@ -460,8 +467,10 @@ bool Scafacos::box_has_changed()
check ScaFaCoS result for error condition
------------------------------------------------------------------------- */
-void Scafacos::check_result(FCSResult result)
+void Scafacos::check_result(void* result_p)
{
+ FCSResult result = *(FCSResult*)result_p;
+
if (!result) return;
std::stringstream ss;
diff --git a/src/USER-SCAFACOS/scafacos.h b/src/USER-SCAFACOS/scafacos.h
index bf07b3b45a..fdf15739a6 100644
--- a/src/USER-SCAFACOS/scafacos.h
+++ b/src/USER-SCAFACOS/scafacos.h
@@ -21,7 +21,7 @@ KSpaceStyle(scafacos,Scafacos)
#define LMP_SCAFACOS_H
#include "kspace.h"
-#include "fcs.h"
+//#include "fcs.h"
namespace LAMMPS_NS {
@@ -35,7 +35,7 @@ class Scafacos : public KSpace {
int modify_param(int, char **);
double memory_usage();
- private:
+ private:
int me;
char *method;
@@ -46,20 +46,19 @@ class Scafacos : public KSpace {
int fmm_tuning_flag;
- FCS fcs; // ScaFaCoS handle
- FCSResult result; // result for each ScaFaCoS call
+ void* fcs; // ScaFaCoS handle
// simulation state: box, natoms
// so ScaFaCoS can detect if changes, e.g. for NPT
- fcs_float old_box_x[3],old_box_y[3],old_box_z[3];
- fcs_float old_origin[3];
- fcs_int old_periodicity[3];
- fcs_int old_natoms;
+ double old_box_x[3],old_box_y[3],old_box_z[3];
+ double old_origin[3];
+ int old_periodicity[3];
+ int old_natoms;
- fcs_float virial_int[9];
+ double virial_int[9];
- void check_result(FCSResult);
+ void check_result(void*);
void setup_handle();
bool box_has_changed();
};
--
GitLab
From 0e292b397f02f1e2e472cbbff55a5cad963075de Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:41:44 -0400
Subject: [PATCH 127/332] even more broken links detected by ePUB to MOBI
conversion
---
doc/src/Build_basics.txt | 4 ++--
doc/src/Run_windows.txt | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index cee78aced3..c9df7915e5 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -216,8 +216,8 @@ LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the "Howto couple"_Howto_couple.html doc
page for more info on coupling LAMMPS to other codes. See the
-"Python"_Python doc page for more info on wrapping and running LAMMPS
-from Python via its library interface.
+"Python"_Python_head.html doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
[CMake variables]:
diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt
index 2b93cc7d49..85c9a6550d 100644
--- a/doc/src/Run_windows.txt
+++ b/doc/src/Run_windows.txt
@@ -33,8 +33,8 @@ in parallel, follow these steps.
Download and install a compatible MPI library binary package:
-for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
-for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
+for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the
--
GitLab
From c8ac88dd8752ddf92fdfdbd4d7fb30748e3cd001 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 19:46:49 -0400
Subject: [PATCH 128/332] update link in LAMMPS theme for Sphinx
---
doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
index 39ee684a0b..1eb53c70a2 100644
--- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
+++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
@@ -18,7 +18,7 @@
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
{% endif %}
<a href="http://lammps.sandia.gov">Website</a>
- <a href="Section_commands.html#comm">Commands</a>
+ <a href="Commands_all.html">Commands</a>
{% endif %}
</li>
</ul>
--
GitLab
From 9e37ea16acfdc9fbb29c0856c145cc8af0e5838b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 20:35:35 -0400
Subject: [PATCH 129/332] fix some speelink ehrrors
---
doc/src/Commands_parse.txt | 4 ++--
doc/src/pair_python.txt | 2 +-
doc/src/pair_style.txt | 2 +-
doc/src/reset_ids.txt | 2 +-
doc/src/run_style.txt | 2 +-
5 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt
index cbe2261986..1d7c754fa7 100644
--- a/doc/src/Commands_parse.txt
+++ b/doc/src/Commands_parse.txt
@@ -14,7 +14,7 @@ LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
-Here are 6 rulse for how each line in the input script is parsed by
+Here are 6 rules for how each line in the input script is parsed by
LAMMPS:
(1) If the last printable character on the line is a "&" character,
@@ -71,7 +71,7 @@ floating-point value. The format string is used to output the result
of the variable expression evaluation. If a format string is not
specified a high-precision "%.20g" is used as the default.
-This can be useful for formatting print output to a desired precion:
+This can be useful for formatting print output to a desired precision:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 23da86fc49..b7130c8a10 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -98,7 +98,7 @@ verify, that the potential definition in the python class and in the
LAMMPS input match.
Here is an example for a single type Lennard-Jones potential class
-{LJCutMelt} in reducted units, which defines an atom type {lj} for
+{LJCutMelt} in reduced units, which defines an atom type {lj} for
which the parameters epsilon and sigma are both 1.0:
class LJCutMelt(LAMMPSPairPotential):
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index b33897c5aa..1441da2b61 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -93,7 +93,7 @@ There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs,
GPUs, and KNLs. The individual style names on the "Commands
pair"_Commands_pair.html doc page are followed by one or more of
-(g,i,k,o,t) to indicate which accerlerated styles exist.
+(g,i,k,o,t) to indicate which accelerated styles exist.
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt
index 391b51fde9..8b217c7b1c 100644
--- a/doc/src/reset_ids.txt
+++ b/doc/src/reset_ids.txt
@@ -23,7 +23,7 @@ for bond, angle, dihedral, improper topology data. This will
create a set of IDs that are numbered contiguously from 1 to N
for a N atoms system.
-This can be useful to do after perfoming a "delete_atoms" command for
+This can be useful to do after performing a "delete_atoms" command for
a molecular system. The delete_atoms compress yes option will not
perform this operation due to the existence of bond topology. It can
also be useful to do after any simulation which has lost atoms,
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 6dd9b56908..9defd1314e 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -318,7 +318,7 @@ bond forces = level 1 (innermost loop)
angle forces = same level as bond forces
dihedral forces = same level as angle forces
improper forces = same level as dihedral forces
-pair forces = leven N (outermost level)
+pair forces = level N (outermost level)
kspace forces = same level as pair forces
inner, middle, outer forces = no default :ul
--
GitLab
From ffb1a9c46acfb03318a8ab56c9324391a090cd13 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 20:36:01 -0400
Subject: [PATCH 130/332] update link in lammps theme for sphinx
---
doc/utils/converters/tests/test_lammps_filters.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/utils/converters/tests/test_lammps_filters.py b/doc/utils/converters/tests/test_lammps_filters.py
index 6c25c23a79..8d2fa2e577 100644
--- a/doc/utils/converters/tests/test_lammps_filters.py
+++ b/doc/utils/converters/tests/test_lammps_filters.py
@@ -47,7 +47,7 @@ class TestStructuralFilters(unittest.TestCase):
self.assertEqual("Title\n\n"
"\n.. _lws: http://lammps.sandia.gov\n"
".. _ld: Manual.html\n"
- ".. _lc: Section_commands.html#comm\n", s)
+ ".. _lc: Commands_all.html\n", s)
def test_filter_multiple_horizontal_rules(self):
s = self.txt2rst.convert(":hline\n"
--
GitLab
From 1bd56261406452cc6e3d601cac2883669b593d0e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 20:43:35 -0400
Subject: [PATCH 131/332] fix some more spelling issues
---
doc/src/Build_basics.txt | 8 ++++----
doc/src/Build_cmake.txt | 2 +-
doc/src/Build_extras.txt | 4 ++--
doc/src/Build_settings.txt | 6 +++---
4 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index c9df7915e5..6924e73417 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -61,7 +61,7 @@ library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
are found, and the name of the library files (MPI_LIB).
-For a serial build, you need to specify the 3 varaibles, as shown
+For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
@@ -145,7 +145,7 @@ By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any "accelerator
packages"_Speed_packages.html you have included in the build.
-You can tell CMake to look for a specific compiler with these varaible
+You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
@@ -247,7 +247,7 @@ Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
-the lib/packages directroy, since they are always built as shared
+the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
@@ -299,7 +299,7 @@ Install LAMMPS after a build :h4,link(install)
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
-that you may need super-user priveleges (e.g. sudo) if the directory
+that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
[CMake variable]:
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
index 08c1c72180..6298ab2576 100644
--- a/doc/src/Build_cmake.txt
+++ b/doc/src/Build_cmake.txt
@@ -50,7 +50,7 @@ make install # optional, copy LAMMPS executable & library elsewhere :pre
:line
-There are 3 variants of CMake: a command-line verison (cmake), a text mode
+There are 3 variants of CMake: a command-line version (cmake), a text mode
UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
any of them interchangeably to configure and create the LAMMPS build
environment. On Linux all the versions produce a Makefile as their
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 5c33a0a4d4..2aa7de2b12 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -340,7 +340,7 @@ NOTE: the use of the MEAM package is discouraged, as it has been
superseded by the USER-MEAMC package, which is a direct translation of
the Fortran code in the MEAM library to C++. The code in USER-MEAMC
should be functionally equivalent to the MEAM package, fully supports
-use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
+use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
not), and has optimizations that make it significantly faster than the
MEAM package.
@@ -470,7 +470,7 @@ lib/python/README for more details.
-D PYTHON_EXECUTABLE=path # path to Python executable to use :pre
-Without this setting, CMake will ues the default Python on your
+Without this setting, CMake will guess the default Python on your
system. To use a different Python version, you can either create a
virtualenv, activate it and then run cmake. Or you can set the
PYTHON_EXECUTABLE variable to specify which Python interpreter should
diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt
index dfe2f900f3..500130ecee 100644
--- a/doc/src/Build_settings.txt
+++ b/doc/src/Build_settings.txt
@@ -101,7 +101,7 @@ Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
-4-byte floats. Double precesion means they are 8-byte doubles. Note
+4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT_SINGLE
@@ -193,7 +193,7 @@ Output of JPG, PNG, and movie files :h4,link(graphics)
The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command
-ouputs movie files in MPEG format. Using these options requires the
+outputs movie files in MPEG format. Using these options requires the
following settings:
[CMake variables]:
@@ -206,7 +206,7 @@ following settings:
# default = yes if CMake can find ffmpeg, else no :pre
Usually these settings are all that is needed. If CMake cannot find
-the graphics header, library, executuable files, you can set these
+the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
--
GitLab
From e632acec297b1594723bfee2c1961b3db4470590 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:30:21 -0400
Subject: [PATCH 132/332] fix a bunch more spelling errors
---
doc/src/Build_extras.txt | 2 +-
doc/src/Build_make.txt | 4 ++--
doc/src/Errors_warnings.txt | 2 +-
doc/src/Howto_barostat.txt | 6 +++---
doc/src/Howto_body.txt | 2 +-
doc/src/Howto_library.txt | 8 ++++----
doc/src/Howto_spins.txt | 6 +++---
doc/src/Intro_overview.txt | 4 ++--
doc/src/Manual_build.txt | 18 +++++++++---------
doc/src/Modify_overview.txt | 2 +-
doc/src/Packages_details.txt | 4 ++--
doc/src/Python_call.txt | 2 +-
doc/src/Python_head.txt | 4 ++--
doc/src/Python_library.txt | 10 +++++-----
doc/src/Run_basics.txt | 2 +-
doc/src/Speed_bench.txt | 6 +++---
doc/src/Speed_gpu.txt | 2 +-
doc/src/Speed_intel.txt | 2 +-
doc/src/Speed_omp.txt | 2 +-
doc/src/atom_modify.txt | 2 +-
doc/src/compute.txt | 2 +-
doc/src/compute_displace_atom.txt | 2 +-
doc/src/compute_entropy_atom.txt | 10 +++++-----
doc/src/compute_property_atom.txt | 2 +-
doc/src/compute_spin.txt | 2 +-
doc/src/delete_atoms.txt | 2 +-
doc/src/dump_modify.txt | 2 +-
doc/src/fix.txt | 4 ++--
doc/src/fix_filter_corotate.txt | 2 +-
doc/src/fix_langevin_spin.txt | 2 +-
doc/src/fix_latte.txt | 2 +-
doc/src/fix_neb.txt | 2 +-
doc/src/fix_nh_uef.txt | 2 +-
doc/src/fix_surface_global.txt | 2 +-
doc/src/pair_buck6d_coul_gauss.txt | 6 +++---
doc/src/pair_coeff.txt | 2 +-
doc/src/pair_ilp_graphene_hbn.txt | 2 +-
doc/src/pair_kolmogorov_crespi_z.txt | 2 +-
doc/src/restart.txt | 2 +-
doc/src/special_bonds.txt | 2 +-
40 files changed, 72 insertions(+), 72 deletions(-)
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 2aa7de2b12..e141c62a3a 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -905,7 +905,7 @@ Eigen3 is a template library, so you do not need to build it.
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre
If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
-inside the CMake build directory. If the Eig3n3 library is already on
+inside the CMake build directory. If the Eigen3 library is already on
your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
is the directory the Eigen3++ include file is in.
diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt
index c00ce1f420..a18d812b59 100644
--- a/doc/src/Build_make.txt
+++ b/doc/src/Build_make.txt
@@ -71,8 +71,8 @@ Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags
for optimized performance. Please note, however, that some of these
customized machine Makefile are contributed by users. Since both
-compilers, OS configs, and LAMMPS itself keep changing, their settings
-may become outdated:
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index dd3402ba86..98b66f2aa5 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -13,7 +13,7 @@ This is an alphabetic list of the WARNING messages LAMMPS prints out
and the reason why. If the explanation here is not sufficient, the
documentation for the offending command may help. Warning messages
also list the source file and line number where the warning was
-generated. For example, a message lile this:
+generated. For example, a message like this:
WARNING: Bond atom missing in box size check (domain.cpp:187) :pre
diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt
index 7c3db89152..3323334600 100644
--- a/doc/src/Howto_barostat.txt
+++ b/doc/src/Howto_barostat.txt
@@ -64,11 +64,11 @@ Thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes pressure
values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default pressure is
-setup by the thermo command itself. It is NOT the presure associated
+setup by the thermo command itself. It is NOT the pressure associated
with any barostatting fix you have defined or with any compute you
-have defined that calculates a presure. The doc pages for the
+have defined that calculates a pressure. The doc pages for the
barostatting fixes explain the ID of the pressure compute they create.
-Thus if you want to view these pressurse, you need to specify them
+Thus if you want to view these pressures, you need to specify them
explicitly via the "thermo_style custom"_thermo_style.html command.
Or you can use the "thermo_modify"_thermo_modify.html command to
re-define what pressure compute is used for default thermodynamic
diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt
index 3535349b46..3e7db9bc8e 100644
--- a/doc/src/Howto_body.txt
+++ b/doc/src/Howto_body.txt
@@ -337,7 +337,7 @@ the sphere that surrounds each vertex. The diameter value can be
different for each body particle. These floating-point values can be
listed on as many lines as you wish; see the
"read_data"_read_data.html command for more details. Because the
-maxmimum vertices per face is hard-coded to be 4
+maximum number of vertices per face is hard-coded to be 4
(i.e. quadrilaterals), faces with more than 4 vertices need to be
split into triangles or quadrilaterals. For triangular faces, the
last vertex index should be set to -1.
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index 741078e7eb..9a9656784c 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -171,16 +171,16 @@ void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
+same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
-resulting vector is not ordered by atom ID. Atom IDs can be requetsed
+resulting vector is not ordered by atom ID. Atom IDs can be requested
by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt
index 1b9adb49a5..b549f99be2 100644
--- a/doc/src/Howto_spins.txt
+++ b/doc/src/Howto_spins.txt
@@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Magnetic spins :h3
-The magnetic spin simualtions are enabled by the SPIN package, whose
+The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
-The model representents the simulation of atomic magnetic spins coupled
+The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
@@ -43,7 +43,7 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
-All the computed magnetic properties can be outputed by two main
+All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or
diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt
index 49c14bc5f0..cd822c778f 100644
--- a/doc/src/Intro_overview.txt
+++ b/doc/src/Intro_overview.txt
@@ -17,7 +17,7 @@ variety of interatomic potentials (force fields) and boundary
conditions. It can model 2d or 3d systems with only a few particles
up to millions or billions.
-LAMMPS can be built and run on a laptop or destop machine, but is
+LAMMPS can be built and run on a laptop or desktop machine, but is
designed for parallel computers. It will run on any parallel machine
that supports the "MPI"_mpi message-passing library. This includes
shared-memory boxes and distributed-memory clusters and
@@ -45,7 +45,7 @@ nature; some long-range models are included as well.
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
-too large. This is in contrast to methods used for modeling plasmas
+too large. This is in contrast to methods used for modeling plasma
or gravitational bodies (e.g. galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques to
diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt
index a6b881cb79..ac12dd7b2e 100644
--- a/doc/src/Manual_build.txt
+++ b/doc/src/Manual_build.txt
@@ -10,15 +10,16 @@ Section"_Manual.html :c
Building the LAMMPS manual :h2
-Depending on how you obtained LAMMPS, the doc directory has
-2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
+Depending on how you obtained LAMMPS, the doc directory has 2 or 3
+sub-directories and optionally 2 PDF files and 2 e-book format files:
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
tools # tools and settings for building the documentation
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
-LAMMPS.epub # Manual in ePUB format :pre
+LAMMPS.epub # Manual in ePUB e-book format
+LAMMPS.mobi # Manual in MOBI e-book format :pre
If you downloaded LAMMPS as a tarball from the web site, all these
directories and files should be included.
@@ -40,7 +41,7 @@ HTML files already exist. This requires various tools including
Sphinx, which the build process will attempt to download and install
on your system, if not already available. See more details below.
-(c) You can genererate an older, simpler, less-fancy style of HTML
+(c) You can generate an older, simpler, less-fancy style of HTML
documentation by typing "make old". This will create an "old"
directory. This can be useful if (b) does not work on your box for
some reason, or you want to quickly view the HTML version of a doc
@@ -61,6 +62,7 @@ make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
+make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data :pre
@@ -68,7 +70,7 @@ make clean-all # remove entire build folder and any cached data :pre
Installing prerequisites for HTML build :h3
-To run the HTML documention build toolchain, Python 3 and virtualenv
+To run the HTML documentation build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
Ubuntu :h4
@@ -115,10 +117,8 @@ ePUB :h4
Same as for HTML. This uses the same tools and configuration
files as the HTML tree.
-For converting the generated ePUB file to a mobi format file
+For converting the generated ePUB file to a MOBI format file
(for e-book readers like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
-You first create the ePUB file with 'make epub' and then do:
-
-ebook-convert LAMMPS.epub LAMMPS.mobi :pre
+You first create the ePUB file and then convert it with 'make mobi'
diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt
index cf94b40281..4ab1eddf21 100644
--- a/doc/src/Modify_overview.txt
+++ b/doc/src/Modify_overview.txt
@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Overview :h3
The best way to add a new feature to LAMMPS is to find a similar
-featureand look at the corresponding source and header files to figure
+feature and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index c415a4058c..188081c8dd 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -851,7 +851,7 @@ multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
verlet/split algorithm for performing long-range Coulombics on one set
-of processors, and the remainder of the force field calcalation on
+of processors, and the remainder of the force field calculation on
another set.
[Supporting info:]
@@ -874,7 +874,7 @@ RIGID package :link(PKG-RIGID),h4
[Contents:]
Fixes which enforce rigid constraints on collections of atoms or
-particles. This includes SHAKE and RATTLE, as well as varous
+particles. This includes SHAKE and RATTLE, as well as various
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 3854552188..3c382de1ba 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -61,7 +61,7 @@ Python code at selected timesteps during a simulation run.
The "pair_style python"_pair_python.html command allows you to define
pairwise potentials as python code which encodes a single pairwise
-interaction. This is useful for rapid-developement and debugging of a
+interaction. This is useful for rapid development and debugging of a
new potential.
To use any of these commands, you only need to build LAMMPS with the
diff --git a/doc/src/Python_head.txt b/doc/src/Python_head.txt
index 1f02368429..54f995c565 100644
--- a/doc/src/Python_head.txt
+++ b/doc/src/Python_head.txt
@@ -62,11 +62,11 @@ library interface provided in src/library.h and src/library.h. That
interface is exposed to Python either when calling LAMMPS from Python
or when calling Python from a LAMMPS input script and then calling
back to LAMMPS from Python code. The library interface is designed to
-be easy to add funcionality to. Thus the Python interface to LAMMPS
+be easy to add functionality to. Thus the Python interface to LAMMPS
is also easy to extend as well.
If you create interesting Python scripts that run LAMMPS or
interesting Python functions that can be called from a LAMMPS input
-script, that you think would be genearlly useful, please post them as
+script, that you think would be generally useful, please post them as
a pull request to our "GitHub site"_https://github.com/lammps/lammps,
and they can be added to the LAMMPS distribution or webpage.
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index 9a3ea93fc3..e76af83962 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -186,20 +186,20 @@ keyword as a float.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
-The set_variable() methosd sets an existing string-style variable to a
+The set_variable() method sets an existing string-style variable to a
new string value, so that subsequent LAMMPS commands can access the
variable.
-The reset_box() emthods resets the size and shape of the simulation
+The reset_box() method resets the size and shape of the simulation
box, e.g. as part of restoring a previously extracted and saved state
of a simulation.
The gather methods collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
+same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
Note that the data returned by the gather methods,
e.g. gather_atoms("x"), is different from the data structure returned
diff --git a/doc/src/Run_basics.txt b/doc/src/Run_basics.txt
index 02139a8c69..1b7387b46b 100644
--- a/doc/src/Run_basics.txt
+++ b/doc/src/Run_basics.txt
@@ -75,7 +75,7 @@ setenv OMP_NUM_THREADS 2 # csh or tcsh :pre
This can also be done via the "package"_package.html command or via
the "-pk command-line switch"_Run_options.html which invokes the
package command. See the "package"_package.html command or
-"Speed"_Speed.html doc pages for more details about which accerlarator
+"Speed"_Speed.html doc pages for more details about which accelerator
packages and which commands support multi-threading.
:line
diff --git a/doc/src/Speed_bench.txt b/doc/src/Speed_bench.txt
index 8e407d14ea..a3d0bf4f46 100644
--- a/doc/src/Speed_bench.txt
+++ b/doc/src/Speed_bench.txt
@@ -11,7 +11,7 @@ Benchmarks :h3
Current LAMMPS performance is discussed on the "Benchmarks
page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
-where timings and parallel efficiencies are listed. The page has
+where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
@@ -77,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated.
Performance on a parallel machine can also be predicted from one-core
or one-node timings if the parallel efficiency can be estimated. The
communication bandwidth and latency of a particular parallel machine
-affects the efficiency. On most machines LAMMPS will give parallel
-efficiencies on these benchmarks above 50% so long as the number of
+affects the efficiency. On most machines LAMMPS will give a parallel
+efficiency on these benchmarks above 50% so long as the number of
atoms/core is a few 100 or greater, and closer to 100% for large
numbers of atoms/core. This is for all-MPI mode with one MPI task per
core. For nodes with accelerator options or hardware (OpenMP, GPU,
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index acef5bf6c1..bddefc5031 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -62,7 +62,7 @@ Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-d
installed. There can be multiple of them for the same or different hardware
(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
as 'platforms'. The GPU library will select the [first] suitable platform,
-but this can be overridded using the device option of the "package"_package.html
+but this can be overridden using the device option of the "package"_package.html
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
platforms and devices with a suitable ICD available.
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index 3b25ade4d2..bf078fb576 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -68,7 +68,7 @@ In most molecular dynamics software, parallelization parameters
to changing the order of operations with finite-precision
calculations. The USER-INTEL package is deterministic. This means
that the results should be reproducible from run to run with the
-{same} parallel configurations and when using determinstic
+{same} parallel configurations and when using deterministic
libraries or library settings (MPI, OpenMP, FFT). However, there
are differences in the USER-INTEL package that can change the
order of operations compared to LAMMPS without acceleration:
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index 0abf54430e..238909d1b4 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -29,7 +29,7 @@ instructions.
[Run with the USER-OMP package from the command line:]
-These example asume one or more 16-core nodes.
+These examples assume one or more 16-core nodes.
env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS
lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 4b4ac3862d..0f0b241b76 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -67,7 +67,7 @@ when required. An example are the bond (angle, etc) methods which
need to find the local index of an atom with a specific global ID
which is a bond (angle, etc) partner. LAMMPS performs this operation
efficiently by creating a "map", which is either an {array} or {hash}
-table, as descibed below.
+table, as described below.
When the {map} keyword is not specified in your input script, LAMMPS
only creates a map for "atom_styles"_atom_style.html for molecular
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 7d9e443e7d..8facb4de63 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -173,7 +173,7 @@ There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
-(g,i,k,o,t) to indicate which accerlerated styles exist.
+(g,i,k,o,t) to indicate which accelerated styles exist.
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle/local"_compute_bond_local.html - theta and energy of each angle
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 669ab9f7ca..7cea62c7b3 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -85,7 +85,7 @@ dump 1 all custom 100 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
refresh c_dsp delay 100 :pre
-The "dump_modify thresh"_dump_modify.html command will only ouptut
+The "dump_modify thresh"_dump_modify.html command will only output
atoms that have displaced more than 0.6 Angstroms on each snapshot
(assuming metal units). The dump_modify {refresh} option triggers a
call to this compute at the end of every dump.
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index b3891841b8..04f0fd0b82 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -14,7 +14,7 @@ compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
ID, group-ID are documented in "compute"_compute.html command :l
entropy/atom = style name of this compute command :l
-sigma = width of gaussians used in the g(r) smoothening :l
+sigma = width of gaussians used in the g(r) smoothing :l
cutoff = cutoff for the g(r) calculation :l
one or more keyword/value pairs may be appended :l
keyword = {avg} or {local}
@@ -49,14 +49,14 @@ This parameter for atom i is computed using the following formula from
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
-atom i can be noisy and therefore it is smoothened using:
+atom i can be noisy and therefore it is smoothed using:
:c,image(Eqs/pair_entropy2.jpg)
where the sum in j goes through the neighbors of atom i, and sigma is a
-parameter to control the smoothening.
+parameter to control the smoothing.
-The input parameters are {sigma} the smoothening parameter, and the
+The input parameters are {sigma} the smoothing parameter, and the
{cutoff} for the calculation of g(r).
If the keyword {avg} has the setting {yes}, then this compute also
@@ -82,7 +82,7 @@ If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
-inhomogeneus systems such as those that have surfaces.
+inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
constant 4.05 Angstroms),
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index 512009093c..bc1e3049fa 100644
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@@ -158,7 +158,7 @@ corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.
For the spin quantities, sp is in the units of the Bohr magneton, spx,
-spy, and spz are adimentional quantities, and fmx, fmy and fmz are
+spy, and spz are adimensional quantities, and fmx, fmy and fmz are
given in rad.THz.
[Restrictions:] none
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 787ff8cdcf..e6185a2dd8 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -48,7 +48,7 @@ variable temp_mag equal c_out_mag\[6\] :pre
thermo 10
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
-This serie of commands evaluates the total magnetization along z, the norm of
+This series of commands evaluates the total magnetization along z, the norm of
the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index 57faf97ad1..a55288e1db 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -84,7 +84,7 @@ connectivity that has already been assigned. However, the
"reset_ids"_reset_ids.html command can be used after this command to
accomplish the same thing.
-Note that the re-assignement of IDs is not really a compression, where
+Note that the re-assignment of IDs is not really a compression, where
gaps in atom IDs are removed by decrementing atom IDs that are larger.
Instead the IDs for all atoms are erased, and new IDs are assigned so
that the atoms owned by individual processors have consecutive IDs, as
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 98bcbc5e55..72f4935916 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -914,7 +914,7 @@ flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
-maxifiles = -1
+maxfiles = -1
nfile = 1
pad = 0
pbc = no
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 9c3a1d0349..ee0d006fe8 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -30,7 +30,7 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a
timestepping or minimization. Examples include updating of atom
positions and velocities due to time integration, controlling
temperature, applying constraint forces to atoms, enforcing boundary
-conditions, computing diagnostics, etc. There are hundredes of fixes
+conditions, computing diagnostics, etc. There are hundreds of fixes
defined in LAMMPS and new ones can be added; see the
"Modify"_Modify.html doc page for details.
@@ -164,7 +164,7 @@ There are also additional accelerated fix styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands fix"_Commands_fix.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
-accerlerated styles exist.
+accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index b30966c2f9..4868761d42 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -47,7 +47,7 @@ this can significantly accelerate the simulation.
The filter computes a cluster decomposition of the molecular structure
following the criteria indicated by the options a, b, t and m. This
process is similar to the approach in "fix shake"_fix_shake.html,
-however, the clusters are not kept contrained. Instead, the position
+however, the clusters are not kept constrained. Instead, the position
is slightly modified only for the computation of long-range forces. A
good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 7bb25e0a68..d4836706e2 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -34,7 +34,7 @@ the following stochastic differential equation:
:c,image(Eqs/fix_langevin_spin_sLLG.jpg)
-with lambda the transverse damping, and eta a random verctor.
+with lambda the transverse damping, and eta a random vector.
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
equation.
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index bd61e29dcb..c97095bcfc 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -44,7 +44,7 @@ Once LAMMPS is built with the LATTE package, you can run the example
input scripts for molecular dynamics or energy minimization that are
found in examples/latte.
-A step-by-step tutorial can be follwed at: "LAMMPS-LATTE
+A step-by-step tutorial can be followed at: "LAMMPS-LATTE
tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
The {peID} argument is not yet supported by fix latte, so it must be
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index d331d9ad75..521dfff12b 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -168,7 +168,7 @@ The difference between these two {estyle} options is as follows. When
{estyle} is specified as {last/efirst}, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
-intermediate repilica may relax "faster" and reach a lower energy than
+intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying {estyle} as {last/efirst/middle} which will alter the
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index ae403cafd1..dc05948de3 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -174,7 +174,7 @@ This fix can be used with the "fix_modify"_fix_modify.html {temp} and
{press} options. The temperature and pressure computes used must be of
type {temp/uef} and {pressure/uef}.
-This fix computes the same global scalar and vecor quantities as "fix
+This fix computes the same global scalar and vector quantities as "fix
npt"_fix_nh.html.
The fix is not invoked during "energy minimization"_minimize.html.
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
index ade64d2056..2ee045141a 100644
--- a/doc/src/fix_surface_global.txt
+++ b/doc/src/fix_surface_global.txt
@@ -6,7 +6,7 @@
:line
-fix wall/surface/globale command :h3
+fix wall/surface/global command :h3
[Description:]
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 4c43978fe5..d9780e0320 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -52,18 +52,18 @@ The latter corrects for artifacts occurring at short distances which
become an issue for soft vdW potentials.
The {buck6d} styles include a smoothing function which is invoked
-according to the global smooting parameter within the specified
+according to the global smoothing parameter within the specified
cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing
within 90% of the cutoff. No smoothing is applied at a value
of 1.0. For the {gauss/dsf} style this smoothing is only applicable
for the dispersion damped Buckingham potential. For the {gauss/long}
styles the smoothing function can also be invoked for the real
-space coulomb interactions which enforce continous energies and
+space coulomb interactions which enforce continuous energies and
forces at the cutoff.
Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long}
evaluate a Coulomb potential using spherical Gaussian type charge
-distributions which effectively dampen electrostatic ineractions
+distributions which effectively dampen electrostatic interactions
for high charges at close distances. The electrostatic potential
is thus evaluated as:
diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt
index 63f85f23d5..88f95b5b2c 100644
--- a/doc/src/pair_coeff.txt
+++ b/doc/src/pair_coeff.txt
@@ -128,7 +128,7 @@ There are also additional accelerated pair styles (not listed on the
distribution for faster performance on CPUs, GPUs, and KNLs. The
individual style names on the "Commands pair"_Commands_pair.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
-accerlerated styles exist.
+accelerated styles exist.
:line
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 02d0db7af2..c74028faa9 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -39,7 +39,7 @@ in "(Kolmogorov)"_#Kolmogorov2.
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
-r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
+r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index f557e6c731..912fca1657 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -30,7 +30,7 @@ which is to take all normals along the z-axis.
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
-It is important to have a suffiently large cutoff to ensure smooth forces.
+It is important to have a sufficiently large cutoff to ensure smooth forces.
Energies are shifted so that they go continously to zero at the cutoff assuming
that the exponential part of {Vij} (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for {Vij} above.
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 7c034f36e0..e0fae3909d 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -49,7 +49,7 @@ as it writes successive restart files.
Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you,
for example, to write out archival restart files every 100000 steps
-using a single filenname, and more frequent temporary restart files
+using a single filename, and more frequent temporary restart files
every 1000 steps, using two filenames. Using restart 0 will turn off
both modes of output.
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index a57b61664d..47544b0b4e 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -64,7 +64,7 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a manybody potential will alter the
-neigborlist and thus can render the computation of those interactions
+neighborlist and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
--
GitLab
From 2d6d635ce0388964f9fdc407f40b1a1dbaa10cef Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:30:40 -0400
Subject: [PATCH 133/332] update list of false positives
---
doc/utils/sphinx-config/false_positives.txt | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index fb08e4e97e..0abd0d7de1 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -308,6 +308,8 @@ Clebsch
Clermont
clo
Clovertown
+cmake
+CMake
cmap
Cmax
cmdlist
@@ -713,7 +715,10 @@ fhg
Fi
figshare
Fij
-filenname
+filename
+filenames
+Filename
+Filenames
fileper
Fincham
Finchham
@@ -1456,6 +1461,7 @@ Mtotal
Muccioli
Mukherjee
Mulders
+multi
multibody
Multibody
multicenter
@@ -2489,6 +2495,7 @@ velocites
Verlag
verlet
Verlet
+versa
ves
vhi
vibrational
@@ -2566,6 +2573,7 @@ whitespace
Wi
Wicaksono
wih
+wildcard
Wirnsberger
wirtes
witin
--
GitLab
From 5da714bcc81cffe0723b210fa80232b21e3f8d7c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:33:40 -0400
Subject: [PATCH 134/332] fix another source of broken links inserted into
processed files
---
doc/utils/converters/lammpsdoc/lammps_filters.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/utils/converters/lammpsdoc/lammps_filters.py b/doc/utils/converters/lammpsdoc/lammps_filters.py
index 11460185db..7b1481ceb9 100644
--- a/doc/utils/converters/lammpsdoc/lammps_filters.py
+++ b/doc/utils/converters/lammpsdoc/lammps_filters.py
@@ -64,7 +64,7 @@ def filter_file_header_until_first_horizontal_line(content):
common_links = "\n.. _lws: http://lammps.sandia.gov\n" \
".. _ld: Manual.html\n" \
- ".. _lc: Section_commands.html#comm\n"
+ ".. _lc: Commands_all.html\n"
if first_hr >= 0:
return content[first_hr+len(hr):].lstrip() + common_links
--
GitLab
From 4278a284e4b5fb19e8a694b29ccd2a1e95e5c9c0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:48:42 -0400
Subject: [PATCH 135/332] fix one more broken link
---
doc/src/Install_patch.txt | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt
index 3d0b27370e..ff9b14c12c 100644
--- a/doc/src/Install_patch.txt
+++ b/doc/src/Install_patch.txt
@@ -17,10 +17,11 @@ how to stay current are on the "Install git"_Install_git.html and
If you prefer to download a tarball, as described on the "Install
git"_Install_tarball.html doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
-a patch file is posted on the "bug and feature page"_bug of the
-website, along with a list of changed files and details about what is
-in the new patch release. This page explains how to apply the patch
-file to your local LAMMPS directory.
+a patch file is posted on the "bug and feature
+page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
+with a list of changed files and details about what is in the new patch
+release. This page explains how to apply the patch file to your local
+LAMMPS directory.
NOTE: You should not apply patch files to a local Git or SVN repo of
LAMMPS, only to an unpacked tarball. Use Git and SVN commands to
--
GitLab
From eca0487dafe1ea5e7df988c32681803966f624b2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:50:56 -0400
Subject: [PATCH 136/332] subdomain -> sub-domain
---
doc/src/fix_lb_fluid.txt | 2 +-
doc/src/replicate.txt | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 1a52397822..d9012d8cb3 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -187,7 +187,7 @@ NOTE: Care must be taken when choosing both a value for dx, and a
simulation domain size. This fix uses the same subdivision of the
simulation domain among processors as the main LAMMPS program. In
order to uniformly cover the simulation domain with lattice sites, the
-lengths of the individual LAMMPS subdomains must all be evenly
+lengths of the individual LAMMPS sub-domains must all be evenly
divisible by dx. If the simulation domain size is cubic, with equal
lengths in all dimensions, and the default value for dx is used, this
will automatically be satisfied.
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 0195dce911..79a481746e 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -14,7 +14,7 @@ replicate nx ny nz {keyword} :pre
nx,ny,nz = replication factors in each dimension :ulb
optional {keyword} = {bbox} :l
- {bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
+ {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
[Examples:]
@@ -46,7 +46,7 @@ image flags that differ by 1. This will allow the bond to be
unwrapped appropriately.
The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's subdomain when assigning
+in replicas that overlap with a processor's sub-domain when assigning
atoms to processors, and thus can result in substantial speedups for
calculations using a large number of processors. It does require
temporarily using more memory.
--
GitLab
From 9a8c09288f04e00732dab2ba926ffd76bca1a15c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 21:54:41 -0400
Subject: [PATCH 137/332] use Hyper-Threading consistently
---
doc/src/Speed_kokkos.txt | 14 +++++++-------
doc/src/package.txt | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index eb787df5d6..c734d642ce 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -93,12 +93,12 @@ The "t Nt" option specifies how many OpenMP threads per MPI task to
use with a node. The default is Nt = 1, which is MPI-only mode. Note
that the product of MPI tasks * OpenMP threads/task should not exceed
the physical number of cores (on a node), otherwise performance will
-suffer. If hyperthreading is enabled, then the product of MPI tasks *
-OpenMP threads/task should not exceed the physical number of cores *
-hardware threads. The "-k on" switch also issues a "package kokkos"
-command (with no additional arguments) which sets various KOKKOS
-options to default values, as discussed on the "package"_package.html
-command doc page.
+suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
+tasks * OpenMP threads/task should not exceed the physical number of
+cores * hardware threads. The "-k on" switch also issues a
+"package kokkos" command (with no additional arguments) which sets
+various KOKKOS options to default values, as discussed on the
+"package"_package.html command doc page.
The "-sf kk" "command-line switch"_Run_options.html will automatically
append the "/kk" suffix to styles that support it. In this manner no
@@ -149,7 +149,7 @@ Intel Knight's Landing (KNL) Xeon Phi:
KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
reserved for the OS, and only 64 or 66 cores are used. Each core has 4
-hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
cores to run on. The product of MPI tasks * OpenMP threads/task should
not exceed this limit, otherwise performance will suffer. Note that
with the KOKKOS package you do not need to specify how many KNLs there
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 8b0581929f..65117ba3c3 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -363,7 +363,7 @@ specified with the OMP_NUM_THREADS environment variable or the {omp}
keyword). The extra thread is dedicated for performing part of the
"PPPM solver"_kspace_style.html computations and communications. This
can improve parallel performance on processors supporting
-Simultaneous Multithreading (SMT) such as Hyperthreading on Intel
+Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
processors. In this mode, one additional thread is generated per MPI
process. LAMMPS will generate a warning in the case that more threads
are used than available in SMT hardware on a node. If the PPPM solver
--
GitLab
From fe6debfe9a0274bd84ef31f7d9987b6d2ba4b366 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:02:01 -0400
Subject: [PATCH 138/332] precompiled -> pre-compiled
---
doc/src/Build_cmake.txt | 2 +-
doc/src/Build_windows.txt | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
index 6298ab2576..31f2cb549e 100644
--- a/doc/src/Build_cmake.txt
+++ b/doc/src/Build_cmake.txt
@@ -188,7 +188,7 @@ module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name :pre
-Most Linux distributions offer precompiled cmake packages through
+Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
"https://cmake.org/download/"_https://cmake.org/download/.
diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt
index da257ccbc8..0caad589fb 100644
--- a/doc/src/Build_windows.txt
+++ b/doc/src/Build_windows.txt
@@ -84,7 +84,7 @@ with the cross-compiler environment on Fedora machines.
Please keep in mind, though, that this only applies to compiling LAMMPS.
Whether the resulting binaries do work correctly is no tested by the
LAMMPS developers. We instead rely on the feedback of the users
-of these precompiled LAMMPS packages for Windows. We will try to resolve
+of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However
this is subject to time constraints and focus on HPC platforms.
--
GitLab
From 683c87347ccf07d7435e14a8bd5b43d7383f5f04 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:02:24 -0400
Subject: [PATCH 139/332] neighborlist -> neighbor list
---
doc/src/Speed_kokkos.txt | 2 +-
doc/src/special_bonds.txt | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index c734d642ce..04cf53691b 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -228,7 +228,7 @@ for details and default settings. Experimenting with its options can
provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
-mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
NOTE: For good performance of the KOKKOS package on GPUs, you must
have Kepler generation GPUs (or later). The Kokkos library exploits
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 47544b0b4e..07b4986673 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -64,7 +64,7 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a manybody potential will alter the
-neighborlist and thus can render the computation of those interactions
+neighbor list and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
--
GitLab
From 96bde51ae45d09fa01212ff08ce5510799ae212a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:03:53 -0400
Subject: [PATCH 140/332] autodetect -> auto-detect
---
doc/src/Build_extras.txt | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index e141c62a3a..088ffd8972 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -687,7 +687,7 @@ the HDF5 library.
No additional settings are needed besides "-D PKG_USER-H5MD=yes".
-This should autodetect the H5MD library on your system. Several
+This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is
installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user
@@ -777,7 +777,7 @@ on your system.
No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
-This should autodetect the NETCDF library if it is installed on your
+This should auto-detect the NETCDF library if it is installed on your
system at standard locations. Several advanced CMake NETCDF options
exist if you need to specify where it was installed. Use the ccmake
(terminal window) or cmake-gui (graphical) tools to see these options
@@ -936,7 +936,7 @@ your system.
No additional settings are needed besides "-D PKG_USER-VTK=yes".
-This should autodetect the VTK library if it is installed on your
+This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist if
you need to specify where it was installed. Use the ccmake (terminal
window) or cmake-gui (graphical) tools to see these options and set
--
GitLab
From 193f46dd9fc92e6fc9a4a5a516fe0ea65e644045 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:04:03 -0400
Subject: [PATCH 141/332] spelling fix
---
doc/src/Packages_standard.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 55d0d616f4..2feb4e142d 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -47,7 +47,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
-"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, n/a, no, no
+"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
--
GitLab
From 4b2629d8ba52cacf66de91681894de3ffeddcae8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:16:34 -0400
Subject: [PATCH 142/332] recompile/recompute/reinit ->
re-compile/re-compute/re-init
---
doc/src/Build_cmake.txt | 2 +-
doc/src/Build_make.txt | 6 +++---
doc/src/Errors_messages.txt | 10 +++++-----
doc/src/Howto_pylammps.txt | 2 +-
doc/src/Packages_details.txt | 2 +-
doc/src/Speed_measure.txt | 2 +-
doc/src/compute_modify.txt | 2 +-
doc/src/compute_rdf.txt | 2 +-
doc/src/compute_smd_tlsph_dt.txt | 2 +-
doc/src/delete_bonds.txt | 2 +-
doc/src/dump_molfile.txt | 2 +-
doc/src/fix_dt_reset.txt | 2 +-
doc/src/fix_ipi.txt | 2 +-
doc/src/fix_modify.txt | 2 +-
doc/src/fix_rigid.txt | 6 +++---
doc/src/fix_smd.txt | 2 +-
doc/src/pair_dsmc.txt | 2 +-
doc/src/pair_python.txt | 2 +-
doc/src/special_bonds.txt | 2 +-
src/KSPACE/msm.cpp | 4 ++--
src/USER-MISC/pair_agni.cpp | 2 +-
21 files changed, 30 insertions(+), 30 deletions(-)
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
index 31f2cb549e..f8b52056fc 100644
--- a/doc/src/Build_cmake.txt
+++ b/doc/src/Build_cmake.txt
@@ -40,7 +40,7 @@ executable called "lmp" and a library called "liblammps.a" in the
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
-LAMMPS or need to recompile LAMMPS repeatedly, installation of the
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
After compilation, you can optionally copy the LAMMPS executable and
diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt
index a18d812b59..ad18695e46 100644
--- a/doc/src/Build_make.txt
+++ b/doc/src/Build_make.txt
@@ -35,16 +35,16 @@ This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
-do development on LAMMPS or need to recompile LAMMPS repeatedly, the
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
-uninstalling packages), you must recompile and relink the LAMMPS
+uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
-recompiled.
+re-compiled.
NOTE: When you build LAMMPS for the first time, a long list of *.d
files will be printed out rapidly. This is not an error; it is the
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index d279b5e975..a74182967c 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -743,7 +743,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
+{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt
Single precision cannot be used with MSM. :dd
@@ -5078,7 +5078,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/point requires atom attribute q} :dt
@@ -5092,7 +5092,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/shielded requires atom attribute q} :dt
@@ -5110,7 +5110,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/slater requires atom attribute q} :dt
@@ -5541,7 +5541,7 @@ See the package gpu command. :dd
{GPUs are requested but Kokkos has not been compiled for CUDA} :dt
-Recompile Kokkos with CUDA support to use GPUs. :dd
+Re-compile Kokkos with CUDA support to use GPUs. :dd
{Ghost velocity forward comm not yet implemented with Kokkos} :dt
diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt
index 8be4b66e78..a12bf13f2e 100644
--- a/doc/src/Howto_pylammps.txt
+++ b/doc/src/Howto_pylammps.txt
@@ -73,7 +73,7 @@ that package into your current Python installation.
cd $LAMMPS_DIR/python
python install.py :pre
-NOTE: Recompiling the shared library requires reinstalling the Python package
+NOTE: Recompiling the shared library requires re-installing the Python package
Installation inside of a virtualenv :h5
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 188081c8dd..3519720911 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1591,7 +1591,7 @@ plugin via the "dump molfile"_dump_molfile.html command. Plugins can
be obtained from a VMD installation which has to match the platform
that you are using to compile LAMMPS for. By adding plugins to VMD,
support for new file formats can be added to LAMMPS (or VMD or other
-programs that use them) without having to recompile the application
+programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found
at
"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 647ff71e36..dd12685dc5 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt
index 192ea0bc9e..5ba2100fba 100644
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
N = # of extra degrees of freedom to subtract
{extra} syntax is identical to {extra/dof}, will be disabled at some point
{dynamic/dof} value = {yes} or {no}
- yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
:ule
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index 04b38682cc..d11ae9e3bf 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -182,7 +182,7 @@ change from zero to one at the location of the spike in g(r).
NOTE: compute rdf can handle dynamic groups and systems where atoms
are added or removed, but this causes that certain normalization
-parameters need to be recomputed in every step and include collective
+parameters need to be re-computed in every step and include collective
communication operations. This will reduce performance and limit
parallel efficiency and scaling. For systems, where only the type
of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html),
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index 92f5923de0..e9ff2e739b 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -25,7 +25,7 @@ Define a computation that outputs the CFL-stable time increment per
particle. This time increment is essentially given by the speed of
sound, divided by the SPH smoothing length. Because both the speed of
sound and the smoothing length typically change during the course of a
-simulation, the stable time increment needs to be recomputed every
+simulation, the stable time increment needs to be re-computed every
time step. This calculation is performed automatically in the
relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt
index b29fa82f2d..4e33604696 100644
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@@ -140,7 +140,7 @@ enough for a processor to acquire the ghost atoms its needs to compute
bond, angle, etc interactions.
If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
-weighting list is not recomputed, this can cause a later "fix
+weighting list is not re-computed, this can cause a later "fix
shake"_fix_shake.html command to fail due to an atom's bonds being
inconsistent with the weighting list. This should only happen if the
group used in the fix command includes both atoms in the bond, in
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index dd2b212f0b..b5f157cf29 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -99,7 +99,7 @@ USER-MOLFILE package only provides the interface code, not the plugins.
These can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD
-or other programs that use them) without having to recompile the
+or other programs that use them) without having to re-compile the
application itself. The plugins are installed in the directory:
<VMDHOME>/plugins/<VMDARCH>/molfile
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index be4fbd255b..0c5a4493ae 100644
--- a/doc/src/fix_dt_reset.txt
+++ b/doc/src/fix_dt_reset.txt
@@ -14,7 +14,7 @@ fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command
dt/reset = style name of this fix command
-N = recompute dt every N timesteps
+N = re-compute dt every N timesteps
Tmin = minimum dt allowed which can be NULL (time units)
Tmax = maximum dt allowed which can be NULL (time units)
Xmax = maximum distance for an atom to move in one timestep (distance units)
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index b115aba7df..64486a9cc7 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -63,7 +63,7 @@ electrostatics, or that contain parameters that depend on box size:
all of these options will be initialized based on the cell size in the
LAMMPS-side initial configuration and kept constant during the run.
This is required to e.g. obtain reproducible and conserved forces.
-If the cell varies too wildly, it may be advisable to reinitialize
+If the cell varies too wildly, it may be advisable to re-initialize
these interactions at each call. This behavior can be requested by
setting the {reset} switch.
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index ddb5f9a4cd..f50747948a 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -21,7 +21,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
- yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{bodyforces} value = {early} or {late}
early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index d489762e80..5d65856735 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -442,11 +442,11 @@ couple none :pre
The keyword/value option pairs are used in the following ways.
The {reinit} keyword determines, whether the rigid body properties
-are reinitialized between run commands. With the option {yes} (the
+are re-initialized between run commands. With the option {yes} (the
default) this is done, with the option {no} this is not done. Turning
-off the reinitialization can be helpful to protect rigid bodies against
+off the re-initialization can be helpful to protect rigid bodies against
unphysical manipulations between runs or when properties cannot be
-easily recomputed (e.g. when read from a file). When using the {infile}
+easily re-computed (e.g. when read from a file). When using the {infile}
keyword, the {reinit} option is automatically set to {no}.
The {langevin} and {temp} and {tparam} keywords perform thermostatting
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index 644c04eadb..774842c7cf 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -77,7 +77,7 @@ normalized. But since it represents the {absolute} displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the {auto} parameter. In this case the direction is
-recomputed in every step, which can be useful for steering a local
+re-computed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index adaeeb8390..8b1ceab858 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -16,7 +16,7 @@ max_cell_size = global maximum cell size for DSMC interactions (distance units)
seed = random # seed (positive integer)
weighting = macroparticle weighting
Tref = reference temperature (temperature units)
-Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
+Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps)
Nsample = sample this many times in recomputing v*sigma_max :ul
[Examples:]
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index b7130c8a10..e8baf14d2e 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -29,7 +29,7 @@ The {python} pair style provides a way to define pairwise additive
potential functions as python script code that is loaded into LAMMPS
from a python file which must contain specific python class definitions.
This allows to rapidly evaluate different potential functions without
-having to modify and recompile LAMMPS. Due to python being an
+having to modify and re-compile LAMMPS. Due to python being an
interpreted language, however, the performance of this pair style is
going to be significantly slower (often between 20x and 100x) than
corresponding compiled code. This penalty can be significantly reduced
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 07b4986673..283aad6c2d 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -110,7 +110,7 @@ simulation.
The two exceptions to this rule are (a) if the {angle} or {dihedral}
keywords are set to {yes} (see below), or (b) if the
"delete_bonds"_delete_bonds.html command is used with the {special}
-option that recomputes the 1-2,1-3,1-4 topologies after bonds are
+option that re-computes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the "delete_bonds"_delete_bonds.html command for more
details.
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index 9f3221449b..efa2c87296 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -177,7 +177,7 @@ void MSM::init()
if (sizeof(FFT_SCALAR) != 8)
error->all(FLERR,"Cannot (yet) use single precision with MSM "
- "(remove -DFFT_SINGLE from Makefile and recompile)");
+ "(remove -DFFT_SINGLE from Makefile and re-compile)");
// extract short-range Coulombic cutoff from pair style
@@ -419,7 +419,7 @@ void MSM::setup()
boxlo = domain->boxlo_lamda;
// ghost grid points depend on direct sum interaction limits,
- // so need to recompute local grid
+ // so need to re-compute local grid
set_grid_local();
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 11bf2ae01e..785146a0d6 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -394,7 +394,7 @@ void PairAGNI::read_file(char *file)
if (nwords == 0) continue;
if (nwords > MAXWORD)
- error->all(FLERR,"Increase MAXWORD and recompile");
+ error->all(FLERR,"Increase MAXWORD and re-compile");
// words = ptrs to all words in line
--
GitLab
From b00046fd34a0af8e9ccd14a38ec8619f9af2d1c8 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:18:27 -0400
Subject: [PATCH 143/332] fix typo
---
doc/src/Commands_all.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index 13db1272b9..aec5a9db8b 100644
--- a/doc/src/Commands_all.txt
+++ b/doc/src/Commands_all.txt
@@ -19,7 +19,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
All commands :h3
-An alphabetic list of all LAMMPS commmands.
+An alphabetic list of all LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
--
GitLab
From 0cd71ee582f7312f57f637064e4a7cf522946c84 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:18:35 -0400
Subject: [PATCH 144/332] more false positives
---
doc/utils/sphinx-config/false_positives.txt | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 0abd0d7de1..8eb37f6135 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -260,6 +260,7 @@ Caro
cartesian
Cates
cbecker
+ccmake
CCu
cd
cdeam
@@ -286,6 +287,9 @@ cgs
Chalopin
Champaign
charmm
+charmmfsw
+charmmfsh
+charmm
CHARMM
checkmark
checkqeq
@@ -412,6 +416,7 @@ Cval
cvar
cvff
cwiggle
+cygwin
Cygwin
Cyrot
cyrstals
@@ -587,6 +592,7 @@ ehanced
ehex
eHEX
Ei
+Eigen
Eigensolve
Eike
eim
@@ -1390,6 +1396,7 @@ Mikami
Militzer
Minary
mincap
+mingw
minima
minimizations
minimizer
--
GitLab
From c0d9d96e09f93660cca2e2b8246c3579cd31f528 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:24:51 -0400
Subject: [PATCH 145/332] better help message in make file
---
doc/Makefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/doc/Makefile b/doc/Makefile
index 797095dfad..9069fa1d60 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -42,7 +42,8 @@ help:
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
- @echo " mobi create MOBI format manual for e-book readers (e.g. Kindle)"
+ @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
+ @echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
--
GitLab
From af35c3bccafdb6e014bee669e209bc975a5fd111 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:28:53 -0400
Subject: [PATCH 146/332] atomID -> atom-ID
---
doc/src/compute_rigid_local.txt | 2 +-
doc/src/fix_bond_react.txt | 2 +-
doc/src/read_data.txt | 8 ++++----
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 9b829a70fc..67c6209bdf 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -92,7 +92,7 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\
This section explains the rigid body attributes that can be specified.
-The {id} attribute is the atomID of the atom which owns the rigid body, which is
+The {id} attribute is the atom-ID of the atom which owns the rigid body, which is
assigned by the "fix rigid/small"_fix_rigid.html command.
The {mol} attribute is the molecule ID of the rigid body. It should
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 327088cb99..8e7cb1bdae 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -34,7 +34,7 @@ react = mandatory argument indicating new reaction specification :l
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
- map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
+ map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l
individual_keyword = {prob} or {stabilize_steps} :l
{prob} values = fraction seed
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index ef899a15b4..6aa30d9e63 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -124,14 +124,14 @@ bond atoms or bad dynamics.
The three choices for the {add} argument affect how the atom IDs and
molecule IDs of atoms in the data file are treated. If {append} is
specified, atoms in the data file are added to the current system,
-with their atom IDs reset so that an atomID = M in the data file
-becomes atomID = N+M, where N is the largest atom ID in the current
+with their atom IDs reset so that an atom-ID = M in the data file
+becomes atom-ID = N+M, where N is the largest atom ID in the current
system. This rule is applied to all occurrences of atom IDs in the
data file, e.g. in the Velocity or Bonds section. This is also done
for molecule IDs, if the atom style does support molecule IDs or
they are enabled via fix property/atom. If {IDoffset} is specified,
then {IDoffset} is a numeric value is given, e.g. 1000, so that an
-atomID = M in the data file becomes atomID = 1000+M. For systems
+atom-ID = M in the data file becomes atom-ID = 1000+M. For systems
with enabled molecule IDs, another numerical argument {MOLoffset}
is required representing the equivalent offset for molecule IDs.
If {merge} is specified, the data file atoms
@@ -139,7 +139,7 @@ are added to the current system without changing their IDs. They are
assumed to merge (without duplication) with the currently defined
atoms. It is up to you to insure there are no multiply defined atom
IDs, as LAMMPS only performs an incomplete check that this is the case
-by insuring the resulting max atomID >= the number of atoms. For
+by insuring the resulting max atom-ID >= the number of atoms. For
molecule IDs, there is no check done at all.
The {offset} and {shift} keywords can only be used if the {add}
--
GitLab
From 440338d769b0dca022a884c11b6d1c0b3cd5af5e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 22 Aug 2018 22:35:35 -0400
Subject: [PATCH 147/332] last round of spelling fixes
---
doc/src/Packages_details.txt | 2 +-
doc/src/compute_ackland_atom.txt | 2 +-
doc/src/fix_bocs.txt | 2 +-
doc/src/fix_rhok.txt | 2 +-
doc/src/neb.txt | 4 ++--
doc/utils/sphinx-config/false_positives.txt | 1 +
6 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 3519720911..381dc2e995 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1370,7 +1370,7 @@ which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
-supported, performance will be suboptimal.
+supported, performance will be sub-optimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index cda4a36b34..46db81eb9e 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -32,7 +32,7 @@ according to the formulation given in "(Ackland)"_#Ackland.
Historically, LAMMPS had two, slightly different implementations of
the algorithm from the paper. With the {legacy} keyword, it is
possible to switch between the pre-2015 ({legacy yes}) and post-2015
-implemention ({legacy no}). The post-2015 variant is the default.
+implementation ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index 7acc22d702..b7d4e7badf 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -56,7 +56,7 @@ value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
-should all be in atomspheres. Furthermore, the table should start/end at a
+should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index a3d1ab702e..f013ebfae1 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -11,7 +11,7 @@ fix rhok command :h3
fix ID group-ID rhok nx ny nz K a :pre
ID, group-ID are documented in "fix"_fix.html command
-nx, ny, nz = k-vektor of collective density field
+nx, ny, nz = k-vector of collective density field
K = spring constant of bias potential
a = anchor point of bias potential :ul
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 57e122fdcd..75d199e0b4 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -338,9 +338,9 @@ energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i.
-When a NEB calculation does not converge properly, the suplementary
+When a NEB calculation does not converge properly, the supplementary
information can help understanding what is going wrong. For instance
-when the path angle becomes accute the definition of tangent used in
+when the path angle becomes accute, the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2.
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 8eb37f6135..febd5c20a0 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -260,6 +260,7 @@ Caro
cartesian
Cates
cbecker
+ccache
ccmake
CCu
cd
--
GitLab
From 4f36f077ff8b451dc2b92a9bd80ff1791ee5bc1b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Aug 2018 10:08:36 -0400
Subject: [PATCH 148/332] whitespace cleanup
---
doc/src/Eqs/pair_atm.tex | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Eqs/pair_atm.tex b/doc/src/Eqs/pair_atm.tex
index 0e05370faf..fce1db99b8 100644
--- a/doc/src/Eqs/pair_atm.tex
+++ b/doc/src/Eqs/pair_atm.tex
@@ -4,6 +4,6 @@
\begin{equation}
E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
-\end{equation}
+\end{equation}
\end{document}
--
GitLab
From c5d3274222a86168312450ba4f6188bb3c47a50d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Aug 2018 10:13:06 -0400
Subject: [PATCH 149/332] restore files
---
doc/src/Packages_details.txt | 2000 ++++++++++++++++++++++++++++++++++
doc/src/Speed_kokkos.txt | 381 +++++++
2 files changed, 2381 insertions(+)
create mode 100644 doc/src/Packages_details.txt
create mode 100644 doc/src/Speed_kokkos.txt
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
new file mode 100644
index 0000000000..892774be38
--- /dev/null
+++ b/doc/src/Packages_details.txt
@@ -0,0 +1,2000 @@
+"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Package details :h3
+
+Here is a brief description of all the standard and user packages in
+LAMMPS. It lists authors (if applicable) and summarizes the package
+contents. It has specific instructions on how to install the package,
+including, if necessary, info on how to download or build any extra
+library it requires. It also gives links to documentation, example
+scripts, and pictures/movies (if available) that illustrate use of the
+package.
+
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
+make). See the "Build package"_Build_package.html doc page for more
+info. A few packages may require additional steps; this is indicated
+in the descriptions below. The "Build extras"_Build_extras.html doc
+page gives those details.
+
+NOTE: To see the complete list of commands a package adds to LAMMPS,
+you can examine the files in its src directory, e.g. "ls
+src/GRANULAR". Files with names that start with fix, compute, atom,
+pair, bond, angle, etc correspond to commands with the same style name
+as contained in the file name.
+
+"ASPHERE"_#PKG-ASPHERE,
+"BODY"_#PKG-BODY,
+"CLASS2"_#PKG-CLASS2,
+"COLLOID"_#PKG-COLLOID,
+"COMPRESS"_#PKG-COMPRESS,
+"CORESHELL"_#PKG-CORESHELL,
+"DIPOLE"_#PKG-DIPOLE,
+"GPU"_#PKG-GPU,
+"GRANULAR"_#PKG-GRANULAR,
+"KIM"_#PKG-KIM,
+"KOKKOS"_#PKG-KOKKOS,
+"KSPACE"_#PKG-KSPACE,
+"LATTE"_#PKG-LATTE,
+"MANYBODY"_#PKG-MANYBODY,
+"MC"_#PKG-MC,
+"MEAM"_#PKG-MEAM,
+"MISC"_#PKG-MISC,
+"MOLECULE"_#PKG-MOLECULE,
+"MPIIO"_#PKG-MPIIO,
+"MSCG"_#PKG-MSCG,
+"OPT"_#PKG-OPT,
+"PERI"_#PKG-PERI,
+"POEMS"_#PKG-POEMS,
+"PYTHON"_#PKG-PYTHON,
+"QEQ"_#PKG-QEQ,
+"REAX"_#PKG-REAX,
+"REPLICA"_#PKG-REPLICA2,
+"RIGID"_#PKG-RIGID,
+"SHOCK"_#PKG-SHOCK,
+"SNAP"_#PKG-SNAP,
+"SPIN"_#PKG-SPIN,
+"SRD"_#PKG-SRD,
+"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
+
+"USER-ATC"_#PKG-USER-ATC,
+"USER-AWPMD"_#PKG-USER-AWPMD,
+"USER-BOCS"_#PKG-USER-BOCS,
+"USER-CGDNA"_#PKG-USER-CGDNA,
+"USER-CGSDK"_#PKG-USER-CGSDK,
+"USER-COLVARS"_#PKG-USER-COLVARS,
+"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
+"USER-DPD"_#PKG-USER-DPD,
+"USER-DRUDE"_#PKG-USER-DRUDE,
+"USER-EFF"_#PKG-USER-EFF,
+"USER-FEP"_#PKG-USER-FEP,
+"USER-H5MD"_#PKG-USER-H5MD,
+"USER-INTEL"_#PKG-USER-INTEL,
+"USER-LB"_#PKG-USER-LB,
+"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
+"USER-MEAMC"_#PKG-USER-MEAMC,
+"USER-MESO"_#PKG-USER-MESO,
+"USER-MGPT"_#PKG-USER-MGPT,
+"USER-MISC"_#PKG-USER-MISC,
+"USER-MOFFF"_#PKG-USER-MOFFF,
+"USER-MOLFILE"_#PKG-USER-MOLFILE,
+"USER-NETCDF"_#PKG-USER-NETCDF,
+"USER-OMP"_#PKG-USER-OMP,
+"USER-PHONON"_#PKG-USER-PHONON,
+"USER-QMMM"_#PKG-USER-QMMM,
+"USER-QTB"_#PKG-USER-QTB,
+"USER-QUIP"_#PKG-USER-QUIP,
+"USER-REAXC"_#PKG-USER-REAXC,
+"USER-SMD"_#PKG-USER-SMD,
+"USER-SMTBQ"_#PKG-USER-SMTBQ,
+"USER-SPH"_#PKG-USER-SPH,
+"USER-TALLY"_#PKG-USER-TALLY,
+"USER-UEF"_#PKG-USER-UEF,
+"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+
+:line
+
+ASPHERE package :link(PKG-ASPHERE),h4
+
+[Contents:]
+
+Computes, time-integration fixes, and pair styles for aspherical
+particle models including ellipsoids, 2d lines, and 3d triangles.
+
+[Supporting info:]
+
+src/ASPHERE: filenames -> commands
+"Howto spherical"_Howto_spherical.html
+"pair_style gayberne"_pair_gayberne.html
+"pair_style resquared"_pair_resquared.html
+"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
+"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf
+examples/ASPHERE
+examples/ellipse
+http://lammps.sandia.gov/movies.html#line
+http://lammps.sandia.gov/movies.html#tri :ul
+
+:line
+
+BODY package :link(PKG-BODY),h4
+
+[Contents:]
+
+Body-style particles with internal structure. Computes,
+time-integration fixes, pair styles, as well as the body styles
+themselves. See the "Howto body"_Howto_body.html doc page for an
+overview.
+
+[Supporting info:]
+
+src/BODY filenames -> commands
+"Howto_body"_Howto_body.html
+"atom_style body"_atom_style.html
+"fix nve/body"_fix_nve_body.html
+"pair_style body/nparticle"_pair_body_nparticle.html
+examples/body :ul
+
+:line
+
+CLASS2 package :link(PKG-CLASS2),h4
+
+[Contents:]
+
+Bond, angle, dihedral, improper, and pair styles for the COMPASS
+CLASS2 molecular force field.
+
+[Supporting info:]
+
+src/CLASS2: filenames -> commands
+"bond_style class2"_bond_class2.html
+"angle_style class2"_angle_class2.html
+"dihedral_style class2"_dihedral_class2.html
+"improper_style class2"_improper_class2.html
+"pair_style lj/class2"_pair_class2.html :ul
+
+:line
+
+COLLOID package :link(PKG-COLLOID),h4
+
+[Contents:]
+
+Coarse-grained finite-size colloidal particles. Pair styles and fix
+wall styles for colloidal interactions. Includes the Fast Lubrication
+Dynamics (FLD) method for hydrodynamic interactions, which is a
+simplified approximation to Stokesian dynamics.
+
+[Authors:] This package includes Fast Lubrication Dynamics pair styles
+which were created by Amit Kumar and Michael Bybee from Jonathan
+Higdon's group at UIUC.
+
+[Supporting info:]
+
+src/COLLOID: filenames -> commands
+"fix wall/colloid"_fix_wall.html
+"pair_style colloid"_pair_colloid.html
+"pair_style yukawa/colloid"_pair_yukawa_colloid.html
+"pair_style brownian"_pair_brownian.html
+"pair_style lubricate"_pair_lubricate.html
+"pair_style lubricateU"_pair_lubricateU.html
+examples/colloid
+examples/srd :ul
+
+:line
+
+COMPRESS package :link(PKG-COMPRESS),h4
+
+[Contents:]
+
+Compressed output of dump files via the zlib compression library,
+using dump styles with a "gz" in their style name.
+
+To use this package you must have the zlib compression library
+available on your system.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/COMPRESS: filenames -> commands
+src/COMPRESS/README
+lib/compress/README
+"dump atom/gz"_dump.html
+"dump cfg/gz"_dump.html
+"dump custom/gz"_dump.html
+"dump xyz/gz"_dump.html :ul
+
+:line
+
+CORESHELL package :link(PKG-CORESHELL),h4
+
+[Contents:]
+
+Compute and pair styles that implement the adiabatic core/shell model
+for polarizability. The pair styles augment Born, Buckingham, and
+Lennard-Jones styles with core/shell capabilities. The "compute
+temp/cs"_compute_temp_cs.html command calculates the temperature of a
+system with core/shell particles. See the "Howto
+coreshell"_Howto_coreshell.html doc page for an overview of how to use
+this package.
+
+[Author:] Hendrik Heenen (Technical U of Munich).
+
+[Supporting info:]
+
+src/CORESHELL: filenames -> commands
+"Howto coreshell"_Howto_coreshell.html
+"Howto polarizable"_Howto_polarizable.html
+"compute temp/cs"_compute_temp_cs.html
+"pair_style born/coul/long/cs"_pair_cs.html
+"pair_style buck/coul/long/cs"_pair_cs.html
+"pair_style lj/cut/coul/long/cs"_pair_lj.html
+examples/coreshell :ul
+
+:line
+
+DIPOLE package :link(PKG-DIPOLE),h4
+
+[Contents:]
+
+An atom style and several pair styles for point dipole models with
+short-range or long-range interactions.
+
+[Supporting info:]
+
+src/DIPOLE: filenames -> commands
+"atom_style dipole"_atom_style.html
+"pair_style lj/cut/dipole/cut"_pair_dipole.html
+"pair_style lj/cut/dipole/long"_pair_dipole.html
+"pair_style lj/long/dipole/long"_pair_dipole.html
+examples/dipole :ul
+
+:line
+
+GPU package :link(PKG-GPU),h4
+
+[Contents:]
+
+Dozens of pair styles and a version of the PPPM long-range Coulombic
+solver optimized for GPUs. All such styles have a "gpu" as a suffix
+in their style name. The GPU code can be compiled with either CUDA or
+OpenCL, however the OpenCL variants are no longer actively maintained
+and only the CUDA versions are regularly tested. The "Speed
+gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
+software is required on your system, and details on how to build and
+use this package. Its styles can be invoked at run time via the "-sf
+gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
+also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
+
+[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
+(Northwestern U) while at ORNL.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/GPU: filenames -> commands
+src/GPU/README
+lib/gpu/README
+"Speed packages"_Speed_packages.html
+"Speed gpu"_Speed_gpu.html
+"Section 2.6 -sf gpu"_Run_options.html
+"Section 2.6 -pk gpu"_Run_options.html
+"package gpu"_package.html
+"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
+
+:line
+
+GRANULAR package :link(PKG-GRANULAR),h4
+
+[Contents:]
+
+Pair styles and fixes for finite-size granular particles, which
+interact with each other and boundaries via frictional and dissipative
+potentials.
+
+[Supporting info:]
+
+src/GRANULAR: filenames -> commands
+"Howto granular"_Howto_granular.html
+"fix pour"_fix_pour.html
+"fix wall/gran"_fix_wall_gran.html
+"pair_style gran/hooke"_pair_gran.html
+"pair_style gran/hertz/history"_pair_gran.html
+examples/granregion
+examples/pour
+bench/in.chute
+http://lammps.sandia.gov/pictures.html#jamming
+http://lammps.sandia.gov/movies.html#hopper
+http://lammps.sandia.gov/movies.html#dem
+http://lammps.sandia.gov/movies.html#brazil
+http://lammps.sandia.gov/movies.html#granregion :ul
+
+:line
+
+KIM package :link(PKG-KIM),h4
+
+[Contents:]
+
+A "pair_style kim"_pair_kim.html command which is a wrapper on the
+Knowledge Base for Interatomic Models (KIM) repository of interatomic
+potentials, enabling any of them to be used in LAMMPS simulations.
+
+To use this package you must have the KIM library available on your
+system.
+
+Information about the KIM project can be found at its website:
+https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
+Elliott (U Minnesota) and James Sethna (Cornell U).
+
+[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
+API which the "pair_style kim"_pair_kim.html command uses. He
+developed the pair style in collaboration with Valeriu Smirichinski (U
+Minnesota).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/KIM: filenames -> commands
+src/KIM/README
+lib/kim/README
+"pair_style kim"_pair_kim.html
+examples/kim :ul
+
+:line
+
+KOKKOS package :link(PKG-KOKKOS),h4
+
+[Contents:]
+
+Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
+styles adapted to compile using the Kokkos library which can convert
+them to OpenMP or CUDA code so that they run efficiently on multicore
+CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
+style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
+details of what hardware and software is required on your system, and
+how to build and use this package. Its styles can be invoked at run
+time via the "-sf kk" or "-suffix kk" "command-line
+switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
+
+You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
+
+[Authors:] The KOKKOS package was created primarily by Christian Trott
+and Stan Moore (Sandia), with contributions from other folks as well.
+It uses the open-source "Kokkos library"_https://github.com/kokkos
+which was developed by Carter Edwards, Christian Trott, and others at
+Sandia, and which is included in the LAMMPS distribution in
+lib/kokkos.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/KOKKOS: filenames -> commands
+src/KOKKOS/README
+lib/kokkos/README
+"Speed packages"_Speed_packages.html
+"Speed kokkos"_Speed_kokkos.html
+"Section 2.6 -k on ..."_Run_options.html
+"Section 2.6 -sf kk"_Run_options.html
+"Section 2.6 -pk kokkos"_Run_options.html
+"package kokkos"_package.html
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
+
+:line
+
+KSPACE package :link(PKG-KSPACE),h4
+
+[Contents:]
+
+A variety of long-range Coulombic solvers, as well as pair styles
+which compute the corresponding short-range pairwise Coulombic
+interactions. These include Ewald, particle-particle particle-mesh
+(PPPM), and multilevel summation method (MSM) solvers.
+
+[Install:]
+
+Building with this package requires a 1d FFT library be present on
+your system for use by the PPPM solvers. This can be the KISS FFT
+library provided with LAMMPS, 3rd party libraries like FFTW, or a
+vendor-supplied FFT library. See the "Build
+settings"_Build_settings.html doc page for details on how to select
+different FFT options for your LAMPMS build.
+
+[Supporting info:]
+
+src/KSPACE: filenames -> commands
+"kspace_style"_kspace_style.html
+"doc/PDF/kspace.pdf"_PDF/kspace.pdf
+"Howto tip3p"_Howto_tip3p.html
+"Howto tip4p"_Howto_tip4p.html
+"Howto spc"_Howto_spc.html
+"pair_style coul"_pair_coul.html
+"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
+examples/peptide
+bench/in.rhodo :ul
+
+:line
+
+LATTE package :link(PKG-LATTE),h4
+
+[Contents:]
+
+A fix command which wraps the LATTE DFTB code, so that molecular
+dynamics can be run with LAMMPS using density-functional tight-binding
+quantum forces calculated by LATTE.
+
+More information on LATTE can be found at this web site:
+"https://github.com/lanl/LATTE"_latte_home. A brief technical
+description is given with the "fix latte"_fix_latte.html command.
+
+:link(latte_home,https://github.com/lanl/LATTE)
+
+[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
+itself is developed at Los Alamos National Laboratory by Marc
+Cawkwell, Anders Niklasson, and Christian Negre.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/LATTE: filenames -> commands
+src/LATTE/README
+lib/latte/README
+"fix latte"_fix_latte.html
+examples/latte
+"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
+
+:line
+
+MANYBODY package :link(PKG-MANYBODY),h4
+
+[Contents:]
+
+A variety of manybody and bond-order potentials. These include
+(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
+
+[Supporting info:]
+
+src/MANYBODY: filenames -> commands
+"Commands pair"_Commands_pair.html page
+examples/comb
+examples/eim
+examples/nb3d
+examples/shear
+examples/streitz
+examples/vashishta
+bench/in.eam :ul
+
+:line
+
+MC package :link(PKG-MC),h4
+
+[Contents:]
+
+Several fixes and a pair style that have Monte Carlo (MC) or MC-like
+attributes. These include fixes for creating, breaking, and swapping
+bonds, for performing atomic swaps, and performing grand-canonical MC
+(GCMC) in conjuction with dynamics.
+
+[Supporting info:]
+
+src/MC: filenames -> commands
+"fix atom/swap"_fix_atom_swap.html
+"fix bond/break"_fix_bond_break.html
+"fix bond/create"_fix_bond_create.html
+"fix bond/swap"_fix_bond_swap.html
+"fix gcmc"_fix_gcmc.html
+"pair_style dsmc"_pair_dsmc.html
+http://lammps.sandia.gov/movies.html#gcmc :ul
+
+:line
+
+MEAM package :link(PKG-MEAM),h4
+
+[Contents:]
+
+A pair style for the modified embedded atom (MEAM) potential.
+
+Please note that the use of the MEAM package is discouraged as
+it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
+which is a direct translation of the MEAM package to C++.
+USER-MEAMC contains additional optimizations making it run faster
+than MEAM on most machines, while providing the identical features
+and user interface.
+
+[Author:] Greg Wagner (Northwestern U) while at Sandia.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+NOTE: You should test building the MEAM library with both the Intel
+and GNU compilers to see if a simulation runs faster with one versus
+the other on your system.
+
+[Supporting info:]
+
+src/MEAM: filenames -> commands
+src/meam/README
+lib/meam/README
+"pair_style meam"_pair_meam.html
+examples/meam :ul
+
+:line
+
+MISC package :link(PKG-MISC),h4
+
+[Contents:]
+
+A variety of compute, fix, pair, dump styles with specialized
+capabilities that don't align with other packages. Do a directory
+listing, "ls src/MISC", to see the list of commands.
+
+NOTE: the MISC package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
+[Supporting info:]
+
+src/MISC: filenames -> commands
+"compute ti"_compute_ti.html
+"fix evaporate"_fix_evaporate.html
+"fix orient/fcc"_fix_orient.html
+"fix ttm"_fix_ttm.html
+"fix thermal/conductivity"_fix_thermal_conductivity.html
+"fix viscosity"_fix_viscosity.html
+examples/KAPPA
+examples/VISCOSITY
+http://lammps.sandia.gov/pictures.html#ttm
+http://lammps.sandia.gov/movies.html#evaporation :ul
+
+:line
+
+MOLECULE package :link(PKG-MOLECULE),h4
+
+[Contents:]
+
+A large number of atom, pair, bond, angle, dihedral, improper styles
+that are used to model molecular systems with fixed covalent bonds.
+The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
+force fields, and a TIP4P water model.
+
+[Supporting info:]
+
+src/MOLECULE: filenames -> commands
+"atom_style"_atom_style.html
+"bond_style"_bond_style.html
+"angle_style"_angle_style.html
+"dihedral_style"_dihedral_style.html
+"improper_style"_improper_style.html
+"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
+"pair_style lj/charmm/coul/charmm"_pair_charmm.html
+"Howto bioFF"_Howto_bioFF.html
+examples/cmap
+examples/dreiding
+examples/micelle,
+examples/peptide
+bench/in.chain
+bench/in.rhodo :ul
+
+:line
+
+MPIIO package :link(PKG-MPIIO),h4
+
+[Contents:]
+
+Support for parallel output/input of dump and restart files via the
+MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
+their style name. Restart files with an ".mpiio" suffix are also
+written and read in parallel.
+
+[Supporting info:]
+
+src/MPIIO: filenames -> commands
+"dump"_dump.html
+"restart"_restart.html
+"write_restart"_write_restart.html
+"read_restart"_read_restart.html :ul
+
+:line
+
+MSCG package :link(PKG-mscg),h4
+
+[Contents:]
+
+A "fix mscg"_fix_mscg.html command which can parameterize a
+Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
+library"_mscg_home.
+
+:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
+
+To use this package you must have the MS-CG library available on your
+system.
+
+[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG
+library was developed by Jacob Wagner in Greg Voth's group at the
+University of Chicago.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/MSCG: filenames -> commands
+src/MSCG/README
+lib/mscg/README
+examples/mscg :ul
+
+:line
+
+OPT package :link(PKG-OPT),h4
+
+[Contents:]
+
+A handful of pair styles which are optimized for improved CPU
+performance on single or multiple cores. These include EAM, LJ,
+CHARMM, and Morse potentials. The styles have an "opt" suffix in
+their style name. The "Speed opt"_Speed_opt.html doc page gives
+details of how to build and use this package. Its styles can be
+invoked at run time via the "-sf opt" or "-suffix opt" "command-line
+switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS,
+"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
+have styles optimized for CPU performance.
+
+[Authors:] James Fischer (High Performance Technologies), David Richie,
+and Vincent Natoli (Stone Ridge Technolgy).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/OPT: filenames -> commands
+"Speed packages"_Speed_packages.html
+"Speed opt"_Speed_opt.html
+"Section 2.6 -sf opt"_Run_options.html
+"Commands pair"_Commands_pair.html for styles followed by (t)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
+
+:line
+
+PERI package :link(PKG-PERI),h4
+
+[Contents:]
+
+An atom style, several pair styles which implement different
+Peridynamics materials models, and several computes which calculate
+diagnostics. Peridynamics is a a particle-based meshless continuum
+model.
+
+[Authors:] The original package was created by Mike Parks (Sandia).
+Additional Peridynamics models were added by Rezwanur Rahman and John
+Foster (UTSA).
+
+[Supporting info:]
+
+src/PERI: filenames -> commands
+"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf
+"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf
+"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf
+"atom_style peri"_atom_style.html
+"pair_style peri/*"_pair_peri.html
+"compute damage/atom"_compute_damage_atom.html
+"compute plasticity/atom"_compute_plasticity_atom.html
+examples/peri
+http://lammps.sandia.gov/movies.html#peri :ul
+
+:line
+
+POEMS package :link(PKG-POEMS),h4
+
+[Contents:]
+
+A fix that wraps the Parallelizable Open source Efficient Multibody
+Software (POEMS) library, which is able to simulate the dynamics of
+articulated body systems. These are systems with multiple rigid
+bodies (collections of particles) whose motion is coupled by
+connections at hinge points.
+
+[Author:] Rudra Mukherjee (JPL) while at RPI.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/POEMS: filenames -> commands
+src/POEMS/README
+lib/poems/README
+"fix poems"_fix_poems.html
+examples/rigid :ul
+
+:line
+
+PYTHON package :link(PKG-PYTHON),h4
+
+[Contents:]
+
+A "python"_python.html command which allow you to execute Python code
+from a LAMMPS input script. The code can be in a separate file or
+embedded in the input script itself. See the "Python
+call"_Python_call.html doc page for an overview of using Python from
+LAMMPS in this manner and all the "Python"_Python_head.html doc pages
+for other ways to use LAMMPS and Python together.
+
+NOTE: Building with the PYTHON package assumes you have a Python
+shared library available on your system, which needs to be a Python 2
+version, 2.6 or later. Python 3 is not yet supported. See the
+lib/python/README for more details.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/PYTHON: filenames -> commands
+"Python call"_Python_head.html
+lib/python/README
+examples/python :ul
+
+:line
+
+QEQ package :link(PKG-QEQ),h4
+
+[Contents:]
+
+Several fixes for performing charge equilibration (QEq) via different
+algorithms. These can be used with pair styles that perform QEq as
+part of their formulation.
+
+[Supporting info:]
+
+src/QEQ: filenames -> commands
+"fix qeq/*"_fix_qeq.html
+examples/qeq
+examples/streitz :ul
+
+:line
+
+REAX package :link(PKG-REAX),h4
+
+[Contents:]
+
+NOTE: the use of the REAX package is discouraged, as it is no longer
+maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
+and possibly the KOKKOS enabled variant of that, which has a more robust
+memory management.
+
+A pair style which wraps a Fortran library which implements the ReaxFF
+potential, which is a universal reactive force field. Also included is
+a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
+as bonds are created and destroyed.
+
+[Author:] Aidan Thompson (Sandia).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/REAX: filenames -> commands
+lib/reax/README
+"pair_style reax"_pair_reax.html
+"fix reax/bonds"_fix_reax_bonds.html
+examples/reax :ul
+
+:line
+
+REPLICA package :link(PKG-REPLICA2),h4
+
+[Contents:]
+
+A collection of multi-replica methods which can be used when running
+multiple LAMMPS simulations (replicas). See the "Howto
+replica"_Howto_replica.html doc page for an overview of how to run
+multi-replica simulations in LAMMPS. Methods in the package include
+nudged elastic band (NEB), parallel replica dynamics (PRD),
+temperature accelerated dynamics (TAD), parallel tempering, and a
+verlet/split algorithm for performing long-range Coulombics on one set
+of processors, and the remainder of the force field calcalation on
+another set.
+
+[Supporting info:]
+
+src/REPLICA: filenames -> commands
+"Howto replica"_Howto_replica.html
+"neb"_neb.html
+"prd"_prd.html
+"tad"_tad.html
+"temper"_temper.html,
+"run_style verlet/split"_run_style.html
+examples/neb
+examples/prd
+examples/tad :ul
+
+:line
+
+RIGID package :link(PKG-RIGID),h4
+
+[Contents:]
+
+Fixes which enforce rigid constraints on collections of atoms or
+particles. This includes SHAKE and RATTLE, as well as varous
+rigid-body integrators for a few large bodies or many small bodies.
+Also several computes which calculate properties of rigid bodies.
+
+[Supporting info:]
+
+src/RIGID: filenames -> commands
+"compute erotate/rigid"_compute_erotate_rigid.html
+fix shake"_fix_shake.html
+"fix rattle"_fix_shake.html
+"fix rigid/*"_fix_rigid.html
+examples/ASPHERE
+examples/rigid
+bench/in.rhodo
+http://lammps.sandia.gov/movies.html#box
+http://lammps.sandia.gov/movies.html#star :ul
+
+:line
+
+SHOCK package :link(PKG-SHOCK),h4
+
+[Contents:]
+
+Fixes for running impact simulations where a shock-wave passes through
+a material.
+
+[Supporting info:]
+
+src/SHOCK: filenames -> commands
+"fix append/atoms"_fix_append_atoms.html
+"fix msst"_fix_msst.html
+"fix nphug"_fix_nphug.html
+"fix wall/piston"_fix_wall_piston.html
+examples/hugoniostat
+examples/msst :ul
+
+:line
+
+SNAP package :link(PKG-SNAP),h4
+
+[Contents:]
+
+A pair style for the spectral neighbor analysis potential (SNAP).
+SNAP is methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. Also several
+computes which analyze attributes of the potential.
+
+[Author:] Aidan Thompson (Sandia).
+
+[Supporting info:]
+
+src/SNAP: filenames -> commands
+"pair_style snap"_pair_snap.html
+"compute sna/atom"_compute_sna_atom.html
+"compute snad/atom"_compute_sna_atom.html
+"compute snav/atom"_compute_sna_atom.html
+examples/snap :ul
+
+:line
+
+SPIN package :link(PKG-SPIN),h4
+
+[Contents:]
+
+Model atomic magnetic spins classically, coupled to atoms moving in
+the usual manner via MD. Various pair, fix, and compute styles.
+
+[Author:] Julian Tranchida (Sandia).
+
+[Supporting info:]
+
+src/SPIN: filenames -> commands
+"Howto spins"_Howto_spins.html
+"pair_style spin/dmi"_pair_spin_dmi.html
+"pair_style spin/exchange"_pair_spin_exchange.html
+"pair_style spin/magelec"_pair_spin_magelec.html
+"pair_style spin/neel"_pair_spin_neel.html
+"fix nve/spin"_fix_nve_spin.html
+"fix precession/spin"_fix_precession_spin.html
+"compute spin"_compute_spin.html
+examples/SPIN :ul
+
+:line
+
+SRD package :link(PKG-SRD),h4
+
+[Contents:]
+
+A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
+method for coarse-graining of a solvent, typically around large
+colloidal particles.
+
+[Supporting info:]
+
+src/SRD: filenames -> commands
+"fix srd"_fix_srd.html
+"fix wall/srd"_fix_wall_srd.html
+examples/srd
+examples/ASPHERE
+http://lammps.sandia.gov/movies.html#tri
+http://lammps.sandia.gov/movies.html#line
+http://lammps.sandia.gov/movies.html#poly :ul
+
+:line
+
+VORONOI package :link(PKG-VORONOI),h4
+
+[Contents:]
+
+A compute command which calculates the Voronoi tesselation of a
+collection of atoms by wrapping the "Voro++ library"_voro_home. This
+can be used to calculate the local volume or each atoms or its near
+neighbors.
+
+:link(voro_home,http://math.lbl.gov/voro++)
+
+To use this package you must have the Voro++ library available on your
+system.
+
+[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++
+library was written by Chris Rycroft (Harvard U) while at UC Berkeley
+and LBNL.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/VORONOI: filenames -> commands
+src/VORONOI/README
+lib/voronoi/README
+"compute voronoi/atom"_compute_voronoi_atom.html
+examples/voronoi :ul
+
+:line
+
+USER-ATC package :link(PKG-USER-ATC),h4
+
+[Contents:]
+
+ATC stands for atoms-to-continuum. This package implements a "fix
+atc"_fix_atc.html command to either couple molecular dynamics with
+continuum finite element equations or perform on-the-fly conversion of
+atomic information to continuum fields.
+
+[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ATC: filenames -> commands
+src/USER-ATC/README
+"fix atc"_fix_atc.html
+examples/USER/atc
+http://lammps.sandia.gov/pictures.html#atc :ul
+
+:line
+
+USER-AWPMD package :link(PKG-USER-AWPMD),h4
+
+[Contents:]
+
+AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This
+package implements an atom, pair, and fix style which allows electrons
+to be treated as explicit particles in a classical molecular dynamics
+model.
+
+[Author:] Ilya Valuev (JIHT, Russia).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-AWPMD: filenames -> commands
+src/USER-AWPMD/README
+"pair_style awpmd/cut"_pair_awpmd.html
+examples/USER/awpmd :ul
+
+:line
+
+USER-BOCS package :link(PKG-USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
+USER-CGDNA package :link(PKG-USER-CGDNA),h4
+
+[Contents:]
+
+Several pair styles, a bond style, and integration fixes for
+coarse-grained models of single- and double-stranded DNA based on the
+oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
+This includes Langevin-type rigid-body integrators with improved
+stability.
+
+[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
+
+[Supporting info:]
+
+src/USER-CGDNA: filenames -> commands
+/src/USER-CGDNA/README
+"pair_style oxdna/*"_pair_oxdna.html
+"pair_style oxdna2/*"_pair_oxdna2.html
+"bond_style oxdna/*"_bond_oxdna.html
+"bond_style oxdna2/*"_bond_oxdna.html
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
+
+:line
+
+USER-CGSDK package :link(PKG-USER-CGSDK),h4
+
+[Contents:]
+
+Several pair styles and an angle style which implement the
+coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
+simulation of ionic liquids, electrolytes, lipids and charged amino
+acids.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Supporting info:]
+
+src/USER-CGSDK: filenames -> commands
+src/USER-CGSDK/README
+"pair_style lj/sdk/*"_pair_sdk.html
+"angle_style sdk"_angle_sdk.html
+examples/USER/cgsdk
+http://lammps.sandia.gov/pictures.html#cg :ul
+
+:line
+
+USER-COLVARS package :link(PKG-USER-COLVARS),h4
+
+[Contents:]
+
+COLVARS stands for collective variables, which can be used to
+implement various enhanced sampling methods, including Adaptive
+Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
+Restraints. A "fix colvars"_fix_colvars.html command is implemented
+which wraps a COLVARS library, which implements these methods.
+simulations.
+
+[Authors:] The COLVARS library is written and maintained by
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
+and Jerome Henin (LISM, CNRS, Marseille, France), originally for
+the NAMD MD code, but with portability in mind. Axel Kohlmeyer
+(Temple U) provided the interface to LAMMPS.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-COLVARS: filenames -> commands
+"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf
+src/USER-COLVARS/README
+lib/colvars/README
+"fix colvars"_fix_colvars.html
+examples/USER/colvars :ul
+
+:line
+
+USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
+
+[Contents:]
+
+Two computes and a fix for calculating x-ray and electron diffraction
+intensities based on kinematic diffraction theory.
+
+[Author:] Shawn Coleman while at the U Arkansas.
+
+[Supporting info:]
+
+src/USER-DIFFRACTION: filenames -> commands
+"compute saed"_compute_saed.html
+"compute xrd"_compute_xrd.html
+"fix saed/vtk"_fix_saed_vtk.html
+examples/USER/diffraction :ul
+
+:line
+
+USER-DPD package :link(PKG-USER-DPD),h4
+
+[Contents:]
+
+DPD stands for dissipative particle dynamics. This package implements
+coarse-grained DPD-based models for energetic, reactive molecular
+crystalline materials. It includes many pair styles specific to these
+systems, including for reactive DPD, where each particle has internal
+state for multiple species and a coupled set of chemical reaction ODEs
+are integrated each timestep. Highly accurate time integrators for
+isothermal, isoenergetic, isobaric and isenthalpic conditions are
+included. These enable long timesteps via the Shardlow splitting
+algorithm.
+
+[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
+Brennan (ARL).
+
+[Supporting info:]
+
+src/USER-DPD: filenames -> commands
+/src/USER-DPD/README
+"compute dpd"_compute_dpd.html
+"compute dpd/atom"_compute_dpd_atom.html
+"fix eos/cv"_fix_eos_table.html
+"fix eos/table"_fix_eos_table.html
+"fix eos/table/rx"_fix_eos_table_rx.html
+"fix shardlow"_fix_shardlow.html
+"fix rx"_fix_rx.html
+"pair_style table/rx"_pair_table_rx.html
+"pair_style dpd/fdt"_pair_dpd_fdt.html
+"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
+"pair_style exp6/rx"_pair_exp6_rx.html
+"pair_style multi/lucy"_pair_multi_lucy.html
+"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
+examples/USER/dpd :ul
+
+:line
+
+USER-DRUDE package :link(PKG-USER-DRUDE),h4
+
+[Contents:]
+
+Fixes, pair styles, and a compute to simulate thermalized Drude
+oscillators as a model of polarization. See the "Howto
+drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
+for an overview of how to use the package. There are auxiliary tools
+for using this package in tools/drude.
+
+[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
+Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
+
+[Supporting info:]
+
+src/USER-DRUDE: filenames -> commands
+"Howto drude"_Howto_drude.html
+"Howto drude2"_Howto_drude2.html
+"Howto polarizable"_Howto_polarizable.html
+src/USER-DRUDE/README
+"fix drude"_fix_drude.html
+"fix drude/transform/*"_fix_drude_transform.html
+"compute temp/drude"_compute_temp_drude.html
+"pair_style thole"_pair_thole.html
+"pair_style lj/cut/thole/long"_pair_thole.html
+examples/USER/drude
+tools/drude :ul
+
+:line
+
+USER-EFF package :link(PKG-USER-EFF),h4
+
+[Contents:]
+
+EFF stands for electron force field which allows a classical MD code
+to model electrons as particles of variable radius. This package
+contains atom, pair, fix and compute styles which implement the eFF as
+described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
+JCC, 2010. The eFF potential was first introduced by Su and Goddard,
+in 2007. There are auxiliary tools for using this package in
+tools/eff; see its README file.
+
+[Author:] Andres Jaramillo-Botero (CalTech).
+
+[Supporting info:]
+
+src/USER-EFF: filenames -> commands
+src/USER-EFF/README
+"atom_style electron"_atom_style.html
+"fix nve/eff"_fix_nve_eff.html
+"fix nvt/eff"_fix_nh_eff.html
+"fix npt/eff"_fix_nh_eff.html
+"fix langevin/eff"_fix_langevin_eff.html
+"compute temp/eff"_compute_temp_eff.html
+"pair_style eff/cut"_pair_eff.html
+"pair_style eff/inline"_pair_eff.html
+examples/USER/eff
+tools/eff/README
+tools/eff
+http://lammps.sandia.gov/movies.html#eff :ul
+
+:line
+
+USER-FEP package :link(PKG-USER-FEP),h4
+
+[Contents:]
+
+FEP stands for free energy perturbation. This package provides
+methods for performing FEP simulations by using a "fix
+adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
+which have a "soft" in their style name. There are auxiliary tools
+for using this package in tools/fep; see its README file.
+
+[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
+
+[Supporting info:]
+
+src/USER-FEP: filenames -> commands
+src/USER-FEP/README
+"fix adapt/fep"_fix_adapt_fep.html
+"compute fep"_compute_fep.html
+"pair_style */soft"_pair_lj_soft.html
+examples/USER/fep
+tools/fep/README
+tools/fep :ul
+
+:line
+
+USER-H5MD package :link(PKG-USER-H5MD),h4
+
+[Contents:]
+
+H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary,
+self-describing file format, used by many scientific simulations.
+H5MD is a format for molecular simulations, built on top of HDF5.
+This package implements a "dump h5md"_dump_h5md.html command to output
+LAMMPS snapshots in this format.
+
+:link(HDF5,http://www.hdfgroup.org/HDF5)
+
+To use this package you must have the HDF5 library available on your
+system.
+
+[Author:] Pierre de Buyl (KU Leuven) created both the package and the
+H5MD format.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-H5MD: filenames -> commands
+src/USER-H5MD/README
+lib/h5md/README
+"dump h5md"_dump_h5md.html :ul
+
+:line
+
+USER-INTEL package :link(PKG-USER-INTEL),h4
+
+[Contents:]
+
+Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
+styles which are optimized for Intel CPUs and KNLs (Knights Landing).
+All of them have an "intel" in their style name. The "Speed
+intel"_Speed_intel.html doc page gives details of what hardware and
+compilers are required on your system, and how to build and use this
+package. Its styles can be invoked at run time via the "-sf intel" or
+"-suffix intel" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
+which have styles optimized for CPUs and KNLs.
+
+You need to have an Intel compiler, version 14 or higher to take full
+advantage of this package. While compilation with GNU compilers is
+supported, performance will be suboptimal.
+
+NOTE: the USER-INTEL package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
+[Author:] Mike Brown (Intel).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-INTEL: filenames -> commands
+src/USER-INTEL/README
+"Speed packages"_Speed_packages.html
+"Speed intel"_Speed_intel.html
+"Section 2.6 -sf intel"_Run_options.html
+"Section 2.6 -pk intel"_Run_options.html
+"package intel"_package.html
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
+src/USER-INTEL/TEST
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
+
+:line
+
+USER-LB package :link(PKG-USER-LB),h4
+
+[Contents:]
+
+Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
+can be used to model MD particles influenced by hydrodynamic forces.
+
+[Authors:] Frances Mackay and Colin Denniston (University of Western
+Ontario).
+
+[Supporting info:]
+
+src/USER-LB: filenames -> commands
+src/USER-LB/README
+"fix lb/fluid"_fix_lb_fluid.html
+"fix lb/momentum"_fix_lb_momentum.html
+"fix lb/viscous"_fix_lb_viscous.html
+examples/USER/lb :ul
+
+:line
+
+USER-MGPT package :link(PKG-USER-MGPT),h4
+
+[Contents:]
+
+A pair style which provides a fast implementation of the quantum-based
+MGPT multi-ion potentials. The MGPT or model GPT method derives from
+first-principles DFT-based generalized pseudopotential theory (GPT)
+through a series of systematic approximations valid for mid-period
+transition metals with nearly half-filled d bands. The MGPT method
+was originally developed by John Moriarty at LLNL. The pair style in
+this package calculates forces and energies using an optimized
+matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
+
+[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
+
+[Supporting info:]
+
+src/USER-MGPT: filenames -> commands
+src/USER-MGPT/README
+"pair_style mgpt"_pair_mgpt.html
+examples/USER/mgpt :ul
+
+:line
+
+USER-MISC package :link(PKG-USER-MISC),h4
+
+[Contents:]
+
+A potpourri of (mostly) unrelated features contributed to LAMMPS by
+users. Each feature is a single fix, compute, pair, bond, angle,
+dihedral, improper, or command style.
+
+[Authors:] The author for each style in the package is listed in the
+src/USER-MISC/README file.
+
+[Supporting info:]
+
+src/USER-MISC: filenames -> commands
+src/USER-MISC/README
+one doc page per individual command listed in src/USER-MISC/README
+examples/USER/misc :ul
+
+:line
+
+USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
+
+[Contents:]
+
+Several fixes and a "manifold" class which enable simulations of
+particles constrained to a manifold (a 2D surface within the 3D
+simulation box). This is done by applying the RATTLE constraint
+algorithm to formulate single-particle constraint functions
+g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
+n = grad(g).
+
+[Author:] Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
+
+[Supporting info:]
+
+src/USER-MANIFOLD: filenames -> commands
+src/USER-MANIFOLD/README
+"Howto manifold"_Howto_manifold.html
+"fix manifoldforce"_fix_manifoldforce.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
+"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
+examples/USER/manifold
+http://lammps.sandia.gov/movies.html#manifold :ul
+
+:line
+
+USER-MEAMC package :link(PKG-USER-MEAMC),h4
+
+[Contents:]
+
+A pair style for the modified embedded atom (MEAM) potential
+translated from the Fortran version in the "MEAM"_MEAM package
+to plain C++. In contrast to the MEAM package, no library
+needs to be compiled and the pair style can be instantiated
+multiple times.
+
+[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
+based on the Fortran version of Greg Wagner (Northwestern U) while at
+Sandia.
+
+[Supporting info:]
+
+src/USER-MEAMC: filenames -> commands
+src/USER-MEAMC/README
+"pair_style meam/c"_pair_meam.html
+examples/meam :ul
+
+:line
+
+USER-MESO package :link(PKG-USER-MESO),h4
+
+[Contents:]
+
+Several extensions of the the dissipative particle dynamics (DPD)
+method. Specifically, energy-conserving DPD (eDPD) that can model
+non-isothermal processes, many-body DPD (mDPD) for simulating
+vapor-liquid coexistence, and transport DPD (tDPD) for modeling
+advection-diffusion-reaction systems. The equations of motion of these
+DPD extensions are integrated through a modified velocity-Verlet (MVV)
+algorithm.
+
+[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
+
+[Supporting info:]
+
+src/USER-MESO: filenames -> commands
+src/USER-MESO/README
+"atom_style edpd"_atom_style.html
+"pair_style edpd"_pair_meso.html
+"pair_style mdpd"_pair_meso.html
+"pair_style tdpd"_pair_meso.html
+"fix mvv/dpd"_fix_mvv_dpd.html
+examples/USER/meso
+http://lammps.sandia.gov/movies.html#mesodpd :ul
+
+:line
+
+USER-MOFFF package :link(PKG-USER-MOFFF),h4
+
+[Contents:]
+
+Pair, angle and improper styles needed to employ the MOF-FF
+force field by Schmid and coworkers with LAMMPS.
+MOF-FF is a first principles derived force field with the primary aim
+to simulate MOFs and related porous framework materials, using spherical
+Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
+2013, 250, 1128-1141.
+For the usage of MOF-FF see the example in the example directory as
+well as the "MOF+"_MOFplus website.
+
+:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
+
+[Author:] Hendrik Heenen (Technical U of Munich),
+Rochus Schmid (Ruhr-University Bochum).
+
+[Supporting info:]
+
+src/USER-MOFFF: filenames -> commands
+src/USER-MOFFF/README
+"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html
+"angle_style class2"_angle_class2.html
+"angle_style cosine/buck6d"_angle_cosine_buck6d.html
+"improper_style inversion/harmonic"_improper_inversion_harmonic.html
+examples/USER/mofff :ul
+
+:line
+
+USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
+
+[Contents:]
+
+A "dump molfile"_dump_molfile.html command which uses molfile plugins
+that are bundled with the "VMD"_vmd_home
+molecular visualization and analysis program, to enable LAMMPS to dump
+snapshots in formats compatible with various molecular simulation
+tools.
+
+:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
+
+To use this package you must have the desired VMD plugins available on
+your system.
+
+Note that this package only provides the interface code, not the
+plugins themselves, which will be accessed when requesting a specific
+plugin via the "dump molfile"_dump_molfile.html command. Plugins can
+be obtained from a VMD installation which has to match the platform
+that you are using to compile LAMMPS for. By adding plugins to VMD,
+support for new file formats can be added to LAMMPS (or VMD or other
+programs that use them) without having to recompile the application
+itself. More information about the VMD molfile plugins can be found
+at
+"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-MOLFILE: filenames -> commands
+src/USER-MOLFILE/README
+lib/molfile/README
+"dump molfile"_dump_molfile.html :ul
+
+:line
+
+USER-NETCDF package :link(PKG-USER-NETCDF),h4
+
+[Contents:]
+
+Dump styles for writing NetCDF formatted dump files. NetCDF is a
+portable, binary, self-describing file format developed on top of
+HDF5. The file contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
+
+To use this package you must have the NetCDF library available on your
+system.
+
+Note that NetCDF files can be directly visualized with the following
+tools:
+
+"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
+"VMD"_vmd_home
+"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
+
+:link(ovito,http://www.ovito.org)
+:link(atomeye,http://www.libatoms.org)
+
+[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-NETCDF: filenames -> commands
+src/USER-NETCDF/README
+lib/netcdf/README
+"dump netcdf"_dump_netcdf.html :ul
+
+:line
+
+USER-OMP package :link(PKG-USER-OMP),h4
+
+[Contents:]
+
+Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
+kspace styles which are altered to enable threading on many-core CPUs
+via OpenMP directives. All of them have an "omp" in their style name.
+The "Speed omp"_Speed_omp.html doc page gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package. Its styles can be invoked at run time via the "-sf omp"
+or "-suffix omp" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
+packages, which have styles optimized for CPUs.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+NOTE: To enable multi-threading support the compile flag "-fopenmp"
+and the link flag "-fopenmp" (for GNU compilers, you have to look up
+the equivalent flags for other compilers) must be used to build LAMMPS.
+When using Intel compilers, also the "-restrict" flag is required.
+The USER-OMP package can be compiled without enabling OpenMP; then
+all code will be compiled as serial and the only improvement over the
+regular styles are some data access optimization. These flags should
+be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
+
+Once you have an appropriate Makefile.machine, you can
+install/un-install the package and build LAMMPS in the usual manner:
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-OMP: filenames -> commands
+src/USER-OMP/README
+"Speed packages"_Speed_packages.html
+"Speed omp"_Speed_omp.html
+"Section 2.6 -sf omp"_Run_options.html
+"Section 2.6 -pk omp"_Run_options.html
+"package omp"_package.html
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
+"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
+
+:line
+
+USER-PHONON package :link(PKG-USER-PHONON),h4
+
+[Contents:]
+
+A "fix phonon"_fix_phonon.html command that calculates dynamical
+matrices, which can then be used to compute phonon dispersion
+relations, directly from molecular dynamics simulations.
+
+[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
+
+[Supporting info:]
+
+src/USER-PHONON: filenames -> commands
+src/USER-PHONON/README
+"fix phonon"_fix_phonon.html
+examples/USER/phonon :ul
+
+:line
+
+USER-QMMM package :link(PKG-USER-QMMM),h4
+
+[Contents:]
+
+A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
+QM/MM simulation, currently only in combination with the "Quantum
+ESPRESSO"_espresso package.
+
+:link(espresso,http://www.quantum-espresso.org)
+
+To use this package you must have Quantum ESPRESSO available on your
+system.
+
+The current implementation only supports an ONIOM style mechanical
+coupling to the Quantum ESPRESSO plane wave DFT package.
+Electrostatic coupling is in preparation and the interface has been
+written in a manner that coupling to other QM codes should be possible
+without changes to LAMMPS itself.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-QMMM: filenames -> commands
+src/USER-QMMM/README
+lib/qmmm/README
+"fix phonon"_fix_phonon.html
+lib/qmmm/example-ec/README
+lib/qmmm/example-mc/README :ul
+
+:line
+
+USER-QTB package :link(PKG-USER-QTB),h4
+
+[Contents:]
+
+Two fixes which provide a self-consistent quantum treatment of
+vibrational modes in a classical molecular dynamics simulation. By
+coupling the MD simulation to a colored thermostat, it introduces zero
+point energy into the system, altering the energy power spectrum and
+the heat capacity to account for their quantum nature. This is useful
+when modeling systems at temperatures lower than their classical
+limits or when temperatures ramp across the classical limits in a
+simulation.
+
+[Author:] Yuan Shen (Stanford U).
+
+[Supporting info:]
+
+src/USER-QTB: filenames -> commands
+src/USER-QTB/README
+"fix qtb"_fix_qtb.html
+"fix qbmsst"_fix_qbmsst.html
+examples/USER/qtb :ul
+
+:line
+
+USER-QUIP package :link(PKG-USER-QUIP),h4
+
+[Contents:]
+
+A "pair_style quip"_pair_quip.html command which wraps the "QUIP
+libAtoms library"_quip, which includes a variety of interatomic
+potentials, including Gaussian Approximation Potential (GAP) models
+developed by the Cambridge University group.
+
+:link(quip,https://github.com/libAtoms/QUIP)
+
+To use this package you must have the QUIP libAtoms library available
+on your system.
+
+[Author:] Albert Bartok (Cambridge University)
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-QUIP: filenames -> commands
+src/USER-QUIP/README
+"pair_style quip"_pair_quip.html
+examples/USER/quip :ul
+
+:line
+
+USER-REAXC package :link(PKG-USER-REAXC),h4
+
+[Contents:]
+
+A pair style which implements the ReaxFF potential in C/C++ (in
+contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
+is universal reactive force field. See the src/USER-REAXC/README file
+for more info on differences between the two packages. Also two fixes
+for monitoring molecules as bonds are created and destroyed.
+
+[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
+
+[Supporting info:]
+
+src/USER-REAXC: filenames -> commands
+src/USER-REAXC/README
+"pair_style reax/c"_pair_reaxc.html
+"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/species"_fix_reaxc_species.html
+examples/reax :ul
+
+:line
+
+USER-SMD package :link(PKG-USER-SMD),h4
+
+[Contents:]
+
+An atom style, fixes, computes, and several pair styles which
+implements smoothed Mach dynamics (SMD) for solids, which is a model
+related to smoothed particle hydrodynamics (SPH) for liquids (see the
+"USER-SPH package"_#PKG-USER-SPH).
+
+This package solves solids mechanics problems via a state of the art
+stabilized meshless method with hourglass control. It can specify
+hydrostatic interactions independently from material strength models,
+i.e. pressure and deviatoric stresses are separated. It provides many
+material models (Johnson-Cook, plasticity with hardening,
+Mie-Grueneisen, Polynomial EOS) and allows new material models to be
+added. It implements rigid boundary conditions (walls) which can be
+specified as surface geometries from *.STL files.
+
+[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-SMD: filenames -> commands
+src/USER-SMD/README
+doc/PDF/SMD_LAMMPS_userguide.pdf
+examples/USER/smd
+http://lammps.sandia.gov/movies.html#smd :ul
+
+:line
+
+USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
+
+[Contents:]
+
+A pair style which implements a Second Moment Tight Binding model with
+QEq charge equilibration (SMTBQ) potential for the description of
+ionocovalent bonds in oxides.
+
+[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
+Tetot (LAAS-CNRS, France).
+
+[Supporting info:]
+
+src/USER-SMTBQ: filenames -> commands
+src/USER-SMTBQ/README
+"pair_style smtbq"_pair_smtbq.html
+examples/USER/smtbq :ul
+
+:line
+
+USER-SPH package :link(PKG-USER-SPH),h4
+
+[Contents:]
+
+An atom style, fixes, computes, and several pair styles which
+implements smoothed particle hydrodynamics (SPH) for liquids. See the
+related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
+(SMD) for solids.
+
+This package contains ideal gas, Lennard-Jones equation of states,
+Tait, and full support for complete (i.e. internal-energy dependent)
+equations of state. It allows for plain or Monaghans XSPH integration
+of the equations of motion. It has options for density continuity or
+density summation to propagate the density field. It has
+"set"_set.html command options to set the internal energy and density
+of particles from the input script and allows the same quantities to
+be output with thermodynamic output or to dump files via the "compute
+property/atom"_compute_property_atom.html command.
+
+[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
+Dynamics, Ernst Mach Institute, Germany).
+
+[Supporting info:]
+
+src/USER-SPH: filenames -> commands
+src/USER-SPH/README
+doc/PDF/SPH_LAMMPS_userguide.pdf
+examples/USER/sph
+http://lammps.sandia.gov/movies.html#sph :ul
+
+:line
+
+USER-TALLY package :link(PKG-USER-TALLY),h4
+
+[Contents:]
+
+Several compute styles that can be called when pairwise interactions
+are calculated to tally information (forces, heat flux, energy,
+stress, etc) about individual interactions.
+
+[Author:] Axel Kohlmeyer (Temple U).
+
+[Supporting info:]
+
+src/USER-TALLY: filenames -> commands
+src/USER-TALLY/README
+"compute */tally"_compute_tally.html
+examples/USER/tally :ul
+
+:line
+
+USER-UEF package :link(PKG-USER-UEF),h4
+
+[Contents:]
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+[Author:] David Nicholson (MIT).
+
+[Supporting info:]
+
+src/USER-UEF: filenames -> commands
+src/USER-UEF/README
+"fix nvt/uef"_fix_nh_uef.html
+"fix npt/uef"_fix_nh_uef.html
+"compute pressure/uef"_compute_pressure_uef.html
+"compute temp/uef"_compute_temp_uef.html
+"dump cfg/uef"_dump_cfg_uef.html
+examples/uef :ul
+
+:line
+
+USER-VTK package :link(PKG-USER-VTK),h4
+
+[Contents:]
+
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+other visualization packages.
+
+:link(vtk,http://www.vtk.org)
+:link(paraview,http://www.paraview.org)
+
+To use this package you must have VTK library available on your
+system.
+
+[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-VTK: filenames -> commands
+src/USER-VTK/README
+lib/vtk/README
+"dump vtk"_dump_vtk.html :ul
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
new file mode 100644
index 0000000000..eb787df5d6
--- /dev/null
+++ b/doc/src/Speed_kokkos.txt
@@ -0,0 +1,381 @@
+"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+KOKKOS package :h3
+
+Kokkos is a templated C++ library that provides abstractions to allow
+a single implementation of an application kernel (e.g. a pair style)
+to run efficiently on different kinds of hardware, such as GPUs, Intel
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
+different backend languages such as CUDA, OpenMP, or Pthreads. The
+Kokkos library also provides data abstractions to adjust (at compile
+time) the memory layout of data structures like 2d and 3d arrays to
+optimize performance on different hardware. For more information on
+Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
+of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
+library was written primarily by Carter Edwards, Christian Trott, and
+Dan Sunderland (all Sandia).
+
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
+styles that use data structures and macros provided by the Kokkos
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
+package was developed primarily by Christian Trott (Sandia) and Stan
+Moore (Sandia) with contributions of various styles by others,
+including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
+(Sandia). For more information on developing using Kokkos abstractions
+see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
+
+Kokkos currently provides support for 3 modes of execution (per MPI
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
+GPUs). You choose the mode at build time to produce an executable
+compatible with specific hardware.
+
+NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
+compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
+Clang 3.5.2 or later is required.
+
+NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
+software version 7.5 or later must be installed on your system. See
+the discussion for the "GPU package"_Speed_gpu.html for details of how
+to check and do this.
+
+NOTE: Kokkos with CUDA currently implicitly assumes, that the MPI
+library is CUDA-aware and has support for GPU-direct. This is not
+always the case, especially when using pre-compiled MPI libraries
+provided by a Linux distribution. This is not a problem when using
+only a single GPU and a single MPI rank on a desktop. When running
+with multiple MPI ranks, you may see segmentation faults without
+GPU-direct support. These can be avoided by adding the flags "-pk
+kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or
+by using the command "package kokkos gpu/direct off"_package.html in
+the input file.
+
+[Building LAMMPS with the KOKKOS package:]
+
+See the "Build extras"_Build_extras.html#kokkos doc page for instructions.
+
+[Running LAMMPS with the KOKKOS package:]
+
+All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+-npernode switches. Ditto for MPICH via -np and -ppn.
+
+[Running on a multi-core CPU:]
+
+Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading
+mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
+kokkos" "command-line switches"_Run_options.html in your mpirun
+command. You must use the "-k on" "command-line
+switch"_Run_options.html to enable the KOKKOS package. It takes
+additional arguments for hardware settings appropriate to your system.
+For OpenMP use:
+
+-k on t Nt :pre
+
+The "t Nt" option specifies how many OpenMP threads per MPI task to
+use with a node. The default is Nt = 1, which is MPI-only mode. Note
+that the product of MPI tasks * OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer. If hyperthreading is enabled, then the product of MPI tasks *
+OpenMP threads/task should not exceed the physical number of cores *
+hardware threads. The "-k on" switch also issues a "package kokkos"
+command (with no additional arguments) which sets various KOKKOS
+options to default values, as discussed on the "package"_package.html
+command doc page.
+
+The "-sf kk" "command-line switch"_Run_options.html will automatically
+append the "/kk" suffix to styles that support it. In this manner no
+modification to the input script is needed. Alternatively, one can run
+with the KOKKOS package by editing the input script as described
+below.
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. However, when running on CPUs, it
+will typically be faster to use "half" neighbor lists and set the
+Newton flag to "on", just as is the case for non-accelerated pair
+styles. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
+
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
+
+If the "newton"_newton.html command is used in the input
+script, it can also override the Newton flag defaults.
+
+[Core and Thread Affinity:]
+
+When using multi-threading, it is important for performance to bind
+both MPI tasks to physical cores, and threads to physical cores, so
+they do not migrate during a simulation.
+
+If you are not certain MPI tasks are being bound (check the defaults
+for your MPI installation), binding can be forced with these flags:
+
+OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre
+
+For binding threads with KOKKOS OpenMP, use thread affinity
+environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
+later, intel 12 or later) setting the environment variable
+OMP_PROC_BIND=true should be sufficient. In general, for best
+performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
+OMP_PLACES=threads. For binding threads with the KOKKOS pthreads
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
+
+[Running on Knight's Landing (KNL) Intel Xeon Phi:]
+
+Here is a quick overview of how to use the KOKKOS package for the
+Intel Knight's Landing (KNL) Xeon Phi:
+
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
+hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+cores to run on. The product of MPI tasks * OpenMP threads/task should
+not exceed this limit, otherwise performance will suffer. Note that
+with the KOKKOS package you do not need to specify how many KNLs there
+are per node; each KNL is simply treated as running some number of MPI
+tasks.
+
+Examples of mpirun commands that follow these rules are shown below.
+
+Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task
+mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task
+mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task
+mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre
+
+The -np setting of the mpirun command sets the number of MPI
+tasks/node. The "-k on t Nt" command-line switch sets the number of
+threads/task as Nt. The product of these two values should be N, i.e.
+256 or 264.
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this will
+typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the Newton flag to "on" may be
+faster. It can also be faster to use non-threaded communication. Use
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
+
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
+
+NOTE: MPI tasks and threads should be bound to cores as described
+above for CPUs.
+
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
+such as Knight's Corner (KNC), your system must be configured to use
+them in "native" mode, not "offload" mode like the USER-INTEL package
+supports.
+
+[Running on GPUs:]
+
+Use the "-k" "command-line switch"_Run_options.html to
+specify the number of GPUs per node. Typically the -np setting of the
+mpirun command should set the number of MPI tasks/node to be equal to
+the number of physical GPUs on the node. You can assign multiple MPI
+tasks to the same GPU with the KOKKOS package, but this is usually
+only faster if significant portions of the input script have not
+been ported to use Kokkos. Using CUDA MPS is recommended in this
+scenario. Using a CUDA-aware MPI library with support for GPU-direct
+is highly recommended. GPU-direct use can be avoided by using
+"-pk kokkos gpu/direct no"_package.html.
+As above for multi-core CPUs (and no GPU), if N is the number of
+physical cores/node, then the number of MPI tasks/node should not
+exceed N.
+
+-k on g Ng :pre
+
+Here are examples of how to use the KOKKOS package for GPUs, assuming
+one or more nodes, each with two GPUs:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
+mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions, along with threaded communication.
+When running on Maxwell or Kepler GPUs, this will typically be
+best. For Pascal GPUs, using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the
+neighbor binsize equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page
+for details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+
+NOTE: For good performance of the KOKKOS package on GPUs, you must
+have Kepler generation GPUs (or later). The Kokkos library exploits
+texture cache options not supported by Telsa generation GPUs (or
+older).
+
+NOTE: When using a GPU, you will achieve the best performance if your
+input script does not use fix or compute styles which are not yet
+Kokkos-enabled. This allows data to stay on the GPU for multiple
+timesteps, without being copied back to the host CPU. Invoking a
+non-Kokkos fix or compute, or performing I/O for
+"thermo"_thermo_style.html or "dump"_dump.html output will cause data
+to be copied back to the CPU incurring a performance penalty.
+
+NOTE: To get an accurate timing breakdown between time spend in pair,
+kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1.
+However, this will reduce performance and is not recommended for production runs.
+
+[Run with the KOKKOS package by editing an input script:]
+
+Alternatively the effect of the "-sf" or "-pk" switches can be
+duplicated by adding the "package kokkos"_package.html or "suffix
+kk"_suffix.html commands to your input script.
+
+The discussion above for building LAMMPS with the KOKKOS package, the
+mpirun/mpiexec command, and setting appropriate thread are the same.
+
+You must still use the "-k on" "command-line switch"_Run_options.html
+to enable the KOKKOS package, and specify its additional arguments for
+hardware options appropriate to your system, as documented above.
+
+You can use the "suffix kk"_suffix.html command, or you can explicitly add a
+"kk" suffix to individual styles in your input script, e.g.
+
+pair_style lj/cut/kk 2.5 :pre
+
+You only need to use the "package kokkos"_package.html command if you
+wish to change any of its option defaults, as set by the "-k on"
+"command-line switch"_Run_options.html.
+
+[Using OpenMP threading and CUDA together (experimental):]
+
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
+used together in a few special cases. In the Makefile, the
+KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
+the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+
+KOKKOS_DEVICES=Cuda,OpenMP :pre
+
+The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
+using the "-sf kk" in the command line gives the default CUDA version
+everywhere. However, if the "/kk/host" suffix is added to a specific
+style in the input script, the Kokkos OpenMP (CPU) version of that
+specific style will be used instead. Set the number of OpenMP threads
+as "t Nt" and the number of GPUs as "g Ng"
+
+-k on t Nt g Ng :pre
+
+For example, the command to run with 1 GPU and 8 OpenMP threads is then:
+
+mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
+
+Conversely, if the "-sf kk/host" is used in the command line and then
+the "/kk" or "/kk/device" suffix is added to a specific style in your
+input script, then only that specific style will run on the GPU while
+everything else will run on the CPU in OpenMP mode. Note that the
+execution of the CPU and GPU styles will NOT overlap, except for a
+special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running
+on the host CPU can overlap with a pair style running on the
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
+in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
+suffix for kspace and bonds, angles, etc. in the input file and the
+"kk" suffix (equal to "kk/device") on the command line. Also make
+sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+so CPU/GPU overlap can occur.
+
+[Speed-ups to expect:]
+
+The performance of KOKKOS running in different modes is a function of
+your hardware, which KOKKOS-enable styles are used, and the problem
+size.
+
+Generally speaking, the following rules of thumb apply:
+
+When running on CPUs only, with a single thread per MPI task,
+performance of a KOKKOS style is somewhere between the standard
+(un-accelerated) styles (MPI-only mode), and those provided by the
+USER-OMP package. However the difference between all 3 is small (less
+than 20%). :ulb,l
+
+When running on CPUs only, with multiple threads per MPI task,
+performance of a KOKKOS style is a bit slower than the USER-OMP
+package. :l
+
+When running large number of atoms per GPU, KOKKOS is typically faster
+than the GPU package. :l
+
+When running on Intel hardware, KOKKOS is not as fast as
+the USER-INTEL package, which is optimized for that hardware. :l
+:ule
+
+See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
+LAMMPS web site for performance of the KOKKOS package on different
+hardware.
+
+[Advanced Kokkos options:]
+
+There are other allowed options when building with the KOKKOS package.
+As explained on the "Build extras"_Build_extras.html#kokkos doc page,
+they can be set either as variables on the make command line or in
+Makefile.machine, or they can be specified as CMake variables. Each
+takes a value shown below. The default value is listed, which is set
+in the lib/kokkos/Makefile.kokkos file.
+
+KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
+KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none}
+KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11}
+KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none}
+KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul
+
+KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
+migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
+used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
+necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
+provides alternative methods via environment variables for binding
+threads to hardware cores. More info on binding threads to cores is
+given on the "Speed omp"_Speed_omp.html doc page.
+
+KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
+on most Unix platforms. This library is not available on all
+platforms.
+
+KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
+within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.
+
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
+building LAMMPS.
+
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
+package must be compiled with the {enable_lambda} option when using
+GPUs.
+
+[Restrictions:]
+
+Currently, there are no precision options with the KOKKOS package. All
+compilation and computation is performed in double precision.
--
GitLab
From 648d8c3d2ae418ef877938d295260b2c058b8b8b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Aug 2018 10:15:17 -0400
Subject: [PATCH 150/332] adapt docs to refactored manual
---
doc/src/pair_atm.txt | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index c2718973ad..e59efe86ab 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
:line
@@ -150,8 +150,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
--
GitLab
From a04008cdfd5bd0f7212669b97fe7581eec771649 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Aug 2018 10:27:40 -0400
Subject: [PATCH 151/332] fully integrate atm pair style into manual
---
doc/src/Commands_pair.txt | 1 +
doc/src/lammps.book | 1 +
doc/src/pairs.txt | 1 +
3 files changed, 3 insertions(+)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index eaf2720613..33890df1fe 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -33,6 +33,7 @@ OPT.
"agni (o)"_pair_agni.html,
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
+"atm"_pair_atm.html,
"awpmd/cut"_pair_awpmd.html,
"beck (go)"_pair_beck.html,
"body/nparticle"_pair_body_nparticle.html,
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 47d05570be..c296ff4039 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -524,6 +524,7 @@ pair_write.html
pair_adp.html
pair_agni.html
pair_airebo.html
+pair_atm.html
pair_awpmd.html
pair_beck.html
pair_body_nparticle.html
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 4c3eef2cd1..d535798482 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -8,6 +8,7 @@ Pair Styles :h1
pair_adp
pair_agni
pair_airebo
+ pair_atm
pair_awpmd
pair_beck
pair_body_nparticle
--
GitLab
From 59d3af44f2fbe29f2848bd9ef9694818afead2a6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 23 Aug 2018 10:27:51 -0400
Subject: [PATCH 152/332] use c++ style system headers
---
src/MANYBODY/pair_atm.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index e960398ab3..c23aa6560d 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -15,10 +15,10 @@
Contributing author: Sergey Lishchuk
------------------------------------------------------------------------- */
-#include "pair_atm.h"
-#include <math.h>
+#include <cmath>
+#include "pair_atm.h"
#include "atom.h"
#include "citeme.h"
#include "comm.h"
--
GitLab
From dd923edf15e40dbff7840167653e24882a857934 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 09:20:02 -0600
Subject: [PATCH 153/332] Fix unused parameters in memory.h (#1076)
---
src/memory.h | 36 ++++++++++++++++++------------------
1 file changed, 18 insertions(+), 18 deletions(-)
diff --git a/src/memory.h b/src/memory.h
index f2faecf6e1..20ea426f90 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -50,7 +50,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **create(TYPE **&array, int n, const char *name)
+ TYPE **create(TYPE **& /*array*/, int /*n*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -68,7 +68,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **grow(TYPE **&array, int n, const char *name)
+ TYPE **grow(TYPE **& /*array*/, int /*n*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -96,7 +96,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **create1d_offset(TYPE **&array, int nlo, int nhi, const char *name)
+ TYPE **create1d_offset(TYPE **& /*array*/, int /*nlo*/, int /*nhi*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -131,7 +131,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create(TYPE ***&array, int n1, int n2, const char *name)
+ TYPE ***create(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -158,7 +158,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***grow(TYPE ***&array, int n1, int n2, const char *name)
+ TYPE ***grow(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -198,7 +198,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create_ragged(TYPE ***&array, int n1, int *n2, const char *name)
+ TYPE ***create_ragged(TYPE ***& /*array*/, int /*n1*/, int * /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -217,7 +217,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi,
+ TYPE ***create2d_offset(TYPE ***& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/,
const char *name) {fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -262,7 +262,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****create(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -297,7 +297,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****grow(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -330,8 +330,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2, int n3, const char *name)
+ TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/,
+ int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -374,8 +374,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2lo, int n2hi, int n3lo, int n3hi,
+ TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/,
+ int /*n2lo*/, int /*n2hi*/, int /*n3lo*/, int /*n3hi*/,
const char *name)
{fail(name); return NULL;}
@@ -432,7 +432,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
+ TYPE *****create(TYPE *****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/,
const char *name)
{fail(name); return NULL;}
@@ -478,8 +478,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create4d_offset(TYPE *****&array, int n1, int n2lo, int n2hi,
- int n3lo, int n3hi, int n4lo, int n4hi,
+ TYPE ****create4d_offset(TYPE *****& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/,
+ int /*n3lo*/, int /*n3hi*/, int /*n4lo*/, int /*n4hi*/,
const char *name)
{fail(name); return NULL;}
@@ -546,8 +546,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ******create(TYPE ******&array, int n1, int n2, int n3, int n4,
- int n5, const char *name)
+ TYPE ******create(TYPE ******& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/,
+ int /*n5*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
--
GitLab
From 9388ed8cd088fab37f8512729274f1bcf7405328 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 09:25:20 -0600
Subject: [PATCH 154/332] Add build files and clang-format config to gitignore
(#1076)
---
.gitignore | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.gitignore b/.gitignore
index 50b970249a..1ce415678e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
*~
*.o
*.so
+*.lo
*.cu_o
*.ptx
*_ptx.h
@@ -32,6 +33,7 @@ log.cite
.Trashes
ehthumbs.db
Thumbs.db
+.clang-format
#cmake
/build*
--
GitLab
From 2eeb8cecb2e658efa9adebe8db17e9634fcc743a Mon Sep 17 00:00:00 2001
From: Rene Halver <r.halver@fz-juelich.de>
Date: Thu, 23 Aug 2018 10:08:31 -0600
Subject: [PATCH 155/332] removed left-over debug messages
---
src/USER-SCAFACOS/scafacos.cpp | 2 --
1 file changed, 2 deletions(-)
diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp
index 92d0612947..52bb0e46c4 100644
--- a/src/USER-SCAFACOS/scafacos.cpp
+++ b/src/USER-SCAFACOS/scafacos.cpp
@@ -126,10 +126,8 @@ void Scafacos::init()
qqrd2e = force->qqrd2e;
if (!initialized) {
- printf("DEBUG: %p\n",&fcs);
result = fcs_init((FCS*)&fcs,method,world);
check_result((void*)&result);
- printf("DEBUG: %p\n",&fcs);
setup_handle();
--
GitLab
From 7238d4af941078ba17d37bf572efc58ff6b5ef25 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 10:08:23 -0600
Subject: [PATCH 156/332] Fix logic warnings (#1076)
---
src/dump_custom.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 4c3950c099..17ad4b89ef 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1023,12 +1023,12 @@ int DumpCustom::count()
} else if (thresh_op[ithresh] == XOR) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
+ if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) ||
(*ptr != 0.0 && values[i] != 0.0))
choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
+ if ((choose[i] && *ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
}
--
GitLab
From e9bc93909817b29a37f32d20fcb96bfa720e30d0 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 09:26:00 -0600
Subject: [PATCH 157/332] Fix more unused parameter warnings (#1076)
---
src/accelerator_kokkos.h | 4 ++--
src/angle_zero.cpp | 2 +-
src/atom.cpp | 4 ++--
src/atom_vec.cpp | 2 +-
src/atom_vec_body.cpp | 3 +++
src/body.cpp | 2 +-
src/bond_zero.cpp | 4 ++--
src/comm_brick.cpp | 4 ++--
src/comm_tiled.cpp | 12 ++++++------
src/compute_aggregate_atom.cpp | 4 ++--
src/compute_bond_local.cpp | 2 +-
src/compute_centro_atom.cpp | 2 +-
src/compute_cluster_atom.cpp | 4 ++--
src/compute_cna_atom.cpp | 2 +-
src/compute_contact_atom.cpp | 2 +-
src/compute_coord_atom.cpp | 4 ++--
src/compute_fragment_atom.cpp | 2 +-
src/compute_group_group.cpp | 2 +-
src/compute_hexorder_atom.cpp | 2 +-
src/compute_orientorder_atom.cpp | 3 +--
src/compute_pair_local.cpp | 2 +-
src/compute_property_local.cpp | 2 +-
src/compute_rdf.cpp | 2 +-
src/compute_temp_com.cpp | 4 ++--
src/compute_temp_deform.cpp | 4 ++--
src/compute_temp_partial.cpp | 10 +++++-----
src/compute_temp_ramp.cpp | 4 ++--
src/compute_temp_region.cpp | 4 ++--
src/dihedral_zero.cpp | 5 ++---
src/domain.cpp | 2 +-
src/dump.cpp | 2 +-
src/dump_image.cpp | 2 +-
src/dump_local.cpp | 2 +-
src/fix.cpp | 2 +-
src/fix_adapt.cpp | 4 ++--
src/fix_addforce.cpp | 2 +-
src/fix_ave_atom.cpp | 4 ++--
src/fix_ave_chunk.cpp | 2 +-
src/fix_ave_correlate.cpp | 2 +-
src/fix_ave_histo.cpp | 2 +-
src/fix_ave_time.cpp | 2 +-
src/fix_aveforce.cpp | 4 ++--
src/fix_balance.cpp | 2 +-
src/fix_drag.cpp | 4 ++--
src/fix_dt_reset.cpp | 2 +-
src/fix_enforce2d.cpp | 4 ++--
src/fix_external.cpp | 4 ++--
src/fix_gravity.cpp | 4 ++--
src/fix_group.cpp | 6 +++---
src/fix_indent.cpp | 4 ++--
src/fix_langevin.cpp | 6 +++---
src/fix_lineforce.cpp | 4 ++--
src/fix_minimize.cpp | 2 +-
src/fix_move.cpp | 10 +++++-----
src/fix_neigh_history.cpp | 2 +-
src/fix_nh.cpp | 8 ++++----
src/fix_nve.cpp | 6 +++---
src/fix_nve_limit.cpp | 6 +++---
src/fix_nve_noforce.cpp | 2 +-
src/fix_nve_sphere.cpp | 2 +-
src/fix_planeforce.cpp | 4 ++--
src/fix_press_berendsen.cpp | 2 +-
src/fix_property_atom.cpp | 16 ++++++++--------
src/fix_read_restart.cpp | 2 +-
src/fix_recenter.cpp | 4 ++--
src/fix_respa.cpp | 2 +-
src/fix_restrain.cpp | 4 ++--
src/fix_setforce.cpp | 4 ++--
src/fix_spring.cpp | 4 ++--
src/fix_spring_chunk.cpp | 4 ++--
src/fix_spring_rg.cpp | 4 ++--
src/fix_spring_self.cpp | 8 ++++----
src/fix_store.cpp | 4 ++--
src/fix_store_force.cpp | 4 ++--
src/fix_store_state.cpp | 6 +++---
src/fix_tmd.cpp | 4 ++--
src/fix_vector.cpp | 2 +-
src/fix_viscous.cpp | 4 ++--
src/fix_wall.cpp | 2 +-
src/fix_wall_region.cpp | 2 +-
src/group.cpp | 2 +-
src/image.cpp | 4 ++--
src/imbalance_var.cpp | 2 +-
src/improper_zero.cpp | 4 ++--
src/integrate.cpp | 2 +-
src/kspace.cpp | 2 +-
src/library.cpp | 2 +-
src/math_extra.cpp | 2 +-
src/neighbor.cpp | 2 +-
src/pair.cpp | 2 +-
src/pair_beck.cpp | 4 ++--
src/pair_born.cpp | 4 ++--
src/pair_buck.cpp | 4 ++--
src/pair_coul_cut.cpp | 4 ++--
src/pair_coul_debye.cpp | 4 ++--
src/pair_coul_dsf.cpp | 6 +++---
src/pair_coul_wolf.cpp | 6 +++---
src/pair_dpd.cpp | 4 ++--
src/pair_gauss.cpp | 4 ++--
src/pair_hybrid.cpp | 2 +-
src/pair_lj96_cut.cpp | 4 ++--
src/pair_lj_cubic.cpp | 6 +++---
src/pair_lj_cut.cpp | 4 ++--
src/pair_lj_expand.cpp | 4 ++--
src/pair_lj_gromacs.cpp | 4 ++--
src/pair_lj_smooth.cpp | 4 ++--
src/pair_lj_smooth_linear.cpp | 4 ++--
src/pair_mie_cut.cpp | 4 ++--
src/pair_morse.cpp | 4 ++--
src/pair_soft.cpp | 4 ++--
src/pair_table.cpp | 4 ++--
src/pair_ufm.cpp | 4 ++--
src/pair_yukawa.cpp | 4 ++--
src/pair_zbl.cpp | 4 ++--
src/rcb.cpp | 4 ++--
src/reader_xyz.cpp | 4 ++--
src/region.cpp | 2 +-
src/reset_ids.cpp | 2 +-
src/respa.cpp | 2 +-
src/variable.cpp | 2 +-
src/velocity.cpp | 8 ++++----
121 files changed, 224 insertions(+), 223 deletions(-)
diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h
index 8bbb6c4788..e64bde24be 100644
--- a/src/accelerator_kokkos.h
+++ b/src/accelerator_kokkos.h
@@ -66,8 +66,8 @@ class AtomKokkos : public Atom {
tagint **k_special;
AtomKokkos(class LAMMPS *lmp) : Atom(lmp) {}
~AtomKokkos() {}
- void sync(const ExecutionSpace space, unsigned int mask) {}
- void modified(const ExecutionSpace space, unsigned int mask) {}
+ void sync(const ExecutionSpace /*space*/, unsigned int /*mask*/) {}
+ void modified(const ExecutionSpace /*space*/, unsigned int /*mask*/) {}
};
class CommKokkos : public CommBrick {
diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp
index e5191c4fb2..d7b7c9cdb5 100644
--- a/src/angle_zero.cpp
+++ b/src/angle_zero.cpp
@@ -148,7 +148,7 @@ void AngleZero::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double AngleZero::single(int type, int i1, int i2, int i3)
+double AngleZero::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/)
{
return 0.0;
}
diff --git a/src/atom.cpp b/src/atom.cpp
index cf4d20a71e..eb2f357890 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -99,7 +99,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// SPIN package
sp = fm = NULL;
-
+
// USER-DPD
uCond = uMech = uChem = uCG = uCGnew = NULL;
@@ -1516,7 +1516,7 @@ void Atom::set_mass(const char *file, int line, int itype, double value)
called from reading of input script
------------------------------------------------------------------------- */
-void Atom::set_mass(const char *file, int line, int narg, char **arg)
+void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
{
if (mass == NULL) error->all(file,line,"Cannot set mass for this atom style");
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index b04bfba34c..a7ca6fcb19 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -66,7 +66,7 @@ void AtomVec::store_args(int narg, char **arg)
no additional args by default
------------------------------------------------------------------------- */
-void AtomVec::process_args(int narg, char **arg)
+void AtomVec::process_args(int narg, char ** /*arg*/)
{
if (narg) error->all(FLERR,"Invalid atom_style command");
}
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index 4d3b5643ae..5a277627ee 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -82,6 +82,9 @@ AtomVecBody::~AtomVecBody()
void AtomVecBody::process_args(int narg, char **arg)
{
+ // suppress unused parameter warning dependent on style_body.h
+ (void)(arg);
+
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
if (0) bptr = NULL;
diff --git a/src/body.cpp b/src/body.cpp
index 42f4ccbdd3..78e2f5d71b 100644
--- a/src/body.cpp
+++ b/src/body.cpp
@@ -21,7 +21,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Body::Body(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Body::Body(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
int n = strlen(arg[0]) + 1;
style = new char[n];
diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp
index 9fd9d4a580..9fcf300b21 100644
--- a/src/bond_zero.cpp
+++ b/src/bond_zero.cpp
@@ -149,8 +149,8 @@ void BondZero::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondZero::single(int type, double rsq, int i, int j,
- double &fforce)
+double BondZero::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/,
+ double & /*fforce*/)
{
return 0.0;
}
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 3aa6d7748c..49c9db172f 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -88,7 +88,7 @@ CommBrick::~CommBrick()
// The call to Comm::copy_arrays() then converts the shallow copy
// into a deep copy of the class with the new layout.
-CommBrick::CommBrick(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
+CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm)
{
if (oldcomm->layout == Comm::LAYOUT_TILED)
error->all(FLERR,"Cannot change to comm_style brick from tiled layout");
@@ -457,7 +457,7 @@ int CommBrick::updown(int dim, int dir, int loc,
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-void CommBrick::forward_comm(int dummy)
+void CommBrick::forward_comm(int /*dummy*/)
{
int n;
MPI_Request request;
diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp
index 584be94bf3..d7d2e4725d 100644
--- a/src/comm_tiled.cpp
+++ b/src/comm_tiled.cpp
@@ -55,7 +55,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
// The call to Comm::copy_arrays() then converts the shallow copy
// into a deep copy of the class with the new layout.
-CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
+CommTiled::CommTiled(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm)
{
style = 1;
layout = oldcomm->layout;
@@ -438,7 +438,7 @@ void CommTiled::setup()
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-void CommTiled::forward_comm(int dummy)
+void CommTiled::forward_comm(int /*dummy*/)
{
int i,irecv,n,nsend,nrecv;
AtomVec *avec = atom->avec;
@@ -1164,7 +1164,7 @@ void CommTiled::reverse_comm_fix(Fix *fix, int size)
NOTE: how to setup one big buf recv with correct offsets ??
------------------------------------------------------------------------- */
-void CommTiled::reverse_comm_fix_variable(Fix *fix)
+void CommTiled::reverse_comm_fix_variable(Fix * /*fix*/)
{
error->all(FLERR,"Reverse comm fix variable not yet supported by CommTiled");
}
@@ -1428,7 +1428,7 @@ void CommTiled::forward_comm_array(int nsize, double **array)
NOTE: this method is currently not used
------------------------------------------------------------------------- */
-int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
+int CommTiled::exchange_variable(int n, double * /*inbuf*/, double *& /*outbuf*/)
{
int nrecv = n;
return nrecv;
@@ -1509,7 +1509,7 @@ void CommTiled::box_drop_brick(int idim, double *lo, double *hi, int &indexme)
no need to split lo/hi box as recurse b/c OK if box extends outside RCB box
------------------------------------------------------------------------- */
-void CommTiled::box_drop_tiled(int idim, double *lo, double *hi, int &indexme)
+void CommTiled::box_drop_tiled(int /*idim*/, double *lo, double *hi, int &indexme)
{
box_drop_tiled_recurse(lo,hi,0,nprocs-1,indexme);
}
@@ -1601,7 +1601,7 @@ void CommTiled::box_other_brick(int idim, int idir,
return other box owned by proc as lo/hi corner pts
------------------------------------------------------------------------- */
-void CommTiled::box_other_tiled(int idim, int idir,
+void CommTiled::box_other_tiled(int /*idim*/, int /*idir*/,
int proc, double *lo, double *hi)
{
double (*split)[2] = rcbinfo[proc].mysplit;
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index 56855fcc29..6c8c8e5d9a 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -98,7 +98,7 @@ void ComputeAggregateAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeAggregateAtom::init_list(int id, NeighList *ptr)
+void ComputeAggregateAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -231,7 +231,7 @@ void ComputeAggregateAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 985e3ef075..56abb9b071 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -337,7 +337,7 @@ int ComputeBondLocal::compute_bonds(int flag)
/* ---------------------------------------------------------------------- */
int ComputeBondLocal::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 48af453635..5096879b32 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -110,7 +110,7 @@ void ComputeCentroAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCentroAtom::init_list(int id, NeighList *ptr)
+void ComputeCentroAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 85934c5e6d..0c34b42671 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -89,7 +89,7 @@ void ComputeClusterAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeClusterAtom::init_list(int id, NeighList *ptr)
+void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -209,7 +209,7 @@ void ComputeClusterAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index a1b97d9404..b8ad3f0f64 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -100,7 +100,7 @@ void ComputeCNAAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCNAAtom::init_list(int id, NeighList *ptr)
+void ComputeCNAAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp
index f3c4513b01..e60a51832a 100644
--- a/src/compute_contact_atom.cpp
+++ b/src/compute_contact_atom.cpp
@@ -80,7 +80,7 @@ void ComputeContactAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeContactAtom::init_list(int id, NeighList *ptr)
+void ComputeContactAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index b86d818d06..33b318ea17 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -153,7 +153,7 @@ void ComputeCoordAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCoordAtom::init_list(int id, NeighList *ptr)
+void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -311,7 +311,7 @@ void ComputeCoordAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,m=0,j;
for (i = 0; i < n; ++i) {
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index b9fb2331ec..bb273f3bdb 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -159,7 +159,7 @@ void ComputeFragmentAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeFragmentAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index dc94db50f6..51f84b020d 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -173,7 +173,7 @@ void ComputeGroupGroup::init()
/* ---------------------------------------------------------------------- */
-void ComputeGroupGroup::init_list(int id, NeighList *ptr)
+void ComputeGroupGroup::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index cb2946beba..6d17ae15bd 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -129,7 +129,7 @@ void ComputeHexOrderAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeHexOrderAtom::init_list(int id, NeighList *ptr)
+void ComputeHexOrderAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index f263fdfaed..8a0a525fdc 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -187,7 +187,7 @@ void ComputeOrientOrderAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeOrientOrderAtom::init_list(int id, NeighList *ptr)
+void ComputeOrientOrderAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -542,4 +542,3 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
return p;
}
-
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 3f1147ed27..e4cbabfd3d 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -139,7 +139,7 @@ void ComputePairLocal::init()
/* ---------------------------------------------------------------------- */
-void ComputePairLocal::init_list(int id, NeighList *ptr)
+void ComputePairLocal::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index ad68459650..ddcf5913ca 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -308,7 +308,7 @@ void ComputePropertyLocal::init()
/* ---------------------------------------------------------------------- */
-void ComputePropertyLocal::init_list(int id, NeighList *ptr)
+void ComputePropertyLocal::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index f2635c0948..0a0e8fb684 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -213,7 +213,7 @@ void ComputeRDF::init()
/* ---------------------------------------------------------------------- */
-void ComputeRDF::init_list(int id, NeighList *ptr)
+void ComputeRDF::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index 35f4512ab2..f2ad40ea43 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -163,7 +163,7 @@ void ComputeTempCOM::compute_vector()
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempCOM::remove_bias(int i, double *v)
+void ComputeTempCOM::remove_bias(int /*i*/, double *v)
{
v[0] -= vbias[0];
v[1] -= vbias[1];
@@ -204,7 +204,7 @@ void ComputeTempCOM::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempCOM::restore_bias(int i, double *v)
+void ComputeTempCOM::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index 8729204e70..39780b5cf6 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -277,7 +277,7 @@ void ComputeTempDeform::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempDeform::restore_bias(int i, double *v)
+void ComputeTempDeform::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
@@ -289,7 +289,7 @@ void ComputeTempDeform::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempDeform::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempDeform::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[0] += b[0];
v[1] += b[1];
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index 4b87a2249e..4425aebdda 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -90,7 +90,7 @@ void ComputeTempPartial::dof_compute()
/* ---------------------------------------------------------------------- */
-int ComputeTempPartial::dof_remove(int i)
+int ComputeTempPartial::dof_remove(int /*i*/)
{
int nper = xflag+yflag+zflag;
return (domain->dimension - nper);
@@ -169,7 +169,7 @@ void ComputeTempPartial::compute_vector()
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempPartial::remove_bias(int i, double *v)
+void ComputeTempPartial::remove_bias(int /*i*/, double *v)
{
if (!xflag) {
vbias[0] = v[0];
@@ -189,7 +189,7 @@ void ComputeTempPartial::remove_bias(int i, double *v)
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempPartial::remove_bias_thr(int i, double *v, double *b)
+void ComputeTempPartial::remove_bias_thr(int /*i*/, double *v, double *b)
{
if (!xflag) {
b[0] = v[0];
@@ -275,7 +275,7 @@ void ComputeTempPartial::reapply_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempPartial::restore_bias(int i, double *v)
+void ComputeTempPartial::restore_bias(int /*i*/, double *v)
{
if (!xflag) v[0] += vbias[0];
if (!yflag) v[1] += vbias[1];
@@ -287,7 +287,7 @@ void ComputeTempPartial::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempPartial::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempPartial::restore_bias_thr(int /*i*/, double *v, double *b)
{
if (!xflag) v[0] += b[0];
if (!yflag) v[1] += b[1];
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index 42d258d8b2..ba572645f3 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -279,7 +279,7 @@ void ComputeTempRamp::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRamp::restore_bias(int i, double *v)
+void ComputeTempRamp::restore_bias(int /*i*/, double *v)
{
v[v_dim] += vbias[v_dim];
}
@@ -289,7 +289,7 @@ void ComputeTempRamp::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempRamp::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempRamp::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[v_dim] += b[v_dim];
}
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index bde70a20f0..4aa4dac0a1 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -253,7 +253,7 @@ void ComputeTempRegion::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRegion::restore_bias(int i, double *v)
+void ComputeTempRegion::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
@@ -265,7 +265,7 @@ void ComputeTempRegion::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempRegion::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempRegion::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[0] += b[0];
v[1] += b[1];
diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp
index bdd2eaadd3..46facdb6db 100644
--- a/src/dihedral_zero.cpp
+++ b/src/dihedral_zero.cpp
@@ -99,13 +99,13 @@ void DihedralZero::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
-void DihedralZero::write_restart(FILE *fp) {}
+void DihedralZero::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
-void DihedralZero::read_restart(FILE *fp)
+void DihedralZero::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
@@ -119,4 +119,3 @@ void DihedralZero::write_data(FILE *fp) {
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d\n",i);
}
-
diff --git a/src/domain.cpp b/src/domain.cpp
index 4c1d12018b..1eb848fe06 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1618,7 +1618,7 @@ void Domain::image_flip(int m, int n, int p)
called from create_atoms() in library.cpp
------------------------------------------------------------------------- */
-int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed)
+int Domain::ownatom(int /*id*/, double *x, imageint *image, int shrinkexceed)
{
double lamda[3];
double *coord,*blo,*bhi,*slo,*shi;
diff --git a/src/dump.cpp b/src/dump.cpp
index 7c171015bb..7cd80dcf71 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -45,7 +45,7 @@ enum{ASCEND,DESCEND};
/* ---------------------------------------------------------------------- */
-Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 60a1f545c9..a488f65161 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -1193,7 +1193,7 @@ void DumpImage::create_image()
/* ---------------------------------------------------------------------- */
int DumpImage::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 0d5172b5c1..8dc0554690 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -326,7 +326,7 @@ int DumpLocal::count()
/* ---------------------------------------------------------------------- */
-void DumpLocal::pack(tagint *dummy)
+void DumpLocal::pack(tagint * /*dummy*/)
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
}
diff --git a/src/fix.cpp b/src/fix.cpp
index a54e295798..051ac12bbe 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -31,7 +31,7 @@ int Fix::instance_total = 0;
/* ---------------------------------------------------------------------- */
-Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
+Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
Pointers(lmp),
id(NULL), style(NULL), extlist(NULL), vector_atom(NULL), array_atom(NULL),
vector_local(NULL), array_local(NULL), eatom(NULL), vatom(NULL)
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 42cd1bd199..950bc24253 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -476,7 +476,7 @@ void FixAdapt::init()
/* ---------------------------------------------------------------------- */
-void FixAdapt::setup_pre_force(int vflag)
+void FixAdapt::setup_pre_force(int /*vflag*/)
{
change_settings();
}
@@ -491,7 +491,7 @@ void FixAdapt::setup_pre_force_respa(int vflag, int ilevel)
/* ---------------------------------------------------------------------- */
-void FixAdapt::pre_force(int vflag)
+void FixAdapt::pre_force(int /*vflag*/)
{
if (nevery == 0) return;
if (update->ntimestep % nevery) return;
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index c2eedccd61..d66457a1f1 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -361,7 +361,7 @@ void FixAddForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAddForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index a8c3be07af..c8cbad75c9 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -283,7 +283,7 @@ void FixAveAtom::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveAtom::setup(int vflag)
+void FixAveAtom::setup(int /*vflag*/)
{
end_of_step();
}
@@ -432,7 +432,7 @@ void FixAveAtom::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixAveAtom::copy_arrays(int i, int j, int delflag)
+void FixAveAtom::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++)
array[j][m] = array[i][m];
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 5f727fd3f7..1aead70644 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -557,7 +557,7 @@ void FixAveChunk::init()
that nchunk may not track it
------------------------------------------------------------------------- */
-void FixAveChunk::setup(int vflag)
+void FixAveChunk::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 418464a248..198caf1514 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -404,7 +404,7 @@ void FixAveCorrelate::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveCorrelate::setup(int vflag)
+void FixAveCorrelate::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 7aa5993899..ce32167b74 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -559,7 +559,7 @@ void FixAveHisto::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveHisto::setup(int vflag)
+void FixAveHisto::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index c3ace29684..53354ee066 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -529,7 +529,7 @@ void FixAveTime::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveTime::setup(int vflag)
+void FixAveTime::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 4432a5dd36..1c87ba5785 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -194,7 +194,7 @@ void FixAveForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAveForce::post_force(int vflag)
+void FixAveForce::post_force(int /*vflag*/)
{
// update region if necessary
@@ -259,7 +259,7 @@ void FixAveForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAveForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAveForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// ave + extra force on selected RESPA level
// just ave on all other levels
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index e748e0ae31..8995a57afe 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -160,7 +160,7 @@ void FixBalance::init()
/* ---------------------------------------------------------------------- */
-void FixBalance::setup(int vflag)
+void FixBalance::setup(int /*vflag*/)
{
// compute final imbalance factor if setup_pre_exchange() invoked balancer
// this is called at end of run setup, before output
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index 6a69dddbf5..e4cf12d1ff 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -90,7 +90,7 @@ void FixDrag::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixDrag::post_force(int vflag)
+void FixDrag::post_force(int /*vflag*/)
{
// apply drag force to atoms in group of magnitude f_mag
// apply in direction (r-r0) if atom is further than delta away
@@ -132,7 +132,7 @@ void FixDrag::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixDrag::post_force_respa(int vflag, int ilevel, int iloop)
+void FixDrag::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index f2a50fd6d1..7566094b48 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -129,7 +129,7 @@ void FixDtReset::init()
/* ---------------------------------------------------------------------- */
-void FixDtReset::setup(int vflag)
+void FixDtReset::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index 791a52c50c..ef7eb3a0ef 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -112,7 +112,7 @@ void FixEnforce2D::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEnforce2D::post_force(int vflag)
+void FixEnforce2D::post_force(int /*vflag*/)
{
double **v = atom->v;
double **f = atom->f;
@@ -164,7 +164,7 @@ void FixEnforce2D::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEnforce2D::post_force_respa(int vflag, int ilevel, int iloop)
+void FixEnforce2D::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index 4fcc842f89..5ac9206e7f 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -129,7 +129,7 @@ void FixExternal::min_setup(int vflag)
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixExternal::pre_reverse(int eflag, int vflag)
+void FixExternal::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
@@ -305,7 +305,7 @@ void FixExternal::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixExternal::copy_arrays(int i, int j, int delflag)
+void FixExternal::copy_arrays(int i, int j, int /*delflag*/)
{
fexternal[j][0] = fexternal[i][0];
fexternal[j][1] = fexternal[i][1];
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 9ace9d45ff..c3e73d86c9 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -247,7 +247,7 @@ void FixGravity::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGravity::post_force(int vflag)
+void FixGravity::post_force(int /*vflag*/)
{
// update gravity due to variables
@@ -300,7 +300,7 @@ void FixGravity::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
+void FixGravity::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 10736964e7..0980ff5456 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -176,7 +176,7 @@ void FixGroup::init()
assign atoms to group
------------------------------------------------------------------------- */
-void FixGroup::setup(int vflag)
+void FixGroup::setup(int /*vflag*/)
{
set_group();
}
@@ -192,7 +192,7 @@ void FixGroup::post_integrate()
/* ---------------------------------------------------------------------- */
-void FixGroup::post_integrate_respa(int ilevel, int iloop)
+void FixGroup::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -259,7 +259,7 @@ void FixGroup::set_group()
/* ---------------------------------------------------------------------- */
-void *FixGroup::extract(const char *str, int &unused)
+void *FixGroup::extract(const char *str, int &/*unused*/)
{
if (strcmp(str,"property") == 0 && propflag) return (void *) idprop;
if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar;
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index ade8cee532..b8e07dfd53 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -182,7 +182,7 @@ void FixIndent::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixIndent::post_force(int vflag)
+void FixIndent::post_force(int /*vflag*/)
{
// indenter values, 0 = energy, 1-3 = force components
// wrap variable evaluations with clear/add
@@ -357,7 +357,7 @@ void FixIndent::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixIndent::post_force_respa(int vflag, int ilevel, int iloop)
+void FixIndent::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index e4c36cc739..d829982274 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -298,7 +298,7 @@ void FixLangevin::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLangevin::post_force(int vflag)
+void FixLangevin::post_force(int /*vflag*/)
{
double *rmass = atom->rmass;
@@ -441,7 +441,7 @@ void FixLangevin::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLangevin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -896,7 +896,7 @@ void FixLangevin::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixLangevin::copy_arrays(int i, int j, int delflag)
+void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++)
franprev[j][m] = franprev[i][m];
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index e90152c4e1..aea1a2a25b 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -80,7 +80,7 @@ void FixLineForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLineForce::post_force(int vflag)
+void FixLineForce::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -98,7 +98,7 @@ void FixLineForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLineForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLineForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index 06a3ac900d..fa39643a1b 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -184,7 +184,7 @@ void FixMinimize::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixMinimize::copy_arrays(int i, int j, int delflag)
+void FixMinimize::copy_arrays(int i, int j, int /*delflag*/)
{
int m,iper,nper,ni,nj;
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 9eadfa5ab4..2f9fb0ebaa 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -453,7 +453,7 @@ void FixMove::init()
set x,v of particles
------------------------------------------------------------------------- */
-void FixMove::initial_integrate(int vflag)
+void FixMove::initial_integrate(int /*vflag*/)
{
int flag;
double ddotr,dx,dy,dz;
@@ -945,7 +945,7 @@ void FixMove::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixMove::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
// outermost level - update v and x
// all other levels - nothing
@@ -955,7 +955,7 @@ void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixMove::final_integrate_respa(int ilevel, int iloop)
+void FixMove::final_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) final_integrate();
}
@@ -1019,7 +1019,7 @@ void FixMove::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixMove::copy_arrays(int i, int j, int delflag)
+void FixMove::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -1238,7 +1238,7 @@ int FixMove::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixMove::size_restart(int nlocal)
+int FixMove::size_restart(int /*nlocal*/)
{
return nrestart;
}
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 3329b604ef..44c2003bf1 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -686,7 +686,7 @@ void FixNeighHistory::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixNeighHistory::copy_arrays(int i, int j, int delflag)
+void FixNeighHistory::copy_arrays(int i, int j, int /*delflag*/)
{
// just copy pointers for partner and valuepartner
// b/c can't overwrite chunk allocation inside ipage_atom,dpage_atom
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 73c70420c5..a1a562f2bb 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -742,7 +742,7 @@ void FixNH::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixNH::setup(int vflag)
+void FixNH::setup(int /*vflag*/)
{
// tdof needed by compute_temp_target()
@@ -827,7 +827,7 @@ void FixNH::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixNH::initial_integrate(int vflag)
+void FixNH::initial_integrate(int /*vflag*/)
{
// update eta_press_dot
@@ -922,7 +922,7 @@ void FixNH::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNH::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
// set timesteps by level
@@ -991,7 +991,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNH::final_integrate_respa(int ilevel, int iloop)
+void FixNH::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index 58e33b9744..959483230e 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -62,7 +62,7 @@ void FixNVE::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVE::initial_integrate(int vflag)
+void FixNVE::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -143,7 +143,7 @@ void FixNVE::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -157,7 +157,7 @@ void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVE::final_integrate_respa(int ilevel, int iloop)
+void FixNVE::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index f659597af7..b4fb43e56f 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -83,7 +83,7 @@ void FixNVELimit::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVELimit::initial_integrate(int vflag)
+void FixNVELimit::initial_integrate(int /*vflag*/)
{
double dtfm,vsq,scale;
@@ -202,7 +202,7 @@ void FixNVELimit::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -213,7 +213,7 @@ void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVELimit::final_integrate_respa(int ilevel, int iloop)
+void FixNVELimit::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index 3403f4f5ec..d4fca9e676 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -54,7 +54,7 @@ void FixNVENoforce::init()
/* ---------------------------------------------------------------------- */
-void FixNVENoforce::initial_integrate(int vflag)
+void FixNVENoforce::initial_integrate(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index fe37324cfb..0bee8b8685 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -97,7 +97,7 @@ void FixNVESphere::init()
/* ---------------------------------------------------------------------- */
-void FixNVESphere::initial_integrate(int vflag)
+void FixNVESphere::initial_integrate(int /*vflag*/)
{
double dtfm,dtirotate,msq,scale,s2,inv_len_mu;
double g[3];
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index f90be6a233..45dc782fcf 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -80,7 +80,7 @@ void FixPlaneForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPlaneForce::post_force(int vflag)
+void FixPlaneForce::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -98,7 +98,7 @@ void FixPlaneForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPlaneForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPlaneForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index 792154e93f..95db004436 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -334,7 +334,7 @@ void FixPressBerendsen::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixPressBerendsen::setup(int vflag)
+void FixPressBerendsen::setup(int /*vflag*/)
{
// trigger virial computation on next timestep
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 5ad4dfa4ba..fc99137c3d 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -292,7 +292,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
return # of lines in section of data file labeled by keyword
------------------------------------------------------------------------- */
-bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
+bigint FixPropertyAtom::read_data_skip_lines(char */*keyword*/)
{
return atom->natoms;
}
@@ -304,7 +304,7 @@ bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
ny = columns = tag + nvalues
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
+void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny)
{
nx = atom->nlocal;
ny = nvalue + 1;
@@ -315,7 +315,7 @@ void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
buf allocated by caller as Nlocal by Nvalues+1
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
+void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
{
int i;
@@ -354,7 +354,7 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
only called by proc 0
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
+void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
{
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
@@ -368,8 +368,8 @@ void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
only called by proc 0
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section(int mth, FILE *fp,
- int n, double **buf, int index)
+void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp,
+ int n, double **buf, int /*index*/)
{
int m;
@@ -443,7 +443,7 @@ void FixPropertyAtom::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
+void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
@@ -644,7 +644,7 @@ int FixPropertyAtom::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixPropertyAtom::size_restart(int nlocal)
+int FixPropertyAtom::size_restart(int /*nlocal*/)
{
return nvalue+1;
}
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index b384234b99..3c3178f4af 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -96,7 +96,7 @@ void FixReadRestart::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixReadRestart::copy_arrays(int i, int j, int delflag)
+void FixReadRestart::copy_arrays(int i, int j, int /*delflag*/)
{
count[j] = count[i];
for (int m = 0; m < count[i]; m++) extra[j][m] = extra[i][m];
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index 49e370ac80..75b383d67a 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -149,7 +149,7 @@ void FixRecenter::init()
/* ---------------------------------------------------------------------- */
-void FixRecenter::initial_integrate(int vflag)
+void FixRecenter::initial_integrate(int /*vflag*/)
{
// target COM
// bounding box around domain works for both orthogonal and triclinic
@@ -211,7 +211,7 @@ void FixRecenter::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
// outermost level - operate recenter
// all other levels - nothing
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index 3b9aad1286..64461ba7ca 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -93,7 +93,7 @@ void FixRespa::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixRespa::copy_arrays(int i, int j, int delflag)
+void FixRespa::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < nlevels; k++) {
f_level[j][k][0] = f_level[i][k][0];
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 6ad229fea7..bb09116374 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -188,7 +188,7 @@ void FixRestrain::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRestrain::post_force(int vflag)
+void FixRestrain::post_force(int /*vflag*/)
{
energy = 0.0;
@@ -204,7 +204,7 @@ void FixRestrain::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRestrain::post_force_respa(int vflag, int ilevel, int iloop)
+void FixRestrain::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index 89b340b0ae..fc8b7aeb59 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -219,7 +219,7 @@ void FixSetForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSetForce::post_force(int vflag)
+void FixSetForce::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -293,7 +293,7 @@ void FixSetForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSetForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSetForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// set force to desired value on requested level, 0.0 on other levels
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index ecb84eeb0f..328a0eeafd 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -159,7 +159,7 @@ void FixSpring::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpring::post_force(int vflag)
+void FixSpring::post_force(int /*vflag*/)
{
if (styleflag == TETHER) spring_tether();
else spring_couple();
@@ -335,7 +335,7 @@ void FixSpring::spring_couple()
/* ---------------------------------------------------------------------- */
-void FixSpring::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpring::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp
index 53e9285a9c..5b5d95b111 100644
--- a/src/fix_spring_chunk.cpp
+++ b/src/fix_spring_chunk.cpp
@@ -144,7 +144,7 @@ void FixSpringChunk::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringChunk::post_force(int vflag)
+void FixSpringChunk::post_force(int /*vflag*/)
{
int i,m;
double dx,dy,dz,r;
@@ -231,7 +231,7 @@ void FixSpringChunk::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringChunk::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringChunk::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index c2e226a343..28c8969006 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -95,7 +95,7 @@ void FixSpringRG::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringRG::post_force(int vflag)
+void FixSpringRG::post_force(int /*vflag*/)
{
// compute current Rg and center-of-mass
@@ -142,7 +142,7 @@ void FixSpringRG::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringRG::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index 1a5c89c6a1..670883af41 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -148,7 +148,7 @@ void FixSpringSelf::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringSelf::post_force(int vflag)
+void FixSpringSelf::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -181,7 +181,7 @@ void FixSpringSelf::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringSelf::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringSelf::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -227,7 +227,7 @@ void FixSpringSelf::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixSpringSelf::copy_arrays(int i, int j, int delflag)
+void FixSpringSelf::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -303,7 +303,7 @@ int FixSpringSelf::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixSpringSelf::size_restart(int nlocal)
+int FixSpringSelf::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 350e120972..9db65d0987 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -229,7 +229,7 @@ void FixStore::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixStore::copy_arrays(int i, int j, int delflag)
+void FixStore::copy_arrays(int i, int j, int /*delflag*/)
{
if (disable) return;
@@ -324,7 +324,7 @@ int FixStore::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixStore::size_restart(int nlocal)
+int FixStore::size_restart(int /*nlocal*/)
{
if (disable) return 1;
return nvalues+1;
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index 5e2150f68d..a841714098 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -95,7 +95,7 @@ void FixStoreForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixStoreForce::post_force(int vflag)
+void FixStoreForce::post_force(int /*vflag*/)
{
if (atom->nmax > nmax) {
nmax = atom->nmax;
@@ -118,7 +118,7 @@ void FixStoreForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixStoreForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixStoreForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 3195e983e3..da899a173c 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -446,7 +446,7 @@ void FixStoreState::init()
/* ---------------------------------------------------------------------- */
-void FixStoreState::setup(int vflag)
+void FixStoreState::setup(int /*vflag*/)
{
// if first invocation, store current values for compute, fix, variable
@@ -580,7 +580,7 @@ void FixStoreState::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixStoreState::copy_arrays(int i, int j, int delflag)
+void FixStoreState::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++) values[j][m] = values[i][m];
}
@@ -646,7 +646,7 @@ int FixStoreState::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixStoreState::size_restart(int nlocal)
+int FixStoreState::size_restart(int /*nlocal*/)
{
return nvalues+1;
}
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 39d4173a63..ea448bd178 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -170,7 +170,7 @@ void FixTMD::init()
/* ---------------------------------------------------------------------- */
-void FixTMD::initial_integrate(int vflag)
+void FixTMD::initial_integrate(int /*vflag*/)
{
double a,b,c,d,e;
double dx,dy,dz,dxkt,dykt,dzkt;
@@ -335,7 +335,7 @@ void FixTMD::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixTMD::copy_arrays(int i, int j, int delflag)
+void FixTMD::copy_arrays(int i, int j, int /*delflag*/)
{
xf[j][0] = xf[i][0];
xf[j][1] = xf[i][1];
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 9b7f016970..6387af7676 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -239,7 +239,7 @@ void FixVector::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixVector::setup(int vflag)
+void FixVector::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index 1d2609c8b6..e845142322 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -109,7 +109,7 @@ void FixViscous::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixViscous::post_force(int vflag)
+void FixViscous::post_force(int /*vflag*/)
{
// apply drag force to atoms in group
// direction is opposed to velocity vector
@@ -134,7 +134,7 @@ void FixViscous::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixViscous::post_force_respa(int vflag, int ilevel, int iloop)
+void FixViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index 096bbe618a..e84d01191d 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -343,7 +343,7 @@ void FixWall::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWall::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWall::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index ea1b62bfa5..ff147d7446 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -287,7 +287,7 @@ void FixWallRegion::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/group.cpp b/src/group.cpp
index dd5e53bb3c..3bc3f3d7bf 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -629,7 +629,7 @@ int Group::find_unused()
do not include molID = 0
------------------------------------------------------------------------- */
-void Group::add_molecules(int igroup, int bit)
+void Group::add_molecules(int /*igroup*/, int bit)
{
// hash = unique molecule IDs of atoms already in group
diff --git a/src/image.cpp b/src/image.cpp
index 301a2af88f..7879a7035e 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -990,7 +990,7 @@ void Image::compute_SSAO()
/* ---------------------------------------------------------------------- */
-void Image::write_JPG(FILE *fp)
+void Image::write_JPG(FILE */*fp*/)
{
#ifdef LAMMPS_JPEG
struct jpeg_compress_struct cinfo;
@@ -1022,7 +1022,7 @@ void Image::write_JPG(FILE *fp)
/* ---------------------------------------------------------------------- */
-void Image::write_PNG(FILE *fp)
+void Image::write_PNG(FILE */*fp*/)
{
#ifdef LAMMPS_PNG
png_structp png_ptr;
diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp
index acb3da8d13..e089b1df0c 100644
--- a/src/imbalance_var.cpp
+++ b/src/imbalance_var.cpp
@@ -52,7 +52,7 @@ int ImbalanceVar::options(int narg, char **arg)
/* -------------------------------------------------------------------- */
-void ImbalanceVar::init(int flag)
+void ImbalanceVar::init(int /*flag*/)
{
id = input->variable->find(name);
if (id < 0) {
diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp
index 25ab3e7bba..86c724e17d 100644
--- a/src/improper_zero.cpp
+++ b/src/improper_zero.cpp
@@ -99,13 +99,13 @@ void ImproperZero::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
-void ImproperZero::write_restart(FILE *fp) {}
+void ImproperZero::write_restart(FILE */*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
-void ImproperZero::read_restart(FILE *fp)
+void ImproperZero::read_restart(FILE */*fp*/)
{
allocate();
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 97d28d6d7c..d6b27e042d 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Integrate::Integrate(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Integrate::Integrate(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)
{
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
diff --git a/src/kspace.cpp b/src/kspace.cpp
index fc8b12288b..ad5c9e42f2 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+KSpace::KSpace(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)
{
order_allocated = 0;
energy = 0.0;
diff --git a/src/library.cpp b/src/library.cpp
index 13e0756866..18f7005116 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -336,7 +336,7 @@ void lammps_free(void *ptr)
customize by adding names
------------------------------------------------------------------------- */
-int lammps_extract_setting(void *ptr, char *name)
+int lammps_extract_setting(void */*ptr*/, char *name)
{
if (strcmp(name,"bigint") == 0) return sizeof(bigint);
if (strcmp(name,"tagint") == 0) return sizeof(tagint);
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index b70986ce91..0bba2ad401 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -590,7 +590,7 @@ void inertia_triangle(double *v0, double *v1, double *v2,
return symmetric inertia tensor as 6-vector in Voigt notation
------------------------------------------------------------------------- */
-void inertia_triangle(double *idiag, double *quat, double mass,
+void inertia_triangle(double *idiag, double *quat, double /*mass*/,
double *inertia)
{
double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3];
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 912a636227..759f84e29f 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -2193,7 +2193,7 @@ void Neighbor::set(int narg, char **arg)
ditto for lastcall and last_setup_bins
------------------------------------------------------------------------- */
-void Neighbor::reset_timestep(bigint ntimestep)
+void Neighbor::reset_timestep(bigint /*ntimestep*/)
{
for (int i = 0; i < nbin; i++)
neigh_bin[i]->last_bin = -1;
diff --git a/src/pair.cpp b/src/pair.cpp
index 5c308cc7ce..18d561bdb5 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -301,7 +301,7 @@ void Pair::init_style()
specific pair style can override this function
------------------------------------------------------------------------- */
-void Pair::init_list(int which, NeighList *ptr)
+void Pair::init_list(int /*which*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index cc8e14bf2c..d9c0fb902c 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -327,9 +327,9 @@ void PairBeck::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBeck::single(int i, int j, int itype, int jtype,
+double PairBeck::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double phi_beck,r,rinv;
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index ce7a255fd4..1a1db9dd90 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -407,8 +407,8 @@ void PairBorn::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBorn::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBorn::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forceborn,phiborn;
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index 450ce291cb..8b6d79234b 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -380,8 +380,8 @@ void PairBuck::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBuck::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBuck::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index edcf26bffe..8741abdb89 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -284,8 +284,8 @@ void PairCoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulCut::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,rinv,forcecoul,phicoul;
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index ee08ab3294..432a015598 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -163,8 +163,8 @@ void PairCoulDebye::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulDebye::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairCoulDebye::single(int i, int j, int /*itype*/, int /*jtype*/,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,rinv,forcecoul,phicoul,screening;
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index f20eae43bd..8cd5f7fece 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -221,7 +221,7 @@ void PairCoulDSF::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairCoulDSF::init_one(int i, int j)
+double PairCoulDSF::init_one(int /*i*/, int /*j*/)
{
return cut_coul;
}
@@ -291,8 +291,8 @@ void PairCoulDSF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairCoulDSF::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,erfcc,erfcd,prefactor,t;
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index cd582f0693..762491166e 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -219,7 +219,7 @@ void PairCoulWolf::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairCoulWolf::init_one(int i, int j)
+double PairCoulWolf::init_one(int /*i*/, int /*j*/)
{
return cut_coul;
}
@@ -290,8 +290,8 @@ void PairCoulWolf::read_restart_settings(FILE *fp)
only the pair part is calculated here
------------------------------------------------------------------------- */
-double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairCoulWolf::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r,prefactor;
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index c209de87ed..5c5fc4254b 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -390,8 +390,8 @@ void PairDPD::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index fe53bcc9e1..426389753b 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -347,8 +347,8 @@ void PairGauss::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGauss::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double philj =
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index dc74dd040d..03747e1de3 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -844,7 +844,7 @@ void PairHybrid::modify_params(int narg, char **arg)
store a local per pair style override for special_lj and special_coul
------------------------------------------------------------------------- */
-void PairHybrid::modify_special(int m, int narg, char **arg)
+void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
{
double special[4];
int i;
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index 28677a393e..457eba0e79 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -678,8 +678,8 @@ void PairLJ96Cut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJ96Cut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJ96Cut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r3inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index 4b140e5f05..770caa6359 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -175,7 +175,7 @@ void PairLJCubic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairLJCubic::settings(int narg, char **arg)
+void PairLJCubic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
@@ -321,9 +321,9 @@ void PairLJCubic::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCubic::single(int i, int j, int itype, int jtype,
+double PairLJCubic::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index bb2db6aa2f..13a546f5a5 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -672,8 +672,8 @@ void PairLJCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index ba72d7d45f..9aa58b3b88 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -396,8 +396,8 @@ void PairLJExpand::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJExpand::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index 6b2219d2c5..495e96c368 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -414,9 +414,9 @@ void PairLJGromacs::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJGromacs::single(int i, int j, int itype, int jtype,
+double PairLJGromacs::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 23256d486e..a12046bb3b 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -425,8 +425,8 @@ void PairLJSmooth::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJSmooth::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJSmooth::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t,tsq,fskin;
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index 592a7f6f41..17c789bcee 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -326,9 +326,9 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJSmoothLinear::single(int i, int j, int itype, int jtype,
+double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,rinv;
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 1f9267ca30..c1e1c1ff50 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -682,8 +682,8 @@ void PairMIECut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMIECut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_mie,
+double PairMIECut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_mie,
double &fforce)
{
double r2inv,rgamR,rgamA,forcemie,phimie;
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index 32ddd723b2..c1031343e1 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -334,8 +334,8 @@ void PairMorse::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorse::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorse::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index f428893fd1..d1c51ac600 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -307,8 +307,8 @@ void PairSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,arg,philj;
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 9e9e41a54c..5c43761cab 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -993,8 +993,8 @@ void PairTable::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairTable::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairTable::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
int itable;
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index 965fe0204e..a9f076f504 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -353,8 +353,8 @@ void PairUFM::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairUFM::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairUFM::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double expuf,phiuf;
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 040664abec..af520fd3da 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -319,8 +319,8 @@ void PairYukawa::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairYukawa::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index 98048f61d0..f23a1e5d56 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -267,8 +267,8 @@ double PairZBL::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
- double dummy1, double dummy2,
+double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*dummy1*/, double /*dummy2*/,
double &fforce)
{
double phi,r,t,eswitch,fswitch;
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 13e27b6fbf..644f879c73 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -1108,7 +1108,7 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
merge of each component of an RCB bounding box
------------------------------------------------------------------------- */
-void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
+void box_merge(void *in, void *inout, int */*len*/, MPI_Datatype */*dptr*/)
{
RCB::BBox *box1 = (RCB::BBox *) in;
@@ -1138,7 +1138,7 @@ void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
all procs must get same proclo,prochi
------------------------------------------------------------------------- */
-void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
+void median_merge(void *in, void *inout, int */*len*/, MPI_Datatype */*dptr*/)
{
RCB::Median *med1 = (RCB::Median *) in;
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index 5cb3476510..37d30bd740 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -117,9 +117,9 @@ void ReaderXYZ::skip()
only called by proc 0
------------------------------------------------------------------------- */
-bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
+bigint ReaderXYZ::read_header(double /*box*/[3][3], int &triclinic,
int fieldinfo, int nfield,
- int *fieldtype, char **fieldlabel,
+ int *fieldtype, char **/*fieldlabel*/,
int scaleflag, int wrapflag, int &fieldflag,
int &xflag, int &yflag, int &zflag)
{
diff --git a/src/region.cpp b/src/region.cpp
index 88a414b134..c52c0181aa 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Region::Region(LAMMPS *lmp, int narg, char **arg) :
+Region::Region(LAMMPS *lmp, int /*narg*/, char **arg) :
Pointers(lmp),
id(NULL), style(NULL), contact(NULL), list(NULL),
xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp
index fd898bd3ab..b2cf7a9bbc 100644
--- a/src/reset_ids.cpp
+++ b/src/reset_ids.cpp
@@ -28,7 +28,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
-void ResetIDs::command(int narg, char **arg)
+void ResetIDs::command(int narg, char **/*arg*/)
{
if (domain->box_exist == 0)
error->all(FLERR,"Reset_ids command before simulation box is defined");
diff --git a/src/respa.cpp b/src/respa.cpp
index 73e280b03d..26bae5a1cb 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -774,7 +774,7 @@ void Respa::recurse(int ilevel)
clear other arrays as needed
------------------------------------------------------------------------- */
-void Respa::force_clear(int newtonflag)
+void Respa::force_clear(int /*newtonflag*/)
{
if (external_force_clear) return;
diff --git a/src/variable.cpp b/src/variable.cpp
index f005221400..a596dedb2a 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -733,7 +733,7 @@ int Variable::find(char *name)
called when atom is created
------------------------------------------------------------------------- */
-void Variable::set_arrays(int i)
+void Variable::set_arrays(int /*i*/)
{
for (int i = 0; i < nvar; i++)
if (reader[i] && style[i] == ATOMFILE)
diff --git a/src/velocity.cpp b/src/velocity.cpp
index f83f778f8b..3a0b95fb4d 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -410,7 +410,7 @@ void Velocity::create(double t_desired, int seed)
/* ---------------------------------------------------------------------- */
-void Velocity::set(int narg, char **arg)
+void Velocity::set(int /*narg*/, char **arg)
{
int xstyle,ystyle,zstyle,varflag;
double vx,vy,vz;
@@ -579,7 +579,7 @@ void Velocity::set(int narg, char **arg)
rescale velocities of a group after computing its temperature
------------------------------------------------------------------------- */
-void Velocity::scale(int narg, char **arg)
+void Velocity::scale(int /*narg*/, char **arg)
{
double t_desired = force->numeric(FLERR,arg[0]);
@@ -628,7 +628,7 @@ void Velocity::scale(int narg, char **arg)
apply a ramped set of velocities
------------------------------------------------------------------------- */
-void Velocity::ramp(int narg, char **arg)
+void Velocity::ramp(int /*narg*/, char **arg)
{
// set scale factors
@@ -705,7 +705,7 @@ void Velocity::ramp(int narg, char **arg)
zero linear or angular momentum of a group
------------------------------------------------------------------------- */
-void Velocity::zero(int narg, char **arg)
+void Velocity::zero(int /*narg*/, char **arg)
{
if (strcmp(arg[0],"linear") == 0) {
if (rfix < 0) zero_momentum();
--
GitLab
From 9eacabd821536f300184d0946d2dfdff9c15c1ac Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 23 Aug 2018 14:43:31 -0600
Subject: [PATCH 158/332] added manpage from debian package
---
doc/lammps.1 | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
create mode 100644 doc/lammps.1
diff --git a/doc/lammps.1 b/doc/lammps.1
new file mode 100644
index 0000000000..d0251bd2a6
--- /dev/null
+++ b/doc/lammps.1
@@ -0,0 +1,41 @@
+.TH LAMMPS "2012-02-23"
+.SH NAME
+.B LAMMPS
+\- Molecular Dynamics Simulator.
+
+.SH SYNOPSIS
+.B lammps
+< in.file
+
+or
+
+mpirun \-np 2
+.B lammps
+< in.file
+
+.SH DESCRIPTION
+.B LAMMPS
+LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
+Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
+materials (biomolecules, polymers) and solid-state materials (metals,
+semiconductors) and coarse-grained or mesoscopic systems. It can be used to
+model atoms or, more generically, as a parallel particle simulator at the
+atomic, meso, or continuum scale.
+
+See http://lammps.sandia.gov/ for documentation.
+
+.SH COPYRIGHT
+© 2003--2012 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL-2'.
--
GitLab
From a10bb4b96f40f3b5574b0fade2cfece8bf4c6fc9 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 23 Aug 2018 15:02:36 -0600
Subject: [PATCH 159/332] cmake: fix link issue with --as-needed
---
cmake/CMakeLists.txt | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 460d177c92..51997593db 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -276,11 +276,14 @@ endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
- if(NOT LAPACK_FOUND)
+ find_package(BLAS)
+ if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
+ else()
+ list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
endif()
--
GitLab
From 3622cb9b2846f675ead2997fffdf5abb7a281475 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 23 Aug 2018 19:16:41 -0600
Subject: [PATCH 160/332] lammps.1: some update
---
doc/lammps.1 | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/lammps.1 b/doc/lammps.1
index d0251bd2a6..0431aeca02 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "2012-02-23"
+.TH LAMMPS "2018-08-22"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
@@ -25,7 +25,7 @@ atomic, meso, or continuum scale.
See http://lammps.sandia.gov/ for documentation.
.SH COPYRIGHT
-© 2003--2012 Sandia Corporation
+© 2003--2018 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
--
GitLab
From 9b4f7090d373de2f6f90bc7a51370ff89db2117f Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 23 Aug 2018 19:19:03 -0600
Subject: [PATCH 161/332] cmake: install manpage, too
---
cmake/CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 460d177c92..96f066a431 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -1058,6 +1058,7 @@ if(BUILD_EXE)
set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+ install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
if(ENABLE_TESTING)
add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
endif()
--
GitLab
From e1ef158b363f6b75a16f0c8ffd0da5c748fb580a Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 24 Aug 2018 06:52:50 -0600
Subject: [PATCH 162/332] cmake: rename manpage when installing
---
cmake/CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 96f066a431..4db879b5b1 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -1058,7 +1058,7 @@ if(BUILD_EXE)
set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
- install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+ install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1)
if(ENABLE_TESTING)
add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
endif()
--
GitLab
From bd1e89ac4c0f82be43484bfc16909104b6cf00bf Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 24 Aug 2018 06:55:59 -0600
Subject: [PATCH 163/332] lammps.1: use -in syntax
---
doc/lammps.1 | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/doc/lammps.1 b/doc/lammps.1
index 0431aeca02..8f0ba78fdd 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -4,14 +4,14 @@
\- Molecular Dynamics Simulator.
.SH SYNOPSIS
-.B lammps
-< in.file
+.B lmp
+-in in.file
or
mpirun \-np 2
-.B lammps
-< in.file
+.B lmp
+-in in.file
.SH DESCRIPTION
.B LAMMPS
--
GitLab
From 44bda245a60bcb273735a0c8cb3d71c12bfbf3e3 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 24 Aug 2018 09:36:39 -0600
Subject: [PATCH 164/332] resolution of cutoff issues
---
doc/src/pair_atm.txt | 13 +++----
examples/atm/in.atm | 2 +-
...9Jul18.atm.g++.1 => log.23Aug18.atm.g++.1} | 36 +++++++++----------
...9Jul18.atm.g++.4 => log.23Aug18.atm.g++.4} | 34 +++++++++---------
src/MANYBODY/pair_atm.cpp | 21 +++--------
src/MANYBODY/pair_atm.h | 3 +-
6 files changed, 47 insertions(+), 62 deletions(-)
rename examples/atm/{log.9Jul18.atm.g++.1 => log.23Aug18.atm.g++.1} (67%)
rename examples/atm/{log.9Jul18.atm.g++.4 => log.23Aug18.atm.g++.4} (69%)
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
index e59efe86ab..63a450c51a 100644
--- a/doc/src/pair_atm.txt
+++ b/doc/src/pair_atm.txt
@@ -10,8 +10,6 @@ pair_style atm command :h3
[Syntax:]
-SJP: add an arg
-
pair_style atm cutoff cutoff_triple :pre
cutoff = cutoff for each pair in 3-body interaction (distance units)
@@ -19,11 +17,10 @@ cutoff_triple = additional cutoff applied to product of 3 pairwise distances (di
[Examples:]
-SJP: is 1.5 a good value?
-pair_style atm 2.5 1.5
+pair_style atm 4.5 2.5
pair_coeff * * * 0.072 :pre
-pair_style hybrid/overlay lj/cut 6.5 atm 2.5 1.5
+pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 1 1 atm 1 0.064
pair_coeff 1 1 atm 2 0.080
@@ -55,9 +52,9 @@ command as in the example above.
The potential for a triplet of atom is calculated only if all 3
distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
-SJP: In addition, the product of the 3 distances r12*r23*r31 <
-cutoff_triple^3 is required, which limits the contribution of the
-potential to ???
+In addition, the product of the 3 distances r12*r23*r31 <
+cutoff_triple^3 is required, which excludes from calculation the
+triplets with small contribution to the interaction.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
diff --git a/examples/atm/in.atm b/examples/atm/in.atm
index 52576c04c9..131528dce3 100644
--- a/examples/atm/in.atm
+++ b/examples/atm/in.atm
@@ -16,7 +16,7 @@ region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
-pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * atm * 0.072
diff --git a/examples/atm/log.9Jul18.atm.g++.1 b/examples/atm/log.23Aug18.atm.g++.1
similarity index 67%
rename from examples/atm/log.9Jul18.atm.g++.1
rename to examples/atm/log.23Aug18.atm.g++.1
index 0613533f33..3373846b31 100644
--- a/examples/atm/log.9Jul18.atm.g++.1
+++ b/examples/atm/log.23Aug18.atm.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (29 Jun 2018)
+LAMMPS (22 Aug 2018)
# Axilrod-Teller-Muto potential example
variable x index 1
@@ -26,9 +26,9 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.00125098 secs
+ Time spent = 0.00126314 secs
-pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * atm * 0.072
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.733482 0 -3.1843694 -3.924644
- 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
- 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
- 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
- 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
- 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
-Loop time of 27.841 on 1 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8899813 0 -3.3408686 -4.2298176
+ 5 1.0337853 -4.8928208 0 -3.3425304 -4.2233154
+ 10 1.0358056 -4.8953304 0 -3.3420104 -4.1897183
+ 15 1.0380938 -4.8990457 0 -3.3422942 -4.1310148
+ 20 1.0389566 -4.9014345 0 -3.3433892 -4.0406616
+ 25 1.0358313 -4.8989663 0 -3.3456079 -3.9093019
+Loop time of 12.2062 on 1 procs for 25 steps with 4000 atoms
-Performance: 155.167 tau/day, 0.898 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 353.920 tau/day, 2.048 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 27.837 | 27.837 | 27.837 | 0.0 | 99.99
+Pair | 12.202 | 12.202 | 12.202 | 0.0 | 99.96
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.01
-Output | 0.00016594 | 0.00016594 | 0.00016594 | 0.0 | 0.00
-Modify | 0.001785 | 0.001785 | 0.001785 | 0.0 | 0.01
-Other | | 0.0006731 | | | 0.00
+Comm | 0.0015621 | 0.0015621 | 0.0015621 | 0.0 | 0.01
+Output | 0.00020814 | 0.00020814 | 0.00020814 | 0.0 | 0.00
+Modify | 0.0019698 | 0.0019698 | 0.0019698 | 0.0 | 0.02
+Other | | 0.0007734 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:29
+Total wall time: 0:00:13
diff --git a/examples/atm/log.9Jul18.atm.g++.4 b/examples/atm/log.23Aug18.atm.g++.4
similarity index 69%
rename from examples/atm/log.9Jul18.atm.g++.4
rename to examples/atm/log.23Aug18.atm.g++.4
index 5627348fab..d5edfe32ba 100644
--- a/examples/atm/log.9Jul18.atm.g++.4
+++ b/examples/atm/log.23Aug18.atm.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (29 Jun 2018)
+LAMMPS (22 Aug 2018)
# Axilrod-Teller-Muto potential example
variable x index 1
@@ -26,9 +26,9 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.000769138 secs
+ Time spent = 0.000785112 secs
-pair_style hybrid/overlay lj/cut 4.5 atm 2.5
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * atm * 0.072
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.733482 0 -3.1843694 -3.924644
- 5 1.0335743 -4.7330528 0 -3.1830789 -3.9119065
- 10 1.0349987 -4.7346788 0 -3.1825689 -3.8769962
- 15 1.0362024 -4.7401425 0 -3.1862275 -3.8225106
- 20 1.0352365 -4.7459627 0 -3.1934962 -3.7403572
- 25 1.0295963 -4.7444397 0 -3.2004313 -3.6132651
-Loop time of 7.22029 on 4 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8921547 0 -3.343042 -4.2340557
+ 5 1.0337949 -4.8947881 0 -3.3444835 -4.2271456
+ 10 1.0358286 -4.8973178 0 -3.3439632 -4.1935779
+ 15 1.0381322 -4.9010593 0 -3.3442503 -4.134913
+ 20 1.0390107 -4.9034854 0 -3.3453589 -4.0446162
+ 25 1.0358988 -4.9010506 0 -3.3475908 -3.9133006
+Loop time of 3.20632 on 4 procs for 25 steps with 4000 atoms
-Performance: 598.314 tau/day, 3.462 timesteps/s
+Performance: 1347.340 tau/day, 7.797 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 7.1346 | 7.1684 | 7.1863 | 0.8 | 99.28
+Pair | 3.1207 | 3.1553 | 3.1859 | 1.5 | 98.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.032945 | 0.0509 | 0.084664 | 9.1 | 0.70
-Output | 0.00010133 | 0.00011051 | 0.00013804 | 0.0 | 0.00
-Modify | 0.00059557 | 0.00060683 | 0.00061274 | 0.0 | 0.01
-Other | | 0.000318 | | | 0.00
+Comm | 0.019466 | 0.05009 | 0.084602 | 12.0 | 1.56
+Output | 7.1049e-05 | 8.2076e-05 | 0.00011325 | 0.0 | 0.00
+Modify | 0.00056338 | 0.00057292 | 0.00058413 | 0.0 | 0.02
+Other | | 0.0003092 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:07
+Total wall time: 0:00:03
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index c23aa6560d..44587dfdff 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -15,9 +15,7 @@
Contributing author: Sergey Lishchuk
------------------------------------------------------------------------- */
-
#include <cmath>
-
#include "pair_atm.h"
#include "atom.h"
#include "citeme.h"
@@ -92,7 +90,6 @@ void PairATM::compute(int eflag, int vflag)
int *type = atom->type;
double cutoff_squared = cut_global*cut_global;
- // SJP: new cutoff
double triple = cut_triple*cut_triple*cut_triple;
double cutoff_triple_sixth = triple*triple;
@@ -142,15 +139,14 @@ void PairATM::compute(int eflag, int vflag)
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
if (rik2 > cutoff_squared) continue;
- // SJP: add this line?
-
- if (rij2*rjk2*rik2 > cutoff_triple_sixth) continue;
+ double r6 = rij2*rjk2*rik2;
+ if (r6 > cutoff_triple_sixth) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
interaction_ddd(nu_local,
- rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+ r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
@@ -200,14 +196,10 @@ void PairATM::allocate()
void PairATM::settings(int narg, char **arg)
{
- // SJP: change to 2 args, require triple <= global
-
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
cut_triple = force->numeric(FLERR,arg[1]);
-
- if (cut_triple > cut_global) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
@@ -324,7 +316,6 @@ void PairATM::read_restart(FILE *fp)
void PairATM::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
- // SJP: 2nd arg
fwrite(&cut_triple,sizeof(double),1,fp);
}
@@ -334,7 +325,6 @@ void PairATM::write_restart_settings(FILE *fp)
void PairATM::read_restart_settings(FILE *fp)
{
- // SJP: 2nd arg
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
@@ -348,13 +338,12 @@ void PairATM::read_restart_settings(FILE *fp)
Axilrod-Teller-Muto (dipole-dipole-dipole) potential
------------------------------------------------------------------------- */
-void PairATM::interaction_ddd(double nu,
+void PairATM::interaction_ddd(double nu, double r6,
double rij2, double rik2, double rjk2,
double *rij, double *rik, double *rjk,
double *fj, double *fk, int eflag, double &eng)
{
- double r6,r5inv,rri,rrj,rrk,rrr;
- r6 = rij2*rik2*rjk2;
+ double r5inv,rri,rrj,rrk,rrr;
r5inv = nu / (r6*r6*sqrt(r6));
rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
index cc868df832..70883a81c7 100644
--- a/src/MANYBODY/pair_atm.h
+++ b/src/MANYBODY/pair_atm.h
@@ -39,12 +39,11 @@ class PairATM : public Pair {
void read_restart_settings(FILE *);
protected:
- // SJP: add 2nd cutoff
double cut_global,cut_triple;
double ***nu;
void allocate();
- void interaction_ddd(double, double, double, double, double *,
+ void interaction_ddd(double, double, double, double, double, double *,
double *, double *, double *, double *, int, double &);
};
--
GitLab
From 1abeec3a43e961694e11178cf39be77f707b0bb0 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 11:13:52 -0600
Subject: [PATCH 165/332] Fix initialization order (#1076)
---
src/USER-MANIFOLD/manifold_gaussian_bump.cpp | 2 +-
src/fix_neigh_history.cpp | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
index a9ee35bbfc..cbb47ef92d 100644
--- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
@@ -25,7 +25,6 @@ public:
cubic_hermite( double x0, double x1, double y0, double y1,
double yp0, double yp1, LAMMPS_NS::Error *err ) :
- x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1),
a( 2*x0 + 2 - 2*x1 ),
b( -3*x0 - 3 + 3*x1 ),
c( 1.0 ),
@@ -34,6 +33,7 @@ public:
u( -3*y0 + 3*y1 - 2*yp0 - yp1 ),
v( yp0 ),
w( y0 ),
+ x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1),
err(err)
{
test();
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 44c2003bf1..9661409a6a 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -35,7 +35,7 @@ enum{DEFAULT,NPARTNER,PERPARTNER}; // also set in fix neigh/history/omp
FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL),
+ pair(NULL), npartner(NULL), partner(NULL), valuepartner(NULL),
ipage_atom(NULL), dpage_atom(NULL), ipage_neigh(NULL), dpage_neigh(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal fix NEIGH_HISTORY command");
--
GitLab
From fd6792c6be42bad83cec2c42016883537c47ef6c Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 12:26:51 -0600
Subject: [PATCH 166/332] Fix unused params in GRANULAR (#1076)
---
src/GRANULAR/fix_freeze.cpp | 4 ++--
src/GRANULAR/fix_wall_gran.cpp | 8 ++++----
src/GRANULAR/fix_wall_gran_region.cpp | 4 ++--
src/GRANULAR/pair_gran_hertz_history.cpp | 4 ++--
src/GRANULAR/pair_gran_hooke.cpp | 4 ++--
src/GRANULAR/pair_gran_hooke_history.cpp | 6 +++---
6 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 0f581be01c..73c1c9fc11 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -83,7 +83,7 @@ void FixFreeze::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixFreeze::post_force(int vflag)
+void FixFreeze::post_force(int /*vflag*/)
{
double **f = atom->f;
double **torque = atom->torque;
@@ -110,7 +110,7 @@ void FixFreeze::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixFreeze::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFreeze::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 368ff99fb7..f0957423f9 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -302,7 +302,7 @@ void FixWallGran::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallGran::post_force(int vflag)
+void FixWallGran::post_force(int /*vflag*/)
{
int i,j;
double dx,dy,dz,del1,del2,delxy,delr,rsq,rwall,meff;
@@ -446,7 +446,7 @@ void FixWallGran::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallGran::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallGran::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -1041,7 +1041,7 @@ void FixWallGran::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixWallGran::copy_arrays(int i, int j, int delflag)
+void FixWallGran::copy_arrays(int i, int j, int /*delflag*/)
{
if (history)
for (int m = 0; m < sheardim; m++)
@@ -1136,7 +1136,7 @@ int FixWallGran::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixWallGran::size_restart(int nlocal)
+int FixWallGran::size_restart(int /*nlocal*/)
{
if (!history) return 0;
return 1 + sheardim;
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index 12fa25714c..4a6be5f3c9 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -130,7 +130,7 @@ void FixWallGranRegion::init()
/* ---------------------------------------------------------------------- */
-void FixWallGranRegion::post_force(int vflag)
+void FixWallGranRegion::post_force(int /*vflag*/)
{
int i,m,nc,iwall;
double dx,dy,dz,rsq,meff;
@@ -347,7 +347,7 @@ void FixWallGranRegion::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixWallGranRegion::copy_arrays(int i, int j, int delflag)
+void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/)
{
int m,n,iwall;
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index 9d4f5c1a9b..d1f3c7bbe1 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -306,9 +306,9 @@ void PairGranHertzHistory::settings(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
+double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum;
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index 4937c2fe8b..5244396ead 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -219,8 +219,8 @@ void PairGranHooke::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum,r,rinv,rsqinv;
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index d70c7391e2..e74d7a0ea5 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -587,9 +587,9 @@ void PairGranHookeHistory::reset_dt()
/* ---------------------------------------------------------------------- */
-double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
+double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum;
@@ -746,7 +746,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
--
GitLab
From 7a2cb108647018b25e18983a53fe4dda3ab508ff Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 12:31:27 -0600
Subject: [PATCH 167/332] Remove unused variable (#1076)
---
src/variable.cpp | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/variable.cpp b/src/variable.cpp
index a596dedb2a..3c54eac1ef 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -3733,7 +3733,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
- else if (narg == 2)
+ else if (narg == 2)
value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
@@ -3744,7 +3744,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
- else if (narg == 2)
+ else if (narg == 2)
value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
@@ -3795,7 +3795,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
- else if (narg == 3)
+ else if (narg == 3)
group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
@@ -3959,7 +3959,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
double *argstack, int &nargstack, int ivar)
{
bigint sx,sxx;
- double value,xvalue,sy,sxy;
+ double value,sy,sxy;
// word not a match to any special function
@@ -4055,7 +4055,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
- if (ifix < 0)
+ if (ifix < 0)
print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
--
GitLab
From 19976bb94fb7e1a9f551a09a8c4cfac7fe6b5f0e Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Thu, 23 Aug 2018 12:38:05 -0600
Subject: [PATCH 168/332] Fixup conditionally used params (#1076)
---
src/image.cpp | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/image.cpp b/src/image.cpp
index 7879a7035e..1e428921a2 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -990,8 +990,9 @@ void Image::compute_SSAO()
/* ---------------------------------------------------------------------- */
-void Image::write_JPG(FILE */*fp*/)
+void Image::write_JPG(FILE *fp)
{
+ (void)(fp); // suppress unused parameter warning
#ifdef LAMMPS_JPEG
struct jpeg_compress_struct cinfo;
struct jpeg_error_mgr jerr;
@@ -1022,8 +1023,9 @@ void Image::write_JPG(FILE */*fp*/)
/* ---------------------------------------------------------------------- */
-void Image::write_PNG(FILE */*fp*/)
+void Image::write_PNG(FILE *fp)
{
+ (void)(fp); // suppress unused parameter warning
#ifdef LAMMPS_PNG
png_structp png_ptr;
png_infop info_ptr;
--
GitLab
From 92a4dc25b1f402a345c41e1f8791a60f6df5acd4 Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Fri, 24 Aug 2018 09:51:38 -0600
Subject: [PATCH 169/332] Fix unused params in packages (#1076)
---
src/ASPHERE/fix_nve_asphere.cpp | 2 +-
src/ASPHERE/fix_nve_asphere_noforce.cpp | 2 +-
src/ASPHERE/fix_nve_line.cpp | 2 +-
src/ASPHERE/fix_nve_tri.cpp | 2 +-
src/BODY/body_nparticle.cpp | 4 +--
src/BODY/body_rounded_polygon.cpp | 4 +--
src/BODY/body_rounded_polyhedron.cpp | 4 +--
src/BODY/fix_nve_body.cpp | 2 +-
src/BODY/fix_wall_body_polygon.cpp | 4 +--
src/BODY/fix_wall_body_polyhedron.cpp | 12 ++++-----
src/BODY/pair_body_rounded_polygon.cpp | 4 +--
src/CLASS2/bond_class2.cpp | 2 +-
src/CLASS2/improper_class2.cpp | 2 +-
src/CLASS2/pair_lj_class2.cpp | 4 +--
src/COLLOID/pair_colloid.cpp | 4 +--
src/COLLOID/pair_lubricate.cpp | 6 ++---
src/COLLOID/pair_lubricateU.cpp | 2 +-
src/COLLOID/pair_yukawa_colloid.cpp | 4 +--
src/KSPACE/pair_coul_long.cpp | 4 +--
src/KSPACE/pair_coul_msm.cpp | 4 +--
src/KSPACE/pppm_disp.cpp | 2 +-
src/KSPACE/remap.cpp | 2 +-
src/LATTE/fix_latte.cpp | 6 ++---
src/MANYBODY/fix_qeq_comb.cpp | 6 ++---
src/MANYBODY/pair_adp.cpp | 6 ++---
src/MANYBODY/pair_airebo.cpp | 8 +++---
src/MANYBODY/pair_comb.cpp | 8 +++---
src/MANYBODY/pair_comb3.cpp | 20 +++++++-------
src/MANYBODY/pair_eam.cpp | 6 ++---
src/MANYBODY/pair_eam_cd.cpp | 2 +-
src/MANYBODY/pair_eim.cpp | 6 ++---
src/MANYBODY/pair_gw.cpp | 2 +-
src/MANYBODY/pair_lcbop.cpp | 6 ++---
src/MANYBODY/pair_nb3b_harmonic.cpp | 4 +--
src/MANYBODY/pair_polymorphic.cpp | 2 +-
src/MANYBODY/pair_rebo.cpp | 2 +-
src/MANYBODY/pair_sw.cpp | 2 +-
src/MANYBODY/pair_tersoff.cpp | 2 +-
src/MANYBODY/pair_vashishta.cpp | 2 +-
src/MC/fix_atom_swap.cpp | 2 +-
src/MC/fix_bond_break.cpp | 4 +--
src/MC/fix_bond_create.cpp | 10 +++----
src/MC/fix_bond_swap.cpp | 2 +-
src/MC/fix_tfmc.cpp | 2 +-
src/MC/pair_dsmc.cpp | 6 ++---
src/MEAM/pair_meam.cpp | 6 ++---
src/MISC/fix_efield.cpp | 2 +-
src/MISC/fix_gld.cpp | 10 +++----
src/MISC/fix_orient_bcc.cpp | 8 +++---
src/MISC/fix_orient_fcc.cpp | 8 +++---
src/MISC/fix_ttm.cpp | 10 +++----
src/MISC/pair_nm_cut.cpp | 4 +--
src/MISC/xdr_compat.cpp | 2 +-
src/MOLECULE/angle_cosine.cpp | 2 +-
src/MOLECULE/angle_cosine_periodic.cpp | 2 +-
src/MOLECULE/bond_fene.cpp | 2 +-
src/MOLECULE/bond_fene_expand.cpp | 2 +-
src/MOLECULE/bond_gromos.cpp | 2 +-
src/MOLECULE/bond_harmonic.cpp | 2 +-
src/MOLECULE/bond_morse.cpp | 2 +-
src/MOLECULE/bond_nonlinear.cpp | 2 +-
src/MOLECULE/bond_quartic.cpp | 2 +-
src/MOLECULE/bond_table.cpp | 2 +-
src/MOLECULE/fix_cmap.cpp | 18 ++++++-------
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 2 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 2 +-
src/MOLECULE/pair_tip4p_cut.cpp | 2 +-
src/PERI/fix_peri_neigh.cpp | 8 +++---
src/PERI/pair_peri_eps.cpp | 4 +--
src/PERI/pair_peri_lps.cpp | 4 +--
src/PERI/pair_peri_pmb.cpp | 4 +--
src/PERI/pair_peri_ves.cpp | 4 +--
src/QEQ/fix_qeq.cpp | 8 +++---
src/QEQ/fix_qeq_dynamic.cpp | 4 +--
src/QEQ/fix_qeq_fire.cpp | 4 +--
src/QEQ/fix_qeq_point.cpp | 2 +-
src/QEQ/fix_qeq_shielded.cpp | 2 +-
src/QEQ/fix_qeq_slater.cpp | 2 +-
src/REPLICA/fix_event.cpp | 2 +-
src/REPLICA/fix_neb.cpp | 2 +-
src/RIGID/fix_rattle.cpp | 4 +--
src/RIGID/fix_rigid.cpp | 8 +++---
src/RIGID/fix_rigid_small.cpp | 8 +++---
src/RIGID/fix_shake.cpp | 4 +--
src/SHOCK/fix_append_atoms.cpp | 4 +--
src/SHOCK/fix_msst.cpp | 4 +--
src/SHOCK/fix_wall_piston.cpp | 2 +-
src/SNAP/compute_sna_atom.cpp | 2 +-
src/SNAP/compute_snad_atom.cpp | 2 +-
src/SNAP/compute_snav_atom.cpp | 2 +-
src/SNAP/sna.cpp | 2 +-
src/SPIN/atom_vec_spin.cpp | 2 +-
src/SPIN/fix_langevin_spin.cpp | 2 +-
src/SPIN/fix_nve_spin.cpp | 2 +-
src/SPIN/fix_precession_spin.cpp | 4 +--
src/SPIN/pair_spin.cpp | 2 +-
src/SPIN/pair_spin_dmi.cpp | 2 +-
src/SPIN/pair_spin_magelec.cpp | 2 +-
src/SRD/fix_srd.cpp | 12 ++++-----
src/USER-BOCS/fix_bocs.cpp | 8 +++---
src/USER-CGDNA/bond_oxdna_fene.cpp | 4 +--
src/USER-CGDNA/fix_nve_dot.cpp | 2 +-
src/USER-CGDNA/fix_nve_dotc_langevin.cpp | 2 +-
src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 2 +-
src/USER-CGDNA/pair_oxdna2_dh.cpp | 2 +-
src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 2 +-
src/USER-CGDNA/pair_oxdna_excv.cpp | 4 +--
src/USER-CGDNA/pair_oxdna_hbond.cpp | 2 +-
src/USER-CGDNA/pair_oxdna_stk.cpp | 2 +-
src/USER-CGDNA/pair_oxdna_xstk.cpp | 2 +-
src/USER-DIFFRACTION/fix_saed_vtk.cpp | 2 +-
src/USER-DPD/fix_dpd_energy.cpp | 2 +-
src/USER-DPD/fix_eos_table_rx.cpp | 4 +--
src/USER-DPD/fix_rx.cpp | 12 ++++-----
src/USER-DPD/fix_shardlow.cpp | 8 +++---
src/USER-DPD/pair_dpd_fdt.cpp | 4 +--
src/USER-DPD/pair_dpd_fdt_energy.cpp | 4 +--
src/USER-DPD/pair_multi_lucy.cpp | 2 +-
src/USER-DPD/pair_multi_lucy_rx.cpp | 2 +-
src/USER-DPD/pair_table_rx.cpp | 2 +-
src/USER-DRUDE/fix_drude.cpp | 2 +-
src/USER-DRUDE/fix_langevin_drude.cpp | 2 +-
src/USER-DRUDE/pair_thole.cpp | 2 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 2 +-
src/USER-EFF/compute_temp_region_eff.cpp | 2 +-
src/USER-EFF/fix_langevin_eff.cpp | 2 +-
src/USER-EFF/fix_nve_eff.cpp | 6 ++---
src/USER-EFF/pair_eff_cut.cpp | 6 ++---
src/USER-FEP/fix_adapt_fep.cpp | 4 +--
src/USER-FEP/pair_coul_cut_soft.cpp | 2 +-
src/USER-FEP/pair_coul_long_soft.cpp | 2 +-
src/USER-FEP/pair_lj_cut_soft.cpp | 4 +--
src/USER-FEP/pair_morse_soft.cpp | 4 +--
src/USER-INTEL/angle_charmm_intel.cpp | 2 +-
src/USER-INTEL/angle_harmonic_intel.cpp | 2 +-
src/USER-INTEL/bond_fene_intel.cpp | 2 +-
src/USER-INTEL/bond_harmonic_intel.cpp | 2 +-
src/USER-INTEL/dihedral_fourier_intel.cpp | 2 +-
src/USER-INTEL/dihedral_harmonic_intel.cpp | 2 +-
src/USER-INTEL/dihedral_opls_intel.cpp | 2 +-
src/USER-INTEL/fix_intel.cpp | 8 +++---
src/USER-INTEL/fix_intel.h | 14 +++++-----
src/USER-INTEL/fix_nve_asphere_intel.cpp | 2 +-
src/USER-INTEL/fix_nve_intel.cpp | 2 +-
src/USER-INTEL/improper_cvff_intel.cpp | 2 +-
src/USER-INTEL/improper_harmonic_intel.cpp | 2 +-
src/USER-INTEL/intel_buffers.cpp | 14 +++++-----
src/USER-INTEL/intel_buffers.h | 10 +++----
src/USER-INTEL/intel_intrinsics_airebo.h | 4 +--
src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 2 +-
src/USER-INTEL/npair_intel.cpp | 4 +--
src/USER-INTEL/pair_airebo_intel.cpp | 14 +++++-----
src/USER-INTEL/pair_eam_intel.cpp | 2 +-
src/USER-INTEL/pair_rebo_intel.cpp | 2 +-
src/USER-INTEL/pair_sw_intel.cpp | 2 +-
src/USER-INTEL/pppm_disp_intel.cpp | 26 +++++++++----------
src/USER-INTEL/pppm_intel.cpp | 2 +-
src/USER-LB/fix_lb_fluid.cpp | 8 +++---
src/USER-LB/fix_lb_pc.cpp | 4 +--
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 2 +-
src/USER-LB/fix_lb_viscous.cpp | 4 +--
src/USER-MANIFOLD/fix_manifoldforce.cpp | 4 +--
src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 4 +--
src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 4 +--
src/USER-MANIFOLD/manifold.h | 2 +-
src/USER-MANIFOLD/manifold_cylinder.cpp | 4 +--
src/USER-MANIFOLD/manifold_cylinder_dent.cpp | 4 +--
src/USER-MANIFOLD/manifold_dumbbell.cpp | 2 +-
src/USER-MANIFOLD/manifold_ellipsoid.cpp | 2 +-
src/USER-MANIFOLD/manifold_gaussian_bump.cpp | 2 +-
src/USER-MANIFOLD/manifold_plane.cpp | 4 +--
src/USER-MANIFOLD/manifold_plane_wiggle.cpp | 2 +-
src/USER-MANIFOLD/manifold_spine.cpp | 2 +-
src/USER-MANIFOLD/manifold_thylakoid.cpp | 4 +--
src/USER-MANIFOLD/manifold_torus.cpp | 2 +-
src/USER-MEAMC/meam_dens_final.cpp | 2 +-
src/USER-MEAMC/meam_dens_init.cpp | 4 +--
src/USER-MEAMC/meam_force.cpp | 2 +-
src/USER-MEAMC/meam_setup_global.cpp | 2 +-
src/USER-MEAMC/pair_meamc.cpp | 6 ++---
src/USER-MESO/fix_edpd_source.cpp | 2 +-
src/USER-MESO/fix_mvv_dpd.cpp | 2 +-
src/USER-MESO/fix_mvv_edpd.cpp | 2 +-
src/USER-MESO/fix_mvv_tdpd.cpp | 2 +-
src/USER-MESO/fix_tdpd_source.cpp | 2 +-
src/USER-MESO/pair_edpd.cpp | 2 +-
src/USER-MESO/pair_mdpd_rhosum.cpp | 8 +++---
src/USER-MESO/pair_tdpd.cpp | 4 +--
src/USER-MGPT/pair_mgpt.cpp | 6 ++---
src/USER-MISC/angle_dipole.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 2 +-
src/USER-MISC/compute_basal_atom.cpp | 2 +-
src/USER-MISC/compute_cnp_atom.cpp | 2 +-
src/USER-MISC/compute_entropy_atom.cpp | 2 +-
src/USER-MISC/fix_addtorque.cpp | 4 +--
src/USER-MISC/fix_ave_correlate_long.cpp | 2 +-
src/USER-MISC/fix_bond_react.cpp | 6 ++---
src/USER-MISC/fix_filter_corotate.cpp | 8 +++---
src/USER-MISC/fix_flow_gauss.cpp | 4 +--
src/USER-MISC/fix_gle.cpp | 10 +++----
src/USER-MISC/fix_grem.cpp | 2 +-
src/USER-MISC/fix_imd.cpp | 4 +--
src/USER-MISC/fix_ipi.cpp | 2 +-
src/USER-MISC/fix_nvk.cpp | 6 ++---
src/USER-MISC/fix_pimd.cpp | 10 +++----
src/USER-MISC/fix_rhok.cpp | 4 +--
src/USER-MISC/fix_smd.cpp | 2 +-
src/USER-MISC/fix_srp.cpp | 8 +++---
src/USER-MISC/fix_ti_spring.cpp | 10 +++----
src/USER-MISC/fix_ttm_mod.cpp | 10 +++----
src/USER-MISC/fix_wall_region_ees.cpp | 4 +--
src/USER-MISC/pair_agni.cpp | 2 +-
src/USER-MISC/pair_buck_mdf.cpp | 4 +--
src/USER-MISC/pair_coul_diel.cpp | 2 +-
src/USER-MISC/pair_coul_shield.cpp | 2 +-
src/USER-MISC/pair_edip.cpp | 2 +-
src/USER-MISC/pair_edip_multi.cpp | 2 +-
src/USER-MISC/pair_extep.cpp | 2 +-
src/USER-MISC/pair_gauss_cut.cpp | 4 +--
src/USER-MISC/pair_ilp_graphene_hbn.cpp | 6 ++---
src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 6 ++---
src/USER-MISC/pair_lennard_mdf.cpp | 4 +--
src/USER-MISC/pair_lj_mdf.cpp | 4 +--
src/USER-MISC/pair_meam_spline.cpp | 10 +++----
src/USER-MISC/pair_meam_sw_spline.cpp | 10 +++----
src/USER-MISC/pair_momb.cpp | 4 +--
src/USER-MISC/pair_morse_smooth_linear.cpp | 4 +--
src/USER-MISC/pair_tersoff_table.cpp | 2 +-
src/USER-MOFFF/angle_cosine_buck6d.cpp | 2 +-
src/USER-PHONON/fix_phonon.cpp | 2 +-
src/USER-QTB/fix_qbmsst.cpp | 6 ++---
src/USER-QTB/fix_qtb.cpp | 6 ++---
src/USER-QUIP/pair_quip.cpp | 4 +--
src/USER-REAXC/fix_qeq_reax.cpp | 10 +++----
src/USER-REAXC/fix_reaxc.cpp | 4 +--
src/USER-REAXC/fix_reaxc_bonds.cpp | 6 ++---
src/USER-REAXC/fix_reaxc_species.cpp | 8 +++---
src/USER-REAXC/pair_reaxc.cpp | 2 +-
src/USER-REAXC/reaxc_allocate.cpp | 14 +++++-----
src/USER-REAXC/reaxc_bond_orders.cpp | 4 +--
src/USER-REAXC/reaxc_bonds.cpp | 4 +--
src/USER-REAXC/reaxc_forces.cpp | 20 +++++++-------
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 2 +-
src/USER-REAXC/reaxc_init_md.cpp | 12 ++++-----
src/USER-REAXC/reaxc_io_tools.cpp | 2 +-
src/USER-REAXC/reaxc_lookup.cpp | 2 +-
src/USER-REAXC/reaxc_multi_body.cpp | 2 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 4 +--
src/USER-REAXC/reaxc_reset_tools.cpp | 2 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 2 +-
src/USER-REAXC/reaxc_traj.cpp | 6 ++---
src/USER-REAXC/reaxc_valence_angles.cpp | 2 +-
src/USER-SMD/atom_vec_smd.cpp | 20 +++++++-------
src/USER-SMD/fix_smd_adjust_dt.cpp | 4 +--
src/USER-SMD/fix_smd_integrate_tlsph.cpp | 2 +-
src/USER-SMD/fix_smd_integrate_ulsph.cpp | 2 +-
.../fix_smd_move_triangulated_surface.cpp | 4 +--
src/USER-SMD/fix_smd_setvel.cpp | 2 +-
.../fix_smd_tlsph_reference_configuration.cpp | 8 +++---
src/USER-SMD/fix_smd_wall_surface.cpp | 2 +-
src/USER-SMD/pair_smd_hertz.cpp | 2 +-
src/USER-SMD/pair_smd_tlsph.cpp | 8 +++---
.../pair_smd_triangulated_surface.cpp | 2 +-
src/USER-SMD/pair_smd_ulsph.cpp | 4 +--
src/USER-SMD/smd_material_models.cpp | 4 +--
src/USER-SMTBQ/pair_smtbq.cpp | 18 ++++++-------
src/USER-SPH/fix_meso.cpp | 4 +--
src/USER-SPH/fix_meso_stationary.cpp | 2 +-
src/USER-SPH/pair_sph_heatconduction.cpp | 6 ++---
src/USER-SPH/pair_sph_idealgas.cpp | 6 ++---
src/USER-SPH/pair_sph_lj.cpp | 6 ++---
src/USER-SPH/pair_sph_rhosum.cpp | 6 ++---
src/USER-SPH/pair_sph_taitwater.cpp | 6 ++---
src/USER-SPH/pair_sph_taitwater_morris.cpp | 6 ++---
src/USER-UEF/fix_nh_uef.cpp | 2 +-
277 files changed, 594 insertions(+), 594 deletions(-)
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index a33848f1a1..61e3c35293 100644
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -62,7 +62,7 @@ void FixNVEAsphere::init()
/* ---------------------------------------------------------------------- */
-void FixNVEAsphere::initial_integrate(int vflag)
+void FixNVEAsphere::initial_integrate(int /*vflag*/)
{
double dtfm;
double inertia[3],omega[3];
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index d944b68f35..9cc430592a 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -64,7 +64,7 @@ void FixNVEAsphereNoforce::init()
/* ---------------------------------------------------------------------- */
-void FixNVEAsphereNoforce::initial_integrate(int vflag)
+void FixNVEAsphereNoforce::initial_integrate(int /*vflag*/)
{
AtomVecEllipsoid::Bonus *bonus;
if (avec) bonus = avec->bonus;
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index c145e99fcb..51a502df89 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -81,7 +81,7 @@ void FixNVELine::init()
/* ---------------------------------------------------------------------- */
-void FixNVELine::initial_integrate(int vflag)
+void FixNVELine::initial_integrate(int /*vflag*/)
{
double dtfm,dtirotate,length,theta;
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index d06063d905..fb9bf64c58 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -75,7 +75,7 @@ void FixNVETri::init()
/* ---------------------------------------------------------------------- */
-void FixNVETri::initial_integrate(int vflag)
+void FixNVETri::initial_integrate(int /*vflag*/)
{
double dtfm;
double omega[3];
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index 684e5768da..10529ad3af 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -195,7 +195,7 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyNparticle::radius_body(int ninteger, int ndouble,
+double BodyNparticle::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -258,7 +258,7 @@ void BodyNparticle::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyNparticle::image(int ibonus, double flag1, double flag2,
+int BodyNparticle::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
double p[3][3];
diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp
index 1e232f0f3f..00a09c912d 100644
--- a/src/BODY/body_rounded_polygon.cpp
+++ b/src/BODY/body_rounded_polygon.cpp
@@ -323,7 +323,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyRoundedPolygon::radius_body(int ninteger, int ndouble,
+double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -392,7 +392,7 @@ void BodyRoundedPolygon::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyRoundedPolygon::image(int ibonus, double flag1, double flag2,
+int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
int j;
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 6a9b97ae23..5ba4bce8e8 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -381,7 +381,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyRoundedPolyhedron::radius_body(int ninteger, int ndouble,
+double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -460,7 +460,7 @@ void BodyRoundedPolyhedron::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyRoundedPolyhedron::image(int ibonus, double flag1, double flag2,
+int BodyRoundedPolyhedron::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
int j, nelements;
diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp
index 0606723cb7..0c74facf34 100644
--- a/src/BODY/fix_nve_body.cpp
+++ b/src/BODY/fix_nve_body.cpp
@@ -54,7 +54,7 @@ void FixNVEBody::init()
/* ---------------------------------------------------------------------- */
-void FixNVEBody::initial_integrate(int vflag)
+void FixNVEBody::initial_integrate(int /*vflag*/)
{
double dtfm;
double omega[3];
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 0e7aaea1e1..f217db774e 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -204,7 +204,7 @@ void FixWallBodyPolygon::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallBodyPolygon::post_force(int vflag)
+void FixWallBodyPolygon::post_force(int /*vflag*/)
{
double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
int i,ni,npi,ifirst,nei,iefirst,side;
@@ -475,7 +475,7 @@ void FixWallBodyPolygon::body2space(int i)
int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
double** x, double** f, double** torque, int side,
- Contact* contact_list, int &num_contacts, double* facc)
+ Contact* contact_list, int &num_contacts, double* /*facc*/)
{
int ni, npi, ifirst, interact;
double xpi[3], xpj[3], dist, eradi, rradi;
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 17e9f0b8b5..b90731acf6 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -211,7 +211,7 @@ void FixWallBodyPolyhedron::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallBodyPolyhedron::post_force(int vflag)
+void FixWallBodyPolyhedron::post_force(int /*vflag*/)
{
double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side;
@@ -485,7 +485,7 @@ void FixWallBodyPolyhedron::body2space(int i)
---------------------------------------------------------------------- */
int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
- int side, double* vwall, double** x, double** v, double** f,
+ int /*side*/, double* vwall, double** x, double** v, double** f,
double** angmom, double** torque)
{
int mode;
@@ -545,8 +545,8 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
---------------------------------------------------------------------- */
int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
- int side, double* vwall, double** x, double** f, double** torque,
- Contact* contact_list, int &num_contacts, double* facc)
+ int side, double* vwall, double** x, double** /*f*/, double** /*torque*/,
+ Contact* /*contact_list*/, int &/*num_contacts*/, double* /*facc*/)
{
int ni, nei, mode, contact;
double rradi;
@@ -584,7 +584,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
double *xmi, double rounded_radius_i, double wall_pos,
- int side, double* vwall, int &contact)
+ int /*side*/, double* vwall, int &contact)
{
int mode,ifirst,iefirst,npi1,npi2;
double d1,d2,xpi1[3],xpi2[3],hi[3];
@@ -698,7 +698,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
------------------------------------------------------------------------- */
void FixWallBodyPolyhedron::contact_forces(int ibody,
- double j_a, double *xi, double *xj, double delx, double dely, double delz,
+ double j_a, double *xi, double */*xj*/, double delx, double dely, double delz,
double fx, double fy, double fz, double** x, double** v, double** angmom,
double** f, double** torque, double* vwall)
{
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 14ef70f476..97d3ad5606 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -598,7 +598,7 @@ void PairBodyRoundedPolygon::body2space(int i)
void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
double delx, double dely, double delz, double rsq,
- double k_n, double k_na, double** x, double** v,
+ double k_n, double k_na, double** /*x*/, double** v,
double** f, int evflag)
{
double eradi,eradj,rradi,rradj;
@@ -1166,7 +1166,7 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody,
void PairBodyRoundedPolygon::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
- double** torque, double &evdwl, double* facc)
+ double** torque, double &/*evdwl*/, double* facc)
{
int ibody,jbody,ibonus,jbonus,ifirst,jefirst,ni,nj;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index c3dc09715c..af20313e0a 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -209,7 +209,7 @@ void BondClass2::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondClass2::single(int type, double rsq, int i, int j, double &fforce)
+double BondClass2::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
{
double r = sqrt(rsq);
double dr = r - r0[type];
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index 3b3811584d..77f594af9d 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -633,7 +633,7 @@ void ImproperClass2::read_restart(FILE *fp)
angle-angle interactions within improper
------------------------------------------------------------------------- */
-void ImproperClass2::angleangle(int eflag, int vflag)
+void ImproperClass2::angleangle(int eflag, int /*vflag*/)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index e255807ab6..6451921dc5 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -377,8 +377,8 @@ void PairLJClass2::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJClass2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index 4448d6e110..c16dbf41af 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -469,8 +469,8 @@ void PairColloid::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double K[9],h[4],g[4];
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index f0f7ce8c14..fc1fa7acc5 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -749,7 +749,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
int PairLubricate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
@@ -797,7 +797,7 @@ void PairLubricate::unpack_forward_comm(int n, int first, double *buf)
if type pair setting, return -2 if no type pairs are set
------------------------------------------------------------------------- */
-int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
+int PairLubricate::pre_adapt(char *name, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/)
{
if (strcmp(name,"mu") == 0) return 0;
return -1;
@@ -809,7 +809,7 @@ int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
if type pair setting, set I-J and J-I coeffs
------------------------------------------------------------------------- */
-void PairLubricate::adapt(int which, int ilo, int ihi, int jlo, int jhi,
+void PairLubricate::adapt(int /*which*/, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/,
double value)
{
mu = value;
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 11fb213157..2d51f2e2b6 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -2010,7 +2010,7 @@ void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
/* ---------------------------------------------------------------------- */
int PairLubricateU::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index 5965fd3aa8..d21bc43524 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -160,9 +160,9 @@ double PairYukawaColloid::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-double PairYukawaColloid::single(int i, int j, int itype, int jtype,
+double PairYukawaColloid::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,rinv,screening,forceyukawa,phi;
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index 4b10782ee6..8db5979b39 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -338,9 +338,9 @@ void PairCoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulLong::single(int i, int j, int itype, int jtype,
+double PairCoulLong::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp
index f5cd9a0445..ab59dfa4c1 100644
--- a/src/KSPACE/pair_coul_msm.cpp
+++ b/src/KSPACE/pair_coul_msm.cpp
@@ -169,9 +169,9 @@ void PairCoulMSM::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-double PairCoulMSM::single(int i, int j, int itype, int jtype,
+double PairCoulMSM::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,egamma,fgamma,prefactor;
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index aea57da326..b8cd52c5fe 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -8052,7 +8052,7 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
extended to non-neutral systems (J. Chem. Phys. 131, 094107).
------------------------------------------------------------------------- */
-void PPPMDisp::slabcorr(int eflag)
+void PPPMDisp::slabcorr(int /*eflag*/)
{
// compute local contribution to global dipole moment
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index 81dd692f4f..26541f121e 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -234,7 +234,7 @@ struct remap_plan_3d *remap_3d_create_plan(
int in_klo, int in_khi,
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
int out_klo, int out_khi,
- int nqty, int permute, int memory, int precision, int usecollective)
+ int nqty, int permute, int memory, int /*precision*/, int usecollective)
{
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index 18502dd013..c9dd0465f8 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -189,7 +189,7 @@ void FixLatte::init()
/* ---------------------------------------------------------------------- */
-void FixLatte::init_list(int id, NeighList *ptr)
+void FixLatte::init_list(int /*id*/, NeighList */*ptr*/)
{
// list = ptr;
}
@@ -223,13 +223,13 @@ void FixLatte::setup_pre_reverse(int eflag, int vflag)
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
-void FixLatte::initial_integrate(int vflag) {}
+void FixLatte::initial_integrate(int /*vflag*/) {}
/* ----------------------------------------------------------------------
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixLatte::pre_reverse(int eflag, int vflag)
+void FixLatte::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index b8d9c7e6df..61bf9bf11c 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -159,7 +159,7 @@ void FixQEQComb::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEQComb::post_force(int vflag)
+void FixQEQComb::post_force(int /*vflag*/)
{
int i,ii,iloop,loopmax,inum,*ilist;
double heatpq,qmass,dtq,dtq2;
@@ -276,7 +276,7 @@ void FixQEQComb::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEQComb::post_force_respa(int vflag, int ilevel, int iloop)
+void FixQEQComb::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -293,7 +293,7 @@ double FixQEQComb::memory_usage()
/* ---------------------------------------------------------------------- */
int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index d0b4d19758..fd496fcae6 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -424,7 +424,7 @@ void PairADP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairADP::settings(int narg, char **arg)
+void PairADP::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -521,7 +521,7 @@ void PairADP::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairADP::init_one(int i, int j)
+double PairADP::init_one(int /*i*/, int /*j*/)
{
// single global cutoff = max of cut from all files read in
// for funcfl could be multiple files
@@ -935,7 +935,7 @@ void PairADP::grab(FILE *fp, int n, double *list)
/* ---------------------------------------------------------------------- */
int PairADP::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 3be27354c1..ac3ed36a83 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -425,7 +425,7 @@ void PairAIREBO::REBO_neigh()
REBO forces and energy
------------------------------------------------------------------------- */
-void PairAIREBO::FREBO(int eflag, int vflag)
+void PairAIREBO::FREBO(int eflag, int /*vflag*/)
{
int i,j,k,m,ii,inum,itype,jtype;
tagint itag,jtag;
@@ -524,7 +524,7 @@ void PairAIREBO::FREBO(int eflag, int vflag)
find 3- and 4-step paths between atoms I,J via REBO neighbor lists
------------------------------------------------------------------------- */
-void PairAIREBO::FLJ(int eflag, int vflag)
+void PairAIREBO::FLJ(int eflag, int /*vflag*/)
{
int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype;
int atomi,atomj,atomk,atomm;
@@ -893,7 +893,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
torsional forces and energy
------------------------------------------------------------------------- */
-void PairAIREBO::TORSION(int eflag, int vflag)
+void PairAIREBO::TORSION(int eflag, int /*vflag*/)
{
int i,j,k,l,ii,inum;
tagint itag,jtag;
@@ -2116,7 +2116,7 @@ but of the vector r_ij.
*/
-double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mod,
+double PairAIREBO::bondorderLJ(int i, int j, double /*rij_mod*/[3], double rijmag_mod,
double VA, double rij[3], double rijmag,
double **f, int vflag_atom)
{
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index de686d4bcf..b205fc46d3 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -432,7 +432,7 @@ void PairComb::allocate()
global settings
------------------------------------------------------------------------- */
-void PairComb::settings(int narg, char **arg)
+void PairComb::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -1542,7 +1542,7 @@ void PairComb::potal_calc(double &calc1, double &calc2, double &calc3)
void PairComb::tri_point(double rsq, int &mr1, int &mr2,
int &mr3, double &sr1, double &sr2,
- double &sr3, int &itype)
+ double &sr3, int &/*itype*/)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
@@ -1572,7 +1572,7 @@ void PairComb::tri_point(double rsq, int &mr1, int &mr2,
void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
double sr1, double sr2, double sr3,
double iq, double jq,
- double potal, double fac11, double fac11e,
+ double /*potal*/, double fac11, double fac11e,
double &pot_tmp, double &pot_d)
{
double r,erfcc,fafbn1,potij,sme2,esucon;
@@ -2002,7 +2002,7 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
/* ---------------------------------------------------------------------- */
int PairComb::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index b4f9c02206..54fd13029b 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -1569,7 +1569,7 @@ void PairComb3::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
- double &fforce,int eflag, double &eng, double iq, double jq)
+ double &fforce,int /*eflag*/, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,Di,Dj;
double caj,vrcs,fvrcs;
@@ -1614,7 +1614,7 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
- double rsqik, double *delrij, double *delrik, int i, double xcn)
+ double rsqik, double *delrij, double *delrik, int /*i*/, double xcn)
{
double rij,rik,costheta,arg,ex_delr,rlm3;
@@ -1661,7 +1661,7 @@ void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
- double *delrij, double *delrik , double &zet_add)
+ double *delrij, double *delrik , double &/*zet_add*/)
{
double comtt;
double pplp0 = paramj->p6p0;
@@ -2109,7 +2109,7 @@ void PairComb3::coord(Param *param, double r, int i,
void PairComb3::cntri_int(int tri_flag, double xval, double yval,
double zval, int ixmin, int iymin, int izmin, double &vval,
- double &dvalx, double &dvaly, double &dvalz, Param *param)
+ double &dvalx, double &dvaly, double &dvalz, Param */*param*/)
{
double x;
vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0;
@@ -2254,7 +2254,7 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1,
double prefac_ij2, double prefac_ij3, double prefac_ij4,
double prefac_ij5, double rsqij, double rsqik, double *delrij,
- double *delrik, double *fi, double *fj,double *fk, int i, double xcn)
+ double *delrik, double *fi, double *fj,double *fk, int /*i*/, double xcn)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
@@ -2867,7 +2867,7 @@ void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
/* ---------------------------------------------------------------------- */
-double PairComb3::rad_init(double rsq2,Param *param,int i,
+double PairComb3::rad_init(double rsq2,Param *param,int /*i*/,
double &radtot, double cnconj)
{
double r, fc1k, radcut;
@@ -2882,7 +2882,7 @@ double PairComb3::rad_init(double rsq2,Param *param,int i,
/* ---------------------------------------------------------------------- */
void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn)
{
int ixmin, iymin, izmin;
int radindx;
@@ -3061,7 +3061,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
/* ---------------------------------------------------------------------- */
void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn)
{
int ixmin, iymin, izmin;
double vtor, dtorx, dtory, dtorz;
@@ -3589,7 +3589,7 @@ void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3,
void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
double iq, double jq, double &fqij, double &fqji,
- int i, int j, int nj)
+ int i, int /*j*/, int nj)
{
double r, tmp_fc;
double Di, Dj, dDi, dDj, Bsi, Bsj, dBsi, dBsj;
@@ -3863,7 +3863,7 @@ double PairComb3::switching_d(double rr)
/* ---------------------------------------------------------------------- */
int PairComb3::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 9e70b19eea..a861f33824 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -347,7 +347,7 @@ void PairEAM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEAM::settings(int narg, char **arg)
+void PairEAM::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -795,7 +795,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
/* ---------------------------------------------------------------------- */
double PairEAM::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int m;
@@ -829,7 +829,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
index 66ebad6244..9b8fd29465 100644
--- a/src/MANYBODY/pair_eam_cd.cpp
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -539,7 +539,7 @@ void PairEAMCD::read_h_coeff(char *filename)
/* ---------------------------------------------------------------------- */
int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index b810d444fc..cc35004778 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -342,7 +342,7 @@ void PairEIM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEIM::settings(int narg, char **arg)
+void PairEIM::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -850,7 +850,7 @@ void PairEIM::array2spline()
/* ---------------------------------------------------------------------- */
void PairEIM::interpolate(int n, double delta, double *f,
- double **spline, double origin)
+ double **spline, double /*origin*/)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
@@ -1087,7 +1087,7 @@ double PairEIM::funccoul(int i, int j, double r)
/* ---------------------------------------------------------------------- */
int PairEIM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index 35f092b580..0aff4970bb 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -257,7 +257,7 @@ void PairGW::allocate()
global settings
------------------------------------------------------------------------- */
-void PairGW::settings(int narg, char **arg)
+void PairGW::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index d334defcc6..57373c4f85 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -121,7 +121,7 @@ void PairLCBOP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairLCBOP::settings(int narg, char **arg) {
+void PairLCBOP::settings(int narg, char **/*arg*/) {
if( narg != 0 ) error->all(FLERR,"Illegal pair_style command");
}
@@ -353,7 +353,7 @@ void PairLCBOP::SR_neigh()
Short range forces and energy
------------------------------------------------------------------------- */
-void PairLCBOP::FSR(int eflag, int vflag)
+void PairLCBOP::FSR(int eflag, int /*vflag*/)
{
int i,j,jj,ii,inum;
tagint itag,jtag;
@@ -449,7 +449,7 @@ void PairLCBOP::FSR(int eflag, int vflag)
compute long range forces and energy
------------------------------------------------------------------------- */
-void PairLCBOP::FLR(int eflag, int vflag)
+void PairLCBOP::FLR(int eflag, int /*vflag*/)
{
int i,j,jj,ii;
tagint itag,jtag;
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index 36be9c2b90..a09f8a23e6 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -174,7 +174,7 @@ void PairNb3bHarmonic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairNb3bHarmonic::settings(int narg, char **arg)
+void PairNb3bHarmonic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -454,7 +454,7 @@ void PairNb3bHarmonic::setup_params()
/* ---------------------------------------------------------------------- */
-void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik,
+void PairNb3bHarmonic::threebody(Param */*paramij*/, Param */*paramik*/,
Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index 2afb08b7a1..ce9af66d30 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -450,7 +450,7 @@ void PairPolymorphic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPolymorphic::settings(int narg, char **arg)
+void PairPolymorphic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp
index 37948f3038..1f31c0b0cd 100644
--- a/src/MANYBODY/pair_rebo.cpp
+++ b/src/MANYBODY/pair_rebo.cpp
@@ -24,7 +24,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) {}
global settings
------------------------------------------------------------------------- */
-void PairREBO::settings(int narg, char **arg)
+void PairREBO::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index 6fbc00204c..da470d568a 100644
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -239,7 +239,7 @@ void PairSW::allocate()
global settings
------------------------------------------------------------------------- */
-void PairSW::settings(int narg, char **arg)
+void PairSW::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 507b07e29a..45068e5c2e 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -280,7 +280,7 @@ void PairTersoff::allocate()
global settings
------------------------------------------------------------------------- */
-void PairTersoff::settings(int narg, char **arg)
+void PairTersoff::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 8506c9a69f..54b184ea39 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -245,7 +245,7 @@ void PairVashishta::allocate()
global settings
------------------------------------------------------------------------- */
-void PairVashishta::settings(int narg, char **arg)
+void PairVashishta::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 4d9377022b..b795b71273 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -695,7 +695,7 @@ void FixAtomSwap::update_swap_atoms_list()
/* ---------------------------------------------------------------------- */
-int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 9a5b59b601..203d6b589b 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -693,7 +693,7 @@ int FixBondBreak::dedup(int nstart, int nstop, tagint *copy)
/* ---------------------------------------------------------------------- */
-void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
+void FixBondBreak::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -701,7 +701,7 @@ void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 8e9db6a18b..17ea7fb3f2 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -258,14 +258,14 @@ void FixBondCreate::init()
/* ---------------------------------------------------------------------- */
-void FixBondCreate::init_list(int id, NeighList *ptr)
+void FixBondCreate::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
-void FixBondCreate::setup(int vflag)
+void FixBondCreate::setup(int /*vflag*/)
{
int i,j,m;
@@ -1206,7 +1206,7 @@ int FixBondCreate::dedup(int nstart, int nstop, tagint *copy)
/* ---------------------------------------------------------------------- */
-void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
+void FixBondCreate::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -1214,7 +1214,7 @@ void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,m,ns;
@@ -1347,7 +1347,7 @@ void FixBondCreate::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixBondCreate::copy_arrays(int i, int j, int delflag)
+void FixBondCreate::copy_arrays(int i, int j, int /*delflag*/)
{
bondcount[j] = bondcount[i];
}
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index d6df4d9a96..9a72667907 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -182,7 +182,7 @@ void FixBondSwap::init()
/* ---------------------------------------------------------------------- */
-void FixBondSwap::init_list(int id, NeighList *ptr)
+void FixBondSwap::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index b821710353..46c5e592ae 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -158,7 +158,7 @@ void FixTFMC::init()
/* ---------------------------------------------------------------------- */
-void FixTFMC::initial_integrate(int vflag)
+void FixTFMC::initial_integrate(int /*vflag*/)
{
double boltz = force->boltz;
double **x = atom->x;
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index 02f9754c2a..c71eaa2295 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -65,7 +65,7 @@ PairDSMC::~PairDSMC()
/* ---------------------------------------------------------------------- */
-void PairDSMC::compute(int eflag, int vflag)
+void PairDSMC::compute(int /*eflag*/, int /*vflag*/)
{
double **x = atom->x;
double *mass = atom->mass;
@@ -405,7 +405,7 @@ void PairDSMC::read_restart_settings(FILE *fp)
the next nrezero timesteps
-------------------------------------------------------------------------*/
-void PairDSMC::recompute_V_sigma_max(int icell)
+void PairDSMC::recompute_V_sigma_max(int /*icell*/)
{
int i,j,k;
double Vsigma_max = 0;
@@ -459,7 +459,7 @@ double PairDSMC::V_sigma(int i, int j)
generate new velocities for collided particles
-------------------------------------------------------------------------*/
-void PairDSMC::scatter_random(int i, int j, int icell)
+void PairDSMC::scatter_random(int i, int j, int /*icell*/)
{
double mag_delv,cos_phi,cos_squared,r,theta;
double delv[3],vcm[3];
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index 687055aa6a..41f1f4ce37 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -325,7 +325,7 @@ void PairMEAM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAM::settings(int narg, char **arg)
+void PairMEAM::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -448,7 +448,7 @@ void PairMEAM::init_list(int id, NeighList *ptr)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAM::init_one(int i, int j)
+double PairMEAM::init_one(int /*i*/, int /*j*/)
{
return cutmax;
}
@@ -734,7 +734,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,m;
diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp
index 1fa141e2bf..004c8ad7bc 100644
--- a/src/MISC/fix_efield.cpp
+++ b/src/MISC/fix_efield.cpp
@@ -412,7 +412,7 @@ void FixEfield::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEfield::post_force_respa(int vflag, int ilevel, int iloop)
+void FixEfield::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 370730133e..2bf02889a5 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -217,7 +217,7 @@ void FixGLD::init()
First half of a timestep (V^{n} -> V^{n+1/2}; X^{n} -> X^{n+1})
------------------------------------------------------------------------- */
-void FixGLD::initial_integrate(int vflag)
+void FixGLD::initial_integrate(int /*vflag*/)
{
double dtfm;
double ftm2v = force->ftm2v;
@@ -444,7 +444,7 @@ void FixGLD::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixGLD::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
@@ -458,7 +458,7 @@ void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixGLD::final_integrate_respa(int ilevel, int iloop)
+void FixGLD::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
final_integrate();
@@ -507,7 +507,7 @@ void FixGLD::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixGLD::copy_arrays(int i, int j, int delflag)
+void FixGLD::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < 3*prony_terms; k++) {
s_gld[j][k] = s_gld[i][k];
@@ -588,7 +588,7 @@ void FixGLD::unpack_restart(int nlocal, int nth)
fixes on a given processor.
------------------------------------------------------------------------- */
-int FixGLD::size_restart(int nlocal)
+int FixGLD::size_restart(int /*nlocal*/)
{
return 3*prony_terms+1;
}
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index c5ba6514a9..9b22e571fe 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -230,7 +230,7 @@ void FixOrientBCC::init()
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::init_list(int id, NeighList *ptr)
+void FixOrientBCC::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -250,7 +250,7 @@ void FixOrientBCC::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::post_force(int vflag)
+void FixOrientBCC::post_force(int /*vflag*/)
{
int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
tagint id_self;
@@ -471,7 +471,7 @@ void FixOrientBCC::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::post_force_respa(int vflag, int ilevel, int iloop)
+void FixOrientBCC::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -488,7 +488,7 @@ double FixOrientBCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientBCC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index 5786571a89..b061627fd8 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -228,7 +228,7 @@ void FixOrientFCC::init()
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::init_list(int id, NeighList *ptr)
+void FixOrientFCC::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -248,7 +248,7 @@ void FixOrientFCC::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::post_force(int vflag)
+void FixOrientFCC::post_force(int /*vflag*/)
{
int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
tagint id_self;
@@ -469,7 +469,7 @@ void FixOrientFCC::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::post_force_respa(int vflag, int ilevel, int iloop)
+void FixOrientFCC::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -486,7 +486,7 @@ double FixOrientFCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientFCC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index 7ffd979e50..c8f33c73b7 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -235,7 +235,7 @@ void FixTTM::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force(int vflag)
+void FixTTM::post_force(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
@@ -287,7 +287,7 @@ void FixTTM::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_setup(int vflag)
+void FixTTM::post_force_setup(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -306,14 +306,14 @@ void FixTTM::post_force_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTTM::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_respa_setup(int vflag, int ilevel, int iloop)
+void FixTTM::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
@@ -685,7 +685,7 @@ int FixTTM::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTTM::size_restart(int nlocal)
+int FixTTM::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index a778d7a5b6..ce077a7a04 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -401,8 +401,8 @@ void PairNMCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairNMCut::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairNMCut::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r,forcenm,phinm;
diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp
index 3987aa02fc..c67925d92a 100644
--- a/src/MISC/xdr_compat.cpp
+++ b/src/MISC/xdr_compat.cpp
@@ -650,7 +650,7 @@ xdrstdio_setpos (XDR *xdrs, unsigned int pos)
}
static xdr_int32_t *
-xdrstdio_inline (XDR *xdrs, int len)
+xdrstdio_inline (XDR */*xdrs*/, int /*len*/)
{
/*
* Must do some work to implement this: must insure
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index e3472dfd7a..7fb7ce4c27 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -172,7 +172,7 @@ void AngleCosine::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double AngleCosine::equilibrium_angle(int i)
+double AngleCosine::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index 4e620b436e..e8dd970b3b 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -222,7 +222,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double AngleCosinePeriodic::equilibrium_angle(int i)
+double AngleCosinePeriodic::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index b6da72bfaf..671290b0ad 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -242,7 +242,7 @@ void BondFENE::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondFENE::single(int type, double rsq, int i, int j,
+double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r0sq = r0[type] * r0[type];
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index 26b699d7bf..3e191683fb 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -253,7 +253,7 @@ void BondFENEExpand::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondFENEExpand::single(int type, double rsq, int i, int j,
+double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp
index 8e989259af..279f4fb2d4 100644
--- a/src/MOLECULE/bond_gromos.cpp
+++ b/src/MOLECULE/bond_gromos.cpp
@@ -190,7 +190,7 @@ void BondGromos::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondGromos::single(int type, double rsq, int i, int j,
+double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double dr = rsq - r0[type]*r0[type];
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index e7f510d2de..f795610b37 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -190,7 +190,7 @@ void BondHarmonic::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonic::single(int type, double rsq, int i, int j,
+double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 35be50e8df..06af28f2b0 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -196,7 +196,7 @@ void BondMorse::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondMorse::single(int type, double rsq, int i, int j,
+double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index 3926c3494b..645b081779 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -191,7 +191,7 @@ void BondNonlinear::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondNonlinear::single(int type, double rsq, int i, int j,
+double BondNonlinear::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index f581c7f331..f200030d6c 100644
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -251,7 +251,7 @@ void BondQuartic::init_style()
return an equilbrium bond length
------------------------------------------------------------------------- */
-double BondQuartic::equilibrium_distance(int i)
+double BondQuartic::equilibrium_distance(int /*i*/)
{
return 0.97;
}
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index 7515f713df..a5c579042b 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -244,7 +244,7 @@ void BondTable::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondTable::single(int type, double rsq, int i, int j,
+double BondTable::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index 5ef2e662ab..2acb20de60 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -295,7 +295,7 @@ void FixCMAP::pre_neighbor()
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixCMAP::pre_reverse(int eflag, int vflag)
+void FixCMAP::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
@@ -604,7 +604,7 @@ void FixCMAP::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixCMAP::post_force_respa(int vflag, int ilevel, int iloop)
+void FixCMAP::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -1163,7 +1163,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf,
/* ---------------------------------------------------------------------- */
-bigint FixCMAP::read_data_skip_lines(char *keyword)
+bigint FixCMAP::read_data_skip_lines(char */*keyword*/)
{
return ncmap;
}
@@ -1173,7 +1173,7 @@ bigint FixCMAP::read_data_skip_lines(char *keyword)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_header(FILE *fp, int mth)
+void FixCMAP::write_data_header(FILE *fp, int /*mth*/)
{
fprintf(fp,BIGINT_FORMAT " cmap crossterms\n",ncmap);
}
@@ -1186,7 +1186,7 @@ void FixCMAP::write_data_header(FILE *fp, int mth)
ny = columns = type + 5 atom IDs
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
+void FixCMAP::write_data_section_size(int /*mth*/, int &nx, int &ny)
{
int i,m;
@@ -1206,7 +1206,7 @@ void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
buf allocated by caller as owned crossterms by 6
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_pack(int mth, double **buf)
+void FixCMAP::write_data_section_pack(int /*mth*/, double **buf)
{
int i,m;
@@ -1237,7 +1237,7 @@ void FixCMAP::write_data_section_pack(int mth, double **buf)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
+void FixCMAP::write_data_section_keyword(int /*mth*/, FILE *fp)
{
fprintf(fp,"\nCMAP\n\n");
}
@@ -1249,7 +1249,7 @@ void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section(int mth, FILE *fp,
+void FixCMAP::write_data_section(int /*mth*/, FILE *fp,
int n, double **buf, int index)
{
for (int i = 0; i < n; i++)
@@ -1383,7 +1383,7 @@ void FixCMAP::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixCMAP::copy_arrays(int i, int j, int delflag)
+void FixCMAP::copy_arrays(int i, int j, int /*delflag*/)
{
num_crossterm[j] = num_crossterm[i];
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index 26ff499dec..c0c885d4d4 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -468,7 +468,7 @@ double PairHbondDreidingLJ::init_one(int i, int j)
double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int k,kk,ktype,knum,m;
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 749053164c..f464d2c621 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -371,7 +371,7 @@ void PairHbondDreidingMorse::init_style()
double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int k,kk,ktype,knum,m;
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index e9f52b8724..79dd79b180 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -443,7 +443,7 @@ void PairTIP4PCut::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairTIP4PCut::init_one(int i, int j)
+double PairTIP4PCut::init_one(int /*i*/, int /*j*/)
{
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 42d86e14b2..2f5d4ac694 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -140,7 +140,7 @@ void FixPeriNeigh::init()
/* ---------------------------------------------------------------------- */
-void FixPeriNeigh::init_list(int id, NeighList *ptr)
+void FixPeriNeigh::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -159,7 +159,7 @@ void FixPeriNeigh::min_setup(int vflag)
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
-void FixPeriNeigh::setup(int vflag)
+void FixPeriNeigh::setup(int /*vflag*/)
{
int i,j,ii,jj,itype,jtype,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -441,7 +441,7 @@ void FixPeriNeigh::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
+void FixPeriNeigh::copy_arrays(int i, int j, int /*delflag*/)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
@@ -514,7 +514,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index 9950c36f41..fe2041d802 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -434,7 +434,7 @@ void PairPeriEPS::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriEPS::settings(int narg, char **arg)
+void PairPeriEPS::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -799,7 +799,7 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
---------------------------------------------------------------------- */
int PairPeriEPS::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 4c48223b07..0ff0423801 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -364,7 +364,7 @@ void PairPeriLPS::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriLPS::settings(int narg, char **arg)
+void PairPeriLPS::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -631,7 +631,7 @@ void PairPeriLPS::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriLPS::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 81461f0b83..772e47f2d6 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -297,7 +297,7 @@ void PairPeriPMB::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriPMB::settings(int narg, char **arg)
+void PairPeriPMB::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -441,7 +441,7 @@ void PairPeriPMB::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double delx0,dely0,delz0,rsq0;
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index a9f620ef4b..a41d55b593 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -411,7 +411,7 @@ void PairPeriVES::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriVES::settings(int narg, char **arg)
+void PairPeriVES::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -697,7 +697,7 @@ void PairPeriVES::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriVES::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 8acf4498f5..f6f41f57bd 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -274,7 +274,7 @@ void FixQEq::reallocate_matrix()
/* ---------------------------------------------------------------------- */
-void FixQEq::init_list(int id, NeighList *ptr)
+void FixQEq::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -329,7 +329,7 @@ void FixQEq::init_storage()
/* ---------------------------------------------------------------------- */
-void FixQEq::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixQEq::pre_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) pre_force(vflag);
}
@@ -471,7 +471,7 @@ void FixQEq::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEq::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int m;
@@ -552,7 +552,7 @@ void FixQEq::grow_arrays(int nmax)
copy values within fictitious charge arrays
------------------------------------------------------------------------- */
-void FixQEq::copy_arrays(int i, int j, int delflag)
+void FixQEq::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index aeb8dd2c59..82112c5c11 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -88,7 +88,7 @@ void FixQEqDynamic::init()
/* ---------------------------------------------------------------------- */
-void FixQEqDynamic::pre_force(int vflag)
+void FixQEqDynamic::pre_force(int /*vflag*/)
{
int i,ii,iloop,inum,*ilist;
double qmass,dtq2;
@@ -247,7 +247,7 @@ double FixQEqDynamic::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int m=0;
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index db63bec206..d1683aa020 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -104,7 +104,7 @@ void FixQEqFire::init()
/* ---------------------------------------------------------------------- */
-void FixQEqFire::pre_force(int vflag)
+void FixQEqFire::pre_force(int /*vflag*/)
{
int inum, *ilist;
int i,ii,iloop;
@@ -311,7 +311,7 @@ double FixQEqFire::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqFire::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int m = 0;
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index bf7130c1d6..db2d800c06 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -67,7 +67,7 @@ void FixQEqPoint::init()
/* ---------------------------------------------------------------------- */
-void FixQEqPoint::pre_force(int vflag)
+void FixQEqPoint::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index 70898fd96c..88cd1ab3ad 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -111,7 +111,7 @@ void FixQEqShielded::init_shielding()
/* ---------------------------------------------------------------------- */
-void FixQEqShielded::pre_force(int vflag)
+void FixQEqShielded::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 4ddcf06357..81fdc73241 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -107,7 +107,7 @@ void FixQEqSlater::extract_streitz()
/* ---------------------------------------------------------------------- */
-void FixQEqSlater::pre_force(int vflag)
+void FixQEqSlater::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index 3b9b49ac57..8fc5de6b16 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -241,7 +241,7 @@ void FixEvent::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixEvent::copy_arrays(int i, int j, int delflag)
+void FixEvent::copy_arrays(int i, int j, int /*delflag*/)
{
xevent[j][0] = xevent[i][0];
xevent[j][1] = xevent[i][1];
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index e5d24da392..dc86c70956 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -270,7 +270,7 @@ void FixNEB::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixNEB::min_post_force(int vflag)
+void FixNEB::min_post_force(int /*vflag*/)
{
double vprev,vnext;
double delxp,delyp,delzp,delxn,delyn,delzn;
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 7ade8d6848..403f3091c6 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -185,7 +185,7 @@ void FixRattle::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRattle::post_force_respa(int vflag, int ilevel, int iloop)
+void FixRattle::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// remember vflag for the coordinate correction in this->final_integrate
@@ -625,7 +625,7 @@ void FixRattle::update_v_half_nocons()
/* ---------------------------------------------------------------------- */
-void FixRattle::update_v_half_nocons_respa(int ilevel)
+void FixRattle::update_v_half_nocons_respa(int /*ilevel*/)
{
// carry out unconstrained velocity update
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 7104d30849..c0f33346bb 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -1096,7 +1096,7 @@ void FixRigid::compute_forces_and_torques()
/* ---------------------------------------------------------------------- */
-void FixRigid::post_force(int vflag)
+void FixRigid::post_force(int /*vflag*/)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
@@ -1141,7 +1141,7 @@ void FixRigid::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRigid::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -1153,7 +1153,7 @@ void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixRigid::final_integrate_respa(int ilevel, int iloop)
+void FixRigid::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
@@ -2478,7 +2478,7 @@ void FixRigid::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixRigid::copy_arrays(int i, int j, int delflag)
+void FixRigid::copy_arrays(int i, int j, int /*delflag*/)
{
body[j] = body[i];
xcmimage[j] = xcmimage[i];
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index c1de89efc7..b2dbd27c46 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -867,7 +867,7 @@ void FixRigidSmall::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::post_force(int vflag)
+void FixRigidSmall::post_force(int /*vflag*/)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
@@ -1004,7 +1004,7 @@ void FixRigidSmall::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -1016,7 +1016,7 @@ void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::final_integrate_respa(int ilevel, int iloop)
+void FixRigidSmall::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
@@ -2999,7 +2999,7 @@ int FixRigidSmall::unpack_exchange(int nlocal, double *buf)
------------------------------------------------------------------------- */
int FixRigidSmall::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 0beef3bfa2..5c0139737c 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -2451,7 +2451,7 @@ void FixShake::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixShake::copy_arrays(int i, int j, int delflag)
+void FixShake::copy_arrays(int i, int j, int /*delflag*/)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
@@ -2528,7 +2528,7 @@ void FixShake::update_arrays(int i, int atom_offset)
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
- double *xgeom, double *vcm, double *quat)
+ double */*xgeom*/, double */*vcm*/, double */*quat*/)
{
int m,flag;
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index d898d2a790..2e515839c5 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -231,7 +231,7 @@ int FixAppendAtoms::setmask()
/* ---------------------------------------------------------------------- */
-void FixAppendAtoms::initial_integrate(int vflag)
+void FixAppendAtoms::initial_integrate(int /*vflag*/)
{
if (update->ntimestep % freq == 0) next_reneighbor = update->ntimestep;
}
@@ -331,7 +331,7 @@ int FixAppendAtoms::get_spatial()
/* ---------------------------------------------------------------------- */
-void FixAppendAtoms::post_force(int vflag)
+void FixAppendAtoms::post_force(int /*vflag*/)
{
double **f = atom->f;
double **v = atom->v;
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index a7890c3afa..c800e8a85d 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -357,7 +357,7 @@ void FixMSST::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixMSST::setup(int vflag)
+void FixMSST::setup(int /*vflag*/)
{
lagrangian_position = 0.0;
@@ -442,7 +442,7 @@ void FixMSST::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixMSST::initial_integrate(int vflag)
+void FixMSST::initial_integrate(int /*vflag*/)
{
int i,k;
double p_msst; // MSST driving pressure
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 7146b46c1e..eb89e19517 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -171,7 +171,7 @@ int FixWallPiston::setmask()
/* ---------------------------------------------------------------------- */
-void FixWallPiston::initial_integrate(int vflag)
+void FixWallPiston::initial_integrate(int /*vflag*/)
{
next_reneighbor = update->ntimestep;
}
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 0d8b0bae14..a2c1f55788 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -184,7 +184,7 @@ void ComputeSNAAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNAAtom::init_list(int id, NeighList *ptr)
+void ComputeSNAAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index b0fef8e1e3..800d1942e3 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -186,7 +186,7 @@ void ComputeSNADAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNADAtom::init_list(int id, NeighList *ptr)
+void ComputeSNADAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index cf66b1c136..2b823f7b8b 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -181,7 +181,7 @@ void ComputeSNAVAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNAVAtom::init_list(int id, NeighList *ptr)
+void ComputeSNAVAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 3150573043..7ed1bc1e23 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -1231,7 +1231,7 @@ void SNA::compute_uarray(double x, double y, double z,
}
void SNA::compute_uarray_omp(double x, double y, double z,
- double z0, double r, int sub_threads)
+ double z0, double r, int /*sub_threads*/)
{
double r0inv;
double a_r, b_r, a_i, b_i;
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 6460a6185f..24c4480e04 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -943,7 +943,7 @@ bigint AtomVecSpin::memory_usage()
return bytes;
}
-void AtomVecSpin::force_clear(int n, size_t nbytes)
+void AtomVecSpin::force_clear(int /*n*/, size_t nbytes)
{
memset(&atom->f[0][0],0,3*nbytes);
memset(&atom->fm[0][0],0,3*nbytes);
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index cb34465482..55b4d8dfec 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -192,7 +192,7 @@ void FixLangevinSpin::add_temperature(double fmi[3])
/* ---------------------------------------------------------------------- */
-void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index b75f03212a..898eb95396 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -258,7 +258,7 @@ void FixNVESpin::init()
/* ---------------------------------------------------------------------- */
-void FixNVESpin::initial_integrate(int vflag)
+void FixNVESpin::initial_integrate(int /*vflag*/)
{
double dtfm;
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index b908478952..d3edb3ae8a 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -169,7 +169,7 @@ void FixPrecessionSpin::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPrecessionSpin::post_force(int vflag)
+void FixPrecessionSpin::post_force(int /*vflag*/)
{
// update mag field with time (potential improvement)
@@ -245,7 +245,7 @@ void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3])
/* ---------------------------------------------------------------------- */
-void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index 398206b26e..929b79bef3 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -63,7 +63,7 @@ PairSpin::~PairSpin() {}
global settings
------------------------------------------------------------------------- */
-void PairSpin::settings(int narg, char **arg)
+void PairSpin::settings(int narg, char **/*arg*/)
{
if (narg < 1 || narg > 2)
error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index 08e2c63e7f..6f8114042e 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -414,7 +414,7 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double eij[3],
+void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3],
double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 6bc1f71947..570c995754 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -380,7 +380,7 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
/* ---------------------------------------------------------------------- */
-void PairSpinMagelec::compute_magelec(int i, int j, double rsq, double eij[3], double fmi[3], double spj[3])
+void PairSpinMagelec::compute_magelec(int i, int j, double /*rsq*/, double eij[3], double fmi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 564c1e98d7..d6053f4aa4 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -440,7 +440,7 @@ void FixSRD::init()
/* ---------------------------------------------------------------------- */
-void FixSRD::setup(int vflag)
+void FixSRD::setup(int /*vflag*/)
{
setup_bounds();
@@ -703,7 +703,7 @@ void FixSRD::pre_neighbor()
when collision occurs, change x,v of SRD, force,torque of BIG particle
------------------------------------------------------------------------- */
-void FixSRD::post_force(int vflag)
+void FixSRD::post_force(int /*vflag*/)
{
int i,m,ix,iy,iz;
@@ -2168,8 +2168,8 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_line_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
+double FixSRD::collision_line_exact(double */*xs*/, double */*xb*/,
+ double */*vs*/, double */*vb*/, Big */*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
@@ -2197,8 +2197,8 @@ double FixSRD::collision_line_exact(double *xs, double *xb,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_tri_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
+double FixSRD::collision_tri_exact(double */*xs*/, double */*xb*/,
+ double */*vs*/, double */*vb*/, Big */*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 7fb8a27110..eacfc83b40 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -790,7 +790,7 @@ void FixBocs::build_cubic_splines( double **data )
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixBocs::setup(int vflag)
+void FixBocs::setup(int /*vflag*/)
{
// tdof needed by compute_temp_target()
@@ -875,7 +875,7 @@ void FixBocs::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixBocs::initial_integrate(int vflag)
+void FixBocs::initial_integrate(int /*vflag*/)
{
// update eta_press_dot
@@ -970,7 +970,7 @@ void FixBocs::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixBocs::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
// set timesteps by level
@@ -1039,7 +1039,7 @@ void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixBocs::final_integrate_respa(int ilevel, int iloop)
+void FixBocs::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index 47d8d8f60b..34a25a9b5a 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -56,7 +56,7 @@ BondOxdnaFene::~BondOxdnaFene()
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
void BondOxdnaFene::compute_interaction_sites(double e1[3],
- double e2[3], double r[3])
+ double /*e2*/[3], double r[3])
{
double d_cs=-0.4;
@@ -316,7 +316,7 @@ void BondOxdnaFene::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondOxdnaFene::single(int type, double rsq, int i, int j,
+double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp
index 63f38a4e12..72b3388793 100644
--- a/src/USER-CGDNA/fix_nve_dot.cpp
+++ b/src/USER-CGDNA/fix_nve_dot.cpp
@@ -62,7 +62,7 @@ void FixNVEDot::init()
/* ---------------------------------------------------------------------- */
-void FixNVEDot::initial_integrate(int vflag)
+void FixNVEDot::initial_integrate(int /*vflag*/)
{
double *shape,*quat;
double fquat[4],conjqm[4],inertia[3];
diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
index 90f7b1caeb..c73801c97a 100644
--- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
+++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
@@ -127,7 +127,7 @@ void FixNVEDotcLangevin::compute_target()
/* ---------------------------------------------------------------------- */
-void FixNVEDotcLangevin::initial_integrate(int vflag)
+void FixNVEDotcLangevin::initial_integrate(int /*vflag*/)
{
double *shape,*quat;
double fquat[4],conjqm[4],inertia[3];
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 151e752692..d31890ea52 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -542,7 +542,7 @@ void PairOxdna2Coaxstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdna2Coaxstk::settings(int narg, char **arg)
+void PairOxdna2Coaxstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 974ade89c1..da6e1f8bbd 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -264,7 +264,7 @@ void PairOxdna2Dh::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdna2Dh::settings(int narg, char **arg)
+void PairOxdna2Dh::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 0eb75fbb43..ca03bcb35c 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -666,7 +666,7 @@ void PairOxdnaCoaxstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaCoaxstk::settings(int narg, char **arg)
+void PairOxdnaCoaxstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index e2b8334078..719a63b5f4 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -92,7 +92,7 @@ PairOxdnaExcv::~PairOxdnaExcv()
compute vector COM-excluded volume interaction sites in oxDNA
------------------------------------------------------------------------- */
void PairOxdnaExcv::compute_interaction_sites(double e1[3],
- double e2[3], double rs[3], double rb[3])
+ double /*e2*/[3], double rs[3], double rb[3])
{
double d_cs=-0.4, d_cb=+0.4;
@@ -441,7 +441,7 @@ void PairOxdnaExcv::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaExcv::settings(int narg, char **arg)
+void PairOxdnaExcv::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index ce1bfe036a..cb9f61bd7e 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -601,7 +601,7 @@ void PairOxdnaHbond::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaHbond::settings(int narg, char **arg)
+void PairOxdnaHbond::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index 8c4498e627..f713e4d27c 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -647,7 +647,7 @@ void PairOxdnaStk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaStk::settings(int narg, char **arg)
+void PairOxdnaStk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index e5b9de81c0..c4c23bf2c9 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -611,7 +611,7 @@ void PairOxdnaXstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaXstk::settings(int narg, char **arg)
+void PairOxdnaXstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index 45bfeca48b..ad9c76ac6b 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -325,7 +325,7 @@ void FixSAEDVTK::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixSAEDVTK::setup(int vflag)
+void FixSAEDVTK::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp
index d89ea7759a..5759a164f5 100644
--- a/src/USER-DPD/fix_dpd_energy.cpp
+++ b/src/USER-DPD/fix_dpd_energy.cpp
@@ -57,7 +57,7 @@ int FixDPDenergy::setmask()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixDPDenergy::initial_integrate(int vflag)
+void FixDPDenergy::initial_integrate(int /*vflag*/)
{
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 73144c0a0f..0bb96d7664 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -178,7 +178,7 @@ int FixEOStableRX::setmask()
/* ---------------------------------------------------------------------- */
-void FixEOStableRX::setup(int vflag)
+void FixEOStableRX::setup(int /*vflag*/)
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
@@ -803,7 +803,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
/* ---------------------------------------------------------------------- */
-int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int ii,jj,m;
double *uChem = atom->uChem;
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index be78989bb5..4dae89b491 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -668,7 +668,7 @@ void FixRX::init_list(int, class NeighList* ptr)
/* ---------------------------------------------------------------------- */
-void FixRX::setup_pre_force(int vflag)
+void FixRX::setup_pre_force(int /*vflag*/)
{
int nlocal = atom->nlocal;
int nghost = atom->nghost;
@@ -727,7 +727,7 @@ void FixRX::setup_pre_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRX::pre_force(int vflag)
+void FixRX::pre_force(int /*vflag*/)
{
TimerType timer_start = getTimeStamp();
@@ -1191,7 +1191,7 @@ void FixRX::rkf45_step (const int neq, const double h, double y[], double y_out[
return;
}
-int FixRX::rkf45_h0 (const int neq, const double t, const double t_stop,
+int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/,
const double hmin, const double hmax,
double& h0, double y[], double rwk[], void* v_params)
{
@@ -1668,7 +1668,7 @@ int FixRX::rhs(double t, const double *y, double *dydt, void *params)
/* ---------------------------------------------------------------------- */
-int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params)
+int FixRX::rhs_dense(double /*t*/, const double *y, double *dydt, void *params)
{
UserRHSData *userData = (UserRHSData *) params;
@@ -1702,7 +1702,7 @@ int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params)
/* ---------------------------------------------------------------------- */
-int FixRX::rhs_sparse(double t, const double *y, double *dydt, void *v_params) const
+int FixRX::rhs_sparse(double /*t*/, const double *y, double *dydt, void *v_params) const
{
UserRHSData *userData = (UserRHSData *) v_params;
@@ -1885,7 +1885,7 @@ void FixRX::computeLocalTemperature()
/* ---------------------------------------------------------------------- */
-int FixRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int ii,jj,m;
double tmp;
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 7fe865c8e6..9e8ee41533 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -145,14 +145,14 @@ void FixShardlow::init()
/* ---------------------------------------------------------------------- */
-void FixShardlow::init_list(int id, NeighList *ptr)
+void FixShardlow::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
-void FixShardlow::setup(int vflag)
+void FixShardlow::setup(int /*vflag*/)
{
bool fixShardlow = false;
@@ -527,7 +527,7 @@ while (ct-- > 0) {
rand_state[id] = RNGstate;
}
-void FixShardlow::initial_integrate(int vflag)
+void FixShardlow::initial_integrate(int /*vflag*/)
{
int ii;
@@ -646,7 +646,7 @@ fprintf(stdout, "\n%6d %6d,%6d %6d: "
/* ---------------------------------------------------------------------- */
-int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int ii,jj,m;
double **v = atom->v;
diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp
index aeade16e7c..12e6d9f257 100644
--- a/src/USER-DPD/pair_dpd_fdt.cpp
+++ b/src/USER-DPD/pair_dpd_fdt.cpp
@@ -433,8 +433,8 @@ void PairDPDfdt::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPDfdt::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPDfdt::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wr,wd,phi;
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 05dc52eac7..42c23e3ad2 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -534,8 +534,8 @@ void PairDPDfdtEnergy::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPDfdtEnergy::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPDfdtEnergy::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wr,wd,phi;
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index 3d204a849e..a7701f4d93 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -781,7 +781,7 @@ void PairMultiLucy::computeLocalDensity()
}
/* ---------------------------------------------------------------------- */
-int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 0070ca82d9..744c1ff64d 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -1019,7 +1019,7 @@ void PairMultiLucyRX::getMixingWeights(int id, double &mixWtSite1old, double &mi
/* ---------------------------------------------------------------------- */
-int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp
index 221944edc5..1e7bc440d1 100644
--- a/src/USER-DPD/pair_table_rx.cpp
+++ b/src/USER-DPD/pair_table_rx.cpp
@@ -439,7 +439,7 @@ void PairTableRX::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
double PairTableRX::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
int itable;
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index 19fd775715..7800efe7ff 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -235,7 +235,7 @@ void FixDrude::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixDrude::copy_arrays(int i, int j, int delflag)
+void FixDrude::copy_arrays(int i, int j, int /*delflag*/)
{
drudeid[j] = drudeid[i];
}
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index 235c5d224b..b9d1139f83 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -157,7 +157,7 @@ void FixLangevinDrude::init()
/* ---------------------------------------------------------------------- */
-void FixLangevinDrude::setup(int vflag)
+void FixLangevinDrude::setup(int /*vflag*/)
{
if (!strstr(update->integrate_style,"verlet"))
error->all(FLERR,"RESPA style not compatible with fix langevin/drude");
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 8c20ee8c42..6901ad1f2d 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -363,7 +363,7 @@ void PairThole::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairThole::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,rinv,r,phicoul;
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index d3856e431d..23abb4f99d 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -290,7 +290,7 @@ void ComputeTempDeformEff::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempDeformEff::restore_bias(int i, double *v)
+void ComputeTempDeformEff::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index 4548914ce1..659bdfca5e 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -263,7 +263,7 @@ void ComputeTempRegionEff::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRegionEff::restore_bias(int i, double *v)
+void ComputeTempRegionEff::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index 2d0eef8e85..d362113997 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -63,7 +63,7 @@ FixLangevinEff::~FixLangevinEff()
/* ---------------------------------------------------------------------- */
-void FixLangevinEff::post_force(int vflag)
+void FixLangevinEff::post_force(int /*vflag*/)
{
if (tallyflag) post_force_tally();
else post_force_no_tally();
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index 584714a44e..699dd9f949 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -68,7 +68,7 @@ void FixNVEEff::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVEEff::initial_integrate(int vflag)
+void FixNVEEff::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -145,7 +145,7 @@ void FixNVEEff::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -159,7 +159,7 @@ void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVEEff::final_integrate_respa(int ilevel, int iloop)
+void FixNVEEff::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index 0379c0264b..b4e9011e33 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -1009,7 +1009,7 @@ void PairEffCut::read_restart_settings(FILE *fp)
these arrays are stored locally by pair style
------------------------------------------------------------------------- */
-void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
+void PairEffCut::min_xf_pointers(int /*ignore*/, double **xextra, double **fextra)
{
// grow arrays if necessary
// need to be atom->nmax in length
@@ -1031,7 +1031,7 @@ void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
calculate and store in min_eradius and min_erforce
------------------------------------------------------------------------- */
-void PairEffCut::min_xf_get(int ignore)
+void PairEffCut::min_xf_get(int /*ignore*/)
{
double *eradius = atom->eradius;
double *erforce = atom->erforce;
@@ -1050,7 +1050,7 @@ void PairEffCut::min_xf_get(int ignore)
propagate the change back to eradius
------------------------------------------------------------------------- */
-void PairEffCut::min_x_set(int ignore)
+void PairEffCut::min_x_set(int /*ignore*/)
{
double *eradius = atom->eradius;
int *spin = atom->spin;
diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp
index 3b8c9d4201..7304bc4ef6 100644
--- a/src/USER-FEP/fix_adapt_fep.cpp
+++ b/src/USER-FEP/fix_adapt_fep.cpp
@@ -387,7 +387,7 @@ void FixAdaptFEP::init()
/* ---------------------------------------------------------------------- */
-void FixAdaptFEP::setup_pre_force(int vflag)
+void FixAdaptFEP::setup_pre_force(int /*vflag*/)
{
change_settings();
}
@@ -402,7 +402,7 @@ void FixAdaptFEP::setup_pre_force_respa(int vflag, int ilevel)
/* ---------------------------------------------------------------------- */
-void FixAdaptFEP::pre_force(int vflag)
+void FixAdaptFEP::pre_force(int /*vflag*/)
{
if (nevery == 0) return;
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index 5bcb5a7522..529ffe6b09 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -347,7 +347,7 @@ void PairCoulCutSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulCutSoft::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double forcecoul,phicoul;
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index 94bb3659fa..e45dbe72d6 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -348,7 +348,7 @@ void PairCoulLongSoft::read_restart_settings(FILE *fp)
double PairCoulLongSoft::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r,grij,expm2,t,erfc,prefactor;
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 4aaa5c2925..a33445f6f8 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -735,8 +735,8 @@ void PairLJCutSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJCutSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double forcelj,philj;
diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp
index 7a897e1870..965d570863 100644
--- a/src/USER-FEP/pair_morse_soft.cpp
+++ b/src/USER-FEP/pair_morse_soft.cpp
@@ -360,8 +360,8 @@ void PairMorseSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorseSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r, dr, dexp, dexp2, dexp3, phi;
diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp
index 672b70b6f6..eddef5bce8 100644
--- a/src/USER-INTEL/angle_charmm_intel.cpp
+++ b/src/USER-INTEL/angle_charmm_intel.cpp
@@ -332,7 +332,7 @@ void AngleCharmmIntel::init_style()
template <class flt_t, class acc_t>
void AngleCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp
index 74639f3aeb..077825332c 100644
--- a/src/USER-INTEL/angle_harmonic_intel.cpp
+++ b/src/USER-INTEL/angle_harmonic_intel.cpp
@@ -314,7 +314,7 @@ void AngleHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void AngleHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp
index 2d70049a89..88fa65f555 100644
--- a/src/USER-INTEL/bond_fene_intel.cpp
+++ b/src/USER-INTEL/bond_fene_intel.cpp
@@ -291,7 +291,7 @@ void BondFENEIntel::init_style()
template <class flt_t, class acc_t>
void BondFENEIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp
index ed9cab082e..f4ab991b1c 100644
--- a/src/USER-INTEL/bond_harmonic_intel.cpp
+++ b/src/USER-INTEL/bond_harmonic_intel.cpp
@@ -262,7 +262,7 @@ void BondHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void BondHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 6ad25f1ce4..7494fef3bf 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -401,7 +401,7 @@ void DihedralFourierIntel::init_style()
template <class flt_t, class acc_t>
void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1, setflag, nterms, memory);
diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp
index b2bf54102c..57361b9527 100644
--- a/src/USER-INTEL/dihedral_harmonic_intel.cpp
+++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp
@@ -396,7 +396,7 @@ void DihedralHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void DihedralHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index 832ce7ed50..ae2810f662 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -416,7 +416,7 @@ void DihedralOPLSIntel::init_style()
template <class flt_t, class acc_t>
void DihedralOPLSIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 7a206f472a..4c703da833 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -349,7 +349,7 @@ void FixIntel::init()
/* ---------------------------------------------------------------------- */
-void FixIntel::setup(int vflag)
+void FixIntel::setup(int /*vflag*/)
{
if (neighbor->style != Neighbor::BIN)
error->all(FLERR,
@@ -539,7 +539,7 @@ void FixIntel::check_neighbor_intel()
/* ---------------------------------------------------------------------- */
-void FixIntel::pre_reverse(int eflag, int vflag)
+void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/)
{
if (_force_array_m != 0) {
if (_need_reduce) {
@@ -652,7 +652,7 @@ template <class ft, class acc_t>
void FixIntel::add_results(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
const int eatom, const int vatom,
- const int offload) {
+ const int /*offload*/) {
start_watch(TIME_PACK);
int f_length;
#ifdef _LMP_INTEL_OFFLOAD
@@ -719,7 +719,7 @@ void FixIntel::add_results(const ft * _noalias const f_in,
template <class ft, class acc_t>
void FixIntel::add_oresults(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
- const int eatom, const int vatom,
+ const int eatom, const int /*vatom*/,
const int out_offset, const int nall) {
lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset;
if (atom->torque) {
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index 79fb23ab3d..e6e09be503 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -74,7 +74,7 @@ class FixIntel : public Fix {
inline int nbor_pack_width() const { return _nbor_pack_width; }
inline void nbor_pack_width(const int w) { _nbor_pack_width = w; }
inline int three_body_neighbor() { return _three_body_neighbor; }
- inline void three_body_neighbor(const int i) { _three_body_neighbor = 1; }
+ inline void three_body_neighbor(const int /*i*/) { _three_body_neighbor = 1; }
inline int need_zero(const int tid) {
if (_need_reduce == 0 && tid > 0) return 1;
@@ -159,8 +159,8 @@ class FixIntel : public Fix {
inline int host_start_neighbor() { return 0; }
inline int host_start_pair() { return 0; }
inline void zero_timers() {}
- inline void start_watch(const int which) {}
- inline double stop_watch(const int which) { return 0.0; }
+ inline void start_watch(const int /*which*/) {}
+ inline double stop_watch(const int /*which*/) { return 0.0; }
double * off_watch_pair() { return NULL; }
double * off_watch_neighbor() { return NULL; }
inline void balance_stamp() {}
@@ -238,7 +238,7 @@ class FixIntel : public Fix {
/* ---------------------------------------------------------------------- */
-void FixIntel::get_buffern(const int offload, int &nlocal, int &nall,
+void FixIntel::get_buffern(const int /*offload*/, int &nlocal, int &nall,
int &minlocal) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers) {
@@ -273,7 +273,7 @@ void FixIntel::get_buffern(const int offload, int &nlocal, int &nall,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<double,double>::vec3_acc_t *f_in,
- double *ev_in, const int offload,
+ double *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
@@ -301,7 +301,7 @@ void FixIntel::add_result_array(IntelBuffers<double,double>::vec3_acc_t *f_in,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<float,double>::vec3_acc_t *f_in,
- double *ev_in, const int offload,
+ double *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
@@ -329,7 +329,7 @@ void FixIntel::add_result_array(IntelBuffers<float,double>::vec3_acc_t *f_in,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<float,float>::vec3_acc_t *f_in,
- float *ev_in, const int offload,
+ float *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp
index 17bbcff771..a83306def5 100644
--- a/src/USER-INTEL/fix_nve_asphere_intel.cpp
+++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp
@@ -79,7 +79,7 @@ void FixNVEAsphereIntel::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixNVEAsphereIntel::initial_integrate(int vflag)
+void FixNVEAsphereIntel::initial_integrate(int /*vflag*/)
{
double dtfm;
double inertia[3],omega[3];
diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/USER-INTEL/fix_nve_intel.cpp
index c0f6da06ae..7dee31d2f4 100644
--- a/src/USER-INTEL/fix_nve_intel.cpp
+++ b/src/USER-INTEL/fix_nve_intel.cpp
@@ -56,7 +56,7 @@ void FixNVEIntel::setup(int vflag)
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVEIntel::initial_integrate(int vflag)
+void FixNVEIntel::initial_integrate(int /*vflag*/)
{
// update v and x of atoms in group
diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp
index e0ef2162d1..025206dc67 100644
--- a/src/USER-INTEL/improper_cvff_intel.cpp
+++ b/src/USER-INTEL/improper_cvff_intel.cpp
@@ -428,7 +428,7 @@ void ImproperCvffIntel::init_style()
template <class flt_t, class acc_t>
void ImproperCvffIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp
index 60cbe16358..dde67e1d76 100644
--- a/src/USER-INTEL/improper_harmonic_intel.cpp
+++ b/src/USER-INTEL/improper_harmonic_intel.cpp
@@ -384,7 +384,7 @@ void ImproperHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void ImproperHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 0f32cb48b2..ada70a18a4 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -109,7 +109,7 @@ void IntelBuffers<flt_t, acc_t>::free_buffers()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow(const int nall, const int nlocal,
const int nthreads,
- const int offload_end)
+ const int /*offload_end*/)
{
free_buffers();
_buf_size = static_cast<double>(nall) * 1.1 + 1;
@@ -200,7 +200,7 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
+void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int /*offload_end*/)
{
#ifdef _LMP_INTEL_OFFLOAD
free_nmax();
@@ -264,7 +264,7 @@ void IntelBuffers<flt_t, acc_t>::free_list_local()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_list_local(NeighList *list,
- const int offload_end)
+ const int /*offload_end*/)
{
free_list_local();
int size = list->get_maxlocal();
@@ -310,10 +310,10 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
+void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList */*list*/,
const int nlocal,
const int nthreads,
- const int offload_end,
+ const int /*offload_end*/,
const int pack_width)
{
free_nbor_list();
@@ -382,7 +382,7 @@ void IntelBuffers<flt_t, acc_t>::free_ccache()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::grow_ccache(const int off_flag,
+void IntelBuffers<flt_t, acc_t>::grow_ccache(const int /*off_flag*/,
const int nthreads,
const int width)
{
@@ -481,7 +481,7 @@ void IntelBuffers<flt_t, acc_t>::free_ncache()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::grow_ncache(const int off_flag,
+void IntelBuffers<flt_t, acc_t>::grow_ncache(const int /*off_flag*/,
const int nthreads)
{
const int nsize = get_max_nbors() * 3;
diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h
index 8040715b2e..397fa77a7e 100644
--- a/src/USER-INTEL/intel_buffers.h
+++ b/src/USER-INTEL/intel_buffers.h
@@ -135,24 +135,24 @@ class IntelBuffers {
void set_ntypes(const int ntypes, const int use_ghost_cut = 0);
- inline int * firstneigh(const NeighList *list) { return _list_alloc; }
- inline int * cnumneigh(const NeighList *list) { return _cnumneigh; }
+ inline int * firstneigh(const NeighList */*list*/) { return _list_alloc; }
+ inline int * cnumneigh(const NeighList */*list*/) { return _cnumneigh; }
inline int * get_atombin() { return _atombin; }
inline int * get_binpacked() { return _binpacked; }
- inline atom_t * get_x(const int offload = 1) {
+ inline atom_t * get_x(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_x;
#endif
return _x;
}
- inline flt_t * get_q(const int offload = 1) {
+ inline flt_t * get_q(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_q;
#endif
return _q;
}
- inline quat_t * get_quat(const int offload = 1) {
+ inline quat_t * get_quat(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_quat;
#endif
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index 4a86d8db29..2c86ad3520 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -2057,8 +2057,8 @@ public:
}
VEC_INLINE static ivec set(
- int i15, int i14, int i13, int i12, int i11, int i10, int i9, int i8,
- int i7, int i6, int i5, int i4, int i3, int i2, int i1, int i0
+ int /*i15*/, int /*i14*/, int /*i13*/, int /*i12*/, int /*i11*/, int /*i10*/, int /*i9*/, int /*i8*/,
+ int /*i7*/, int /*i6*/, int /*i5*/, int /*i4*/, int /*i3*/, int /*i2*/, int /*i1*/, int i0
) {
return i0;
}
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index ae961e84b5..8be2165deb 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -106,7 +106,7 @@ void NPairFullBinGhostIntel::fbi(NeighList * list,
/* ---------------------------------------------------------------------- */
template<class flt_t, class acc_t, int need_ic>
-void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
+void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
IntelBuffers<flt_t,acc_t> * buffers,
const int pstart, const int pend) {
if (pend-pstart == 0) return;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index 355c8db199..d59cd2304a 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -54,10 +54,10 @@ NPairIntel::~NPairIntel() {
template <class flt_t, class acc_t, int offload_noghost, int need_ic,
int FULL, int TRI, int THREE>
-void NPairIntel::bin_newton(const int offload, NeighList *list,
+void NPairIntel::bin_newton(const int /*offload*/, NeighList *list,
IntelBuffers<flt_t,acc_t> *buffers,
const int astart, const int aend,
- const int offload_end) {
+ const int /*offload_end*/) {
if (aend-astart == 0) return;
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index 07f33f7ebe..601144a3c0 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -2200,7 +2200,7 @@ typedef typename intr_types<flt_t, acc_t>::bvec bvec;
VEC_INLINE inline
static void aut_loadatoms_vec(
AtomAIREBOT<flt_t> * atoms, ivec j_vec,
- fvec *x, fvec * y, fvec * z, bvec * type_mask, int * map, ivec map_i,
+ fvec *x, fvec * y, fvec * z, bvec * type_mask, int * /*map*/, ivec map_i,
ivec c_1
) {
const ivec c_4 = ivec::set1(4);
@@ -2413,7 +2413,7 @@ static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
}
static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- bvec active_mask, int itype, fvec cosjik,
+ bvec /*active_mask*/, int itype, fvec cosjik,
fvec Nij, fvec *dgdc, fvec *dgdN) {
int i;
flt_t * gDom = NULL;
@@ -2835,7 +2835,7 @@ static void aut_frebo_data_writeback(
static void aut_frebo_N_spline_force(
KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
struct aut_frebo_data * _noalias data, int itype, int jtype, ivec vi,
- ivec vj, fvec VA, fvec dN, fvec dNconj, fvec Nconj) {
+ ivec /*vj*/, fvec VA, fvec dN, fvec dNconj, fvec Nconj) {
ivec c_i1 = ivec::set1(1);
fvec c_2 = fvec::set1(2);
fvec c_TOL = fvec::set1(TOL);
@@ -2999,8 +2999,8 @@ static fvec aut_frebo_sum_omega(
KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
struct aut_frebo_data * _noalias i_data,
struct aut_frebo_data * _noalias j_data,
- int itype, int jtype,
- ivec vi, ivec vj,
+ int /*itype*/, int /*jtype*/,
+ ivec /*vi*/, ivec /*vj*/,
fvec r23x, fvec r23y, fvec r23z, fvec r23mag,
fvec VA, fvec fij[3]
) {
@@ -3284,7 +3284,7 @@ static void aut_torsion_vec(
KernelArgsAIREBOT<flt_t,acc_t> * ka,
struct aut_frebo_data * i_data,
struct aut_frebo_data * j_data,
- ivec i, ivec j, fvec wij, fvec dwij
+ ivec /*i*/, ivec /*j*/, fvec wij, fvec dwij
) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -4134,7 +4134,7 @@ exceed_limits:
/*
* Attempt to look up an element in the hash-map.
*/
-static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * /*ka*/,
struct aut_airebo_lj_test_path_result_data * test_path_result,
bvec need_search, ivec i_bc, ivec j,
LennardJonesPathAIREBOT<flt_t> path[fvec::VL]
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index 201277e68d..11ae442c0e 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -784,7 +784,7 @@ void PairEAMIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
/* ---------------------------------------------------------------------- */
int PairEAMIntel::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
return pack_forward_comm(n, list, buf, fp);
diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/USER-INTEL/pair_rebo_intel.cpp
index bc7197000b..3decc0154b 100644
--- a/src/USER-INTEL/pair_rebo_intel.cpp
+++ b/src/USER-INTEL/pair_rebo_intel.cpp
@@ -28,7 +28,7 @@ PairREBOIntel::PairREBOIntel(LAMMPS *lmp) : PairAIREBOIntel(lmp) {}
global settings
------------------------------------------------------------------------- */
-void PairREBOIntel::settings(int narg, char **arg)
+void PairREBOIntel::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp
index d1d52270be..aff8ba88a7 100644
--- a/src/USER-INTEL/pair_sw_intel.cpp
+++ b/src/USER-INTEL/pair_sw_intel.cpp
@@ -173,7 +173,7 @@ template <int SPQ,int ONETYPE,int EFLAG,class flt_t,class acc_t>
void PairSWIntel::eval(const int offload, const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc, const int astart,
- const int aend, const int pad_width)
+ const int aend, const int /*pad_width*/)
{
const int inum = aend - astart;
if (inum == 0) return;
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index 0a41e5d8a5..c7edc15a49 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -723,7 +723,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
double sft, int** p2g, int nup, int nlow,
int nxlo, int nylo, int nzlo,
int nxhi, int nyhi, int nzhi,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> */*buffers*/)
{
int nlocal = atom->nlocal;
int nthr = comm->nthreads;
@@ -790,7 +790,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// clear 3d density array
@@ -940,7 +940,7 @@ void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// clear 3d density array
@@ -1091,7 +1091,7 @@ void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// clear 3d density array
@@ -1225,7 +1225,7 @@ void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
FFT_SCALAR * _noalias global_density = &(density_brick_none[0][nzlo_out_6][nylo_out_6][nxlo_out_6]);
@@ -1373,7 +1373,7 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1520,7 +1520,7 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1725,7 +1725,7 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1869,7 +1869,7 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2069,7 +2069,7 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2282,7 +2282,7 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2594,7 +2594,7 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2755,7 +2755,7 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index 46a55e558a..e5540e6377 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -255,7 +255,7 @@ void PPPMIntel::compute_first(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PPPMIntel::compute_second(int eflag, int vflag)
+void PPPMIntel::compute_second(int /*eflag*/, int /*vflag*/)
{
int i,j;
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 7a0bd0572e..fecd6f2b25 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -646,7 +646,7 @@ void FixLbFluid::init(void)
}
-void FixLbFluid::setup(int vflag)
+void FixLbFluid::setup(int /*vflag*/)
{
//--------------------------------------------------------------------------
// Need to calculate the force on the fluid for a restart run.
@@ -655,7 +655,7 @@ void FixLbFluid::setup(int vflag)
calc_fluidforce();
}
-void FixLbFluid::initial_integrate(int vflag)
+void FixLbFluid::initial_integrate(int /*vflag*/)
{
//--------------------------------------------------------------------------
// Print a header labelling any output printed to the screen.
@@ -711,7 +711,7 @@ void FixLbFluid::initial_integrate(int vflag)
streamout();
}
-void FixLbFluid::post_force(int vflag)
+void FixLbFluid::post_force(int /*vflag*/)
{
if(fixviscouslb==1)
calc_fluidforce();
@@ -741,7 +741,7 @@ void FixLbFluid::grow_arrays(int nmax)
//==========================================================================
// copy values within local atom-based array
//==========================================================================
-void FixLbFluid::copy_arrays(int i, int j, int delflag)
+void FixLbFluid::copy_arrays(int i, int j, int /*delflag*/)
{
hydroF[j][0] = hydroF[i][0];
hydroF[j][1] = hydroF[i][1];
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index 9fd0dab51d..c5c12d6c11 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -118,7 +118,7 @@ void FixLbPC::init()
}
/* ---------------------------------------------------------------------- */
-void FixLbPC::initial_integrate(int vflag) {
+void FixLbPC::initial_integrate(int /*vflag*/) {
double dtfm;
@@ -285,7 +285,7 @@ void FixLbPC::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixLbPC::copy_arrays(int i, int j, int delflag)
+void FixLbPC::copy_arrays(int i, int j, int /*delflag*/)
{
force_old[j][0] = force_old[i][0];
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index dddd060fa4..2601539727 100644
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -1454,7 +1454,7 @@ void FixLbRigidPCSphere::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixLbRigidPCSphere::copy_arrays(int i, int j, int delflag)
+void FixLbRigidPCSphere::copy_arrays(int i, int j, int /*delflag*/)
{
body[j] = body[i];
up[j][0] = up[i][0];
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index 8ee4d8419e..afe23477be 100644
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -109,7 +109,7 @@ void FixLbViscous::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLbViscous::post_force(int vflag)
+void FixLbViscous::post_force(int /*vflag*/)
{
// apply drag force to atoms in group
// direction is opposed to velocity vector
@@ -132,7 +132,7 @@ void FixLbViscous::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLbViscous::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLbViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index 04172d5c92..4e717ce556 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -149,7 +149,7 @@ void FixManifoldForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixManifoldForce::post_force(int vflag)
+void FixManifoldForce::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -177,7 +177,7 @@ void FixManifoldForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixManifoldForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixManifoldForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 4dcc3f9704..3c6c70f6df 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -307,7 +307,7 @@ void FixNVEManifoldRattle::update_var_params()
/* -----------------------------------------------------------------------------
---------------------------------------------------------------------------*/
-int FixNVEManifoldRattle::dof(int igroup)
+int FixNVEManifoldRattle::dof(int /*igroup*/)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -348,7 +348,7 @@ double FixNVEManifoldRattle::memory_usage()
/* -----------------------------------------------------------------------------
---------------------------------------------------------------------------*/
-void FixNVEManifoldRattle::initial_integrate(int vflag)
+void FixNVEManifoldRattle::initial_integrate(int /*vflag*/)
{
update_var_params();
nve_x_rattle(igroup, groupbit);
diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
index 973a5bcf43..2a204d2048 100644
--- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
@@ -229,7 +229,7 @@ void FixNVTManifoldRattle::init()
-void FixNVTManifoldRattle::setup(int vflag)
+void FixNVTManifoldRattle::setup(int /*vflag*/)
{
compute_temp_target();
@@ -371,7 +371,7 @@ void FixNVTManifoldRattle::nh_v_temp()
// Most of this logic is based on fix_nh:
-void FixNVTManifoldRattle::initial_integrate(int vflag)
+void FixNVTManifoldRattle::initial_integrate(int /*vflag*/)
{
update_var_params();
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index 6eb09010ef..b0727c346d 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -61,7 +61,7 @@ namespace user_manifold {
virtual const char *id() = 0;
- virtual void set_atom_id( tagint a_id ){}
+ virtual void set_atom_id( tagint /*a_id*/ ){}
virtual int nparams() = 0;
// double *get_params(){ return params; };
diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/USER-MANIFOLD/manifold_cylinder.cpp
index c13581c640..28062d7a27 100644
--- a/src/USER-MANIFOLD/manifold_cylinder.cpp
+++ b/src/USER-MANIFOLD/manifold_cylinder.cpp
@@ -5,8 +5,8 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int argc,
- char **argv ) : manifold(lmp)
+manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int /*argc*/,
+ char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
index 21d4087d7c..4df4c833d3 100644
--- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
+++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
@@ -8,8 +8,8 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int argc,
- char **argv ) : manifold(lmp)
+manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int /*argc*/,
+ char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp
index fa7edc6e4a..c40a5fff9f 100644
--- a/src/USER-MANIFOLD/manifold_dumbbell.cpp
+++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp
@@ -6,7 +6,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp)
+manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/USER-MANIFOLD/manifold_ellipsoid.cpp
index f590123dc3..d5e7bb146e 100644
--- a/src/USER-MANIFOLD/manifold_ellipsoid.cpp
+++ b/src/USER-MANIFOLD/manifold_ellipsoid.cpp
@@ -4,7 +4,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int narg, char **argv ) : manifold(lmp)
+manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int /*narg*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
index cbb47ef92d..b95162740b 100644
--- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
@@ -133,7 +133,7 @@ public:
// Manifold itself:
manifold_gaussian_bump::manifold_gaussian_bump(class LAMMPS* lmp,
- int narg, char **arg)
+ int /*narg*/, char **/*arg*/)
: manifold(lmp), lut_z(NULL), lut_zp(NULL) {}
diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/USER-MANIFOLD/manifold_plane.cpp
index d33617fbfb..45a1f4b46e 100644
--- a/src/USER-MANIFOLD/manifold_plane.cpp
+++ b/src/USER-MANIFOLD/manifold_plane.cpp
@@ -4,7 +4,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_plane::manifold_plane( LAMMPS *lmp, int argc, char **argv ) :
+manifold_plane::manifold_plane( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) :
manifold(lmp)
{}
@@ -16,7 +16,7 @@ double manifold_plane::g( const double *x )
}
-void manifold_plane::n( const double *x, double *n )
+void manifold_plane::n( const double */*x*/, double *n )
{
n[0] = params[0];
n[1] = params[1];
diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
index ccf0a794da..983702b6f3 100644
--- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
+++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
@@ -5,7 +5,7 @@
using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int argc, char **argv ) :
+manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) :
manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp
index 308190c528..0ca4c67002 100644
--- a/src/USER-MANIFOLD/manifold_spine.cpp
+++ b/src/USER-MANIFOLD/manifold_spine.cpp
@@ -8,7 +8,7 @@ using namespace user_manifold;
-manifold_spine::manifold_spine( LAMMPS *lmp, int argc, char **argv )
+manifold_spine::manifold_spine( LAMMPS *lmp, int /*argc*/, char **/*argv*/ )
: manifold(lmp)
{
power = 4;
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp
index b7eb155ba2..16c4e696d5 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp
@@ -12,7 +12,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int narg, char ** arg)
+manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int /*narg*/, char ** /*arg*/)
: manifold(lmp)
{
// You can NOT depend on proper construction of the domains in
@@ -117,7 +117,7 @@ void manifold_thylakoid::n( const double *x, double *n )
}
}
-thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int *err_flag, std::size_t *idx )
+thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int */*err_flag*/, std::size_t *idx )
{
for( std::size_t i = 0; i < parts.size(); ++i ){
diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp
index 44a17725b5..0b4ca24370 100644
--- a/src/USER-MANIFOLD/manifold_torus.cpp
+++ b/src/USER-MANIFOLD/manifold_torus.cpp
@@ -6,7 +6,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_torus::manifold_torus( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp)
+manifold_torus::manifold_torus( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index de188e497d..2be215c282 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -5,7 +5,7 @@ using namespace LAMMPS_NS;
void
MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
- double* eatom, int ntype, int* type, int* fmap, int& errorflag)
+ double* eatom, int /*ntype*/, int* type, int* fmap, int& errorflag)
{
int i, elti;
int m;
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index e1a7509ab3..4bbaa42596 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -93,7 +93,7 @@ MEAM::meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,
void
MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh,
- int* firstneigh, int numneigh_full, int* firstneigh_full, int ntype, int* type, int* fmap)
+ int* firstneigh, int numneigh_full, int* firstneigh_full, int /*ntype*/, int* type, int* fmap)
{
int jn, j, kn, k;
int elti, eltj, eltk;
@@ -256,7 +256,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
void
-MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
double* scrfcn, double* fcpair)
{
int jn, j, m, n, p, elti, eltj;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 85314dd8a2..06fbb57adb 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -7,7 +7,7 @@ using namespace LAMMPS_NS;
void
MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
- double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+ double* eatom, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom)
{
int j, jn, k, kn, kk, m, n, p, q;
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 7f8ad3d81f..503ee65496 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -3,7 +3,7 @@
using namespace LAMMPS_NS;
void
-MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
+MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha,
double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
int* ibar)
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 027e4c27a7..da0e4c1d28 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -195,7 +195,7 @@ void PairMEAMC::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMC::settings(int narg, char **arg)
+void PairMEAMC::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -312,7 +312,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMC::init_one(int i, int j)
+double PairMEAMC::init_one(int /*i*/, int /*j*/)
{
return cutmax;
}
@@ -598,7 +598,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAMC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,m;
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 8b03e05181..24bef2b1f7 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -87,7 +87,7 @@ void FixEDPDSource::init()
/* ---------------------------------------------------------------------- */
-void FixEDPDSource::post_force(int vflag)
+void FixEDPDSource::post_force(int /*vflag*/)
{
double **x = atom->x;
double *edpd_flux = atom->edpd_flux;
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index c97a2d779c..f663165f78 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -72,7 +72,7 @@ void FixMvvDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvDPD::initial_integrate(int vflag)
+void FixMvvDPD::initial_integrate(int /*vflag*/)
{
double dtfm;
double **x = atom->x;
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index 89a831e121..8719d0d262 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -78,7 +78,7 @@ void FixMvvEDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvEDPD::initial_integrate(int vflag)
+void FixMvvEDPD::initial_integrate(int /*vflag*/)
{
double dtfm,dtT;
// update v and x and cc of atoms in group
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index e16171800b..24b1bbcf48 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -76,7 +76,7 @@ void FixMvvTDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvTDPD::initial_integrate(int vflag)
+void FixMvvTDPD::initial_integrate(int /*vflag*/)
{
double dtfm;
// update v and x and cc of atoms in group
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index 64964a4c98..89e8005b43 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -88,7 +88,7 @@ void FixTDPDSource::init()
/* ---------------------------------------------------------------------- */
-void FixTDPDSource::post_force(int vflag)
+void FixTDPDSource::post_force(int /*vflag*/)
{
double **x = atom->x;
double **cc_flux = atom->cc_flux;
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index 351637a842..5ed63a2a8b 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -530,7 +530,7 @@ void PairEDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairEDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
double *T = atom->edpd_temp;
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index 1264d03ed3..d705285584 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -186,7 +186,7 @@ void PairMDPDRhoSum::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairMDPDRhoSum::settings(int narg, char **arg) {
+void PairMDPDRhoSum::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,"Illegal number of setting arguments for pair_style mdpd/rhosum");
}
@@ -236,8 +236,8 @@ double PairMDPDRhoSum::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce) {
+double PairMDPDRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
+ double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
@@ -246,7 +246,7 @@ double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc) {
+ int /*pbc_flag*/, int */*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index b8bbf6d622..821d8c0486 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -465,8 +465,8 @@ void PairTDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairTDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairTDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp
index bac405bcbb..347bc9cc69 100644
--- a/src/USER-MGPT/pair_mgpt.cpp
+++ b/src/USER-MGPT/pair_mgpt.cpp
@@ -79,7 +79,7 @@ static double gettime(int x = 0) {
return 0.0;
}
#else
-static double gettime(int x = 0) { return 0.0; }
+static double gettime(int /*x*/ = 0) { return 0.0; }
#endif
@@ -1805,7 +1805,7 @@ void PairMGPT::allocate()
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
-void PairMGPT::settings(int narg, char **arg)
+void PairMGPT::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(__FILE__,__LINE__,"Illegal pair_style command");
}
@@ -2025,7 +2025,7 @@ void PairMGPT::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMGPT::init_one(int i, int j)
+double PairMGPT::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index bcb631c61f..c4186da472 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -229,7 +229,7 @@ void AngleDipole::write_data(FILE *fp)
used by ComputeAngleLocal
------------------------------------------------------------------------- */
-double AngleDipole::single(int type, int iRef, int iDip, int iDummy)
+double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
{
double **x = atom->x; // position vector
double **mu = atom->mu; // point-dipole components and moment magnitude
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index 7148c5438d..b34f71e888 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -203,7 +203,7 @@ void BondHarmonicShift::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonicShift::single(int type, double rsq, int i, int j,
+double BondHarmonicShift::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 20c8a1a300..a58df70878 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -205,7 +205,7 @@ void BondHarmonicShiftCut::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonicShiftCut::single(int type, double rsq, int i, int j,
+double BondHarmonicShiftCut::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
fforce = 0.0;
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index a17aefe71b..bcf41591eb 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -105,7 +105,7 @@ void ComputeAcklandAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeAcklandAtom::init_list(int id, NeighList *ptr)
+void ComputeAcklandAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 4d8627a11f..3b9b38343d 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -85,7 +85,7 @@ void ComputeBasalAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeBasalAtom::init_list(int id, NeighList *ptr)
+void ComputeBasalAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp
index 51cf3ab07a..6fa16f1a9a 100644
--- a/src/USER-MISC/compute_cnp_atom.cpp
+++ b/src/USER-MISC/compute_cnp_atom.cpp
@@ -121,7 +121,7 @@ void ComputeCNPAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCNPAtom::init_list(int id, NeighList *ptr)
+void ComputeCNPAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp
index 922f2aaf5e..4946bc437e 100644
--- a/src/USER-MISC/compute_entropy_atom.cpp
+++ b/src/USER-MISC/compute_entropy_atom.cpp
@@ -151,7 +151,7 @@ void ComputeEntropyAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeEntropyAtom::init_list(int id, NeighList *ptr)
+void ComputeEntropyAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index 654911769c..2cd1ac7527 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -164,7 +164,7 @@ void FixAddTorque::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddTorque::post_force(int vflag)
+void FixAddTorque::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -252,7 +252,7 @@ void FixAddTorque::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddTorque::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAddTorque::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index da6d041287..0ce6121bf9 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -412,7 +412,7 @@ void FixAveCorrelateLong::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveCorrelateLong::setup(int vflag)
+void FixAveCorrelateLong::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 5ce1f11475..cd7918f4dd 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -588,7 +588,7 @@ void FixBondReact::init()
/* ---------------------------------------------------------------------- */
-void FixBondReact::init_list(int id, NeighList *ptr)
+void FixBondReact::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -2621,7 +2621,7 @@ double FixBondReact::compute_vector(int n)
/* ---------------------------------------------------------------------- */
-void FixBondReact::post_integrate_respa(int ilevel, int iloop)
+void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -2629,7 +2629,7 @@ void FixBondReact::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index 91c7033513..4a6b3226d4 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -705,7 +705,7 @@ double FixFilterCorotate::compute_array(int,int)
return 1;
}
-void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixFilterCorotate::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1)
{
@@ -717,7 +717,7 @@ void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop)
}
}
-void FixFilterCorotate::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFilterCorotate::post_force_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1)
{
@@ -1699,7 +1699,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
}
int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
double**f = atom->f;
@@ -1839,7 +1839,7 @@ double FixFilterCorotate::memory_usage()
* copy values within local atom-based arrays
* ------------------------------------------------------------------------- */
-void FixFilterCorotate::copy_arrays(int i, int j, int delflag)
+void FixFilterCorotate::copy_arrays(int i, int j, int /*delflag*/)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp
index 6a1e508030..b6366ec509 100644
--- a/src/USER-MISC/fix_flow_gauss.cpp
+++ b/src/USER-MISC/fix_flow_gauss.cpp
@@ -155,7 +155,7 @@ void FixFlowGauss::setup(int vflag)
/* ----------------------------------------------------------------------
this is where Gaussian dynamics constraint is applied
------------------------------------------------------------------------- */
-void FixFlowGauss::post_force(int vflag)
+void FixFlowGauss::post_force(int /*vflag*/)
{
double **f = atom->f;
double **v = atom->v;
@@ -222,7 +222,7 @@ void FixFlowGauss::post_force(int vflag)
}
-void FixFlowGauss::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFlowGauss::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 584b33bfe7..0b08fab4ca 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -582,7 +582,7 @@ void FixGLE::gle_integrate()
energy += deltae*0.5*force->mvv2e;
}
-void FixGLE::initial_integrate(int vflag)
+void FixGLE::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -685,7 +685,7 @@ void FixGLE::final_integrate()
}
/* ---------------------------------------------------------------------- */
-void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixGLE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -699,7 +699,7 @@ void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop)
else { final_integrate();}
}
-void FixGLE::final_integrate_respa(int ilevel, int iloop)
+void FixGLE::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -793,7 +793,7 @@ void FixGLE::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixGLE::copy_arrays(int i, int j, int delflag)
+void FixGLE::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < 3*ns; k++) gle_s[j][k] = gle_s[i][k];
}
@@ -868,7 +868,7 @@ void FixGLE::unpack_restart(int nlocal, int nth)
fixes on a given processor.
------------------------------------------------------------------------- */
-int FixGLE::size_restart(int nlocal)
+int FixGLE::size_restart(int /*nlocal*/)
{
return 3*ns+1;
}
diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp
index a5f8c34448..635acf705c 100644
--- a/src/USER-MISC/fix_grem.cpp
+++ b/src/USER-MISC/fix_grem.cpp
@@ -256,7 +256,7 @@ void FixGrem::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGrem::post_force(int vflag)
+void FixGrem::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index abf9e7cb0b..1c3eafdc46 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -811,7 +811,7 @@ void FixIMD::ioworker()
/* ---------------------------------------------------------------------- */
/* Main IMD protocol handler:
* Send coodinates, energies, and add IMD forces to atoms. */
-void FixIMD::post_force(int vflag)
+void FixIMD::post_force(int /*vflag*/)
{
/* check for reconnect */
if (imd_inactive) {
@@ -1153,7 +1153,7 @@ void FixIMD::post_force(int vflag)
}
/* ---------------------------------------------------------------------- */
-void FixIMD::post_force_respa(int vflag, int ilevel, int iloop)
+void FixIMD::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
/* only process IMD on the outmost RESPA level. */
if (ilevel == nlevels_respa-1) post_force(vflag);
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index c4750ce49e..32892d87a8 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -269,7 +269,7 @@ void FixIPI::init()
neighbor->every = 1;
}
-void FixIPI::initial_integrate(int vflag)
+void FixIPI::initial_integrate(int /*vflag*/)
{
/* This is called at the beginning of the integration loop,
* and will be used to read positions from the socket. Then,
diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp
index dbf7b56fe2..2ac2a7c9fc 100644
--- a/src/USER-MISC/fix_nvk.cpp
+++ b/src/USER-MISC/fix_nvk.cpp
@@ -94,7 +94,7 @@ void FixNVK::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVK::initial_integrate(int vflag)
+void FixNVK::initial_integrate(int /*vflag*/)
{
double sm;
double a,b,sqtb,s,sdot;
@@ -190,7 +190,7 @@ void FixNVK::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVK::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel];
@@ -204,7 +204,7 @@ void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVK::final_integrate_respa(int ilevel, int iloop)
+void FixNVK::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel];
final_integrate();
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index e65ae6ae28..506590f02c 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -214,7 +214,7 @@ void FixPIMD::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPIMD::initial_integrate(int vflag)
+void FixPIMD::initial_integrate(int /*vflag*/)
{
nhc_update_v();
nhc_update_x();
@@ -229,7 +229,7 @@ void FixPIMD::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixPIMD::post_force(int flag)
+void FixPIMD::post_force(int /*flag*/)
{
for(int i=0; i<atom->nlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np;
@@ -686,7 +686,7 @@ void FixPIMD::comm_exec(double **ptr)
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
@@ -744,7 +744,7 @@ void FixPIMD::grow_arrays(int nmax)
/* ---------------------------------------------------------------------- */
-void FixPIMD::copy_arrays(int i, int j, int delflag)
+void FixPIMD::copy_arrays(int i, int j, int /*delflag*/)
{
int i_pos = i*3;
int j_pos = j*3;
@@ -832,7 +832,7 @@ int FixPIMD::maxsize_restart()
/* ---------------------------------------------------------------------- */
-int FixPIMD::size_restart(int nlocal)
+int FixPIMD::size_restart(int /*nlocal*/)
{
return size_peratom_cols+1;
}
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
index bbc4ce417a..78d63b79a8 100644
--- a/src/USER-MISC/fix_rhok.cpp
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -144,7 +144,7 @@ FixRhok::min_setup( int inVFlag )
// Modify the forces calculated in the main force loop of ordinary MD
void
-FixRhok::post_force( int inVFlag )
+FixRhok::post_force( int /*inVFlag*/ )
{
double **x = atom->x;
double **f = atom->f;
@@ -206,7 +206,7 @@ FixRhok::post_force( int inVFlag )
// Forces in RESPA loop
void
-FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop )
+FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ )
{
if( inILevel == mNLevelsRESPA - 1 )
post_force( inVFlag );
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index a42690c280..cbebdebdbf 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -461,7 +461,7 @@ void FixSMD::restart(char *buf)
/* ---------------------------------------------------------------------- */
-void FixSMD::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSMD::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index e4d85e8674..ebc161ff99 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -145,7 +145,7 @@ void FixSRP::init()
insert bond particles
------------------------------------------------------------------------- */
-void FixSRP::setup_pre_force(int zz)
+void FixSRP::setup_pre_force(int /*zz*/)
{
double **x = atom->x;
double **xold;
@@ -394,7 +394,7 @@ void FixSRP::grow_arrays(int nmax)
called when move to new proc
------------------------------------------------------------------------- */
-void FixSRP::copy_arrays(int i, int j, int delflag)
+void FixSRP::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2; m++)
array[j][m] = array[i][m];
@@ -589,7 +589,7 @@ int FixSRP::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixSRP::size_restart(int nlocal)
+int FixSRP::size_restart(int /*nlocal*/)
{
return 3;
}
@@ -632,7 +632,7 @@ void FixSRP::restart(char *buf)
pair srp sets the bond type in this fix
------------------------------------------------------------------------- */
-int FixSRP::modify_param(int narg, char **arg)
+int FixSRP::modify_param(int /*narg*/, char **arg)
{
if (strcmp(arg[0],"btype") == 0) {
btype = atoi(arg[1]);
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 5812142763..305e29e033 100644
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -167,7 +167,7 @@ void FixTISpring::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::post_force(int vflag)
+void FixTISpring::post_force(int /*vflag*/)
{
// do not calculate forces during equilibration
if ((update->ntimestep - t0) < t_equil) return;
@@ -200,7 +200,7 @@ void FixTISpring::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTISpring::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -214,7 +214,7 @@ void FixTISpring::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::initial_integrate(int vflag)
+void FixTISpring::initial_integrate(int /*vflag*/)
{
// Update the coupling parameter value if needed
if ((update->ntimestep - t0) < t_equil) return;
@@ -278,7 +278,7 @@ void FixTISpring::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixTISpring::copy_arrays(int i, int j, int delflag)
+void FixTISpring::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -354,7 +354,7 @@ int FixTISpring::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTISpring::size_restart(int nlocal)
+int FixTISpring::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index 1e1e62b638..65f8e90ec3 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -357,7 +357,7 @@ void FixTTMMod::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force(int vflag)
+void FixTTMMod::post_force(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
@@ -451,7 +451,7 @@ void FixTTMMod::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_setup(int vflag)
+void FixTTMMod::post_force_setup(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -468,14 +468,14 @@ void FixTTMMod::post_force_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTTMMod::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int iloop)
+void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
@@ -916,7 +916,7 @@ int FixTTMMod::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTTMMod::size_restart(int nlocal)
+int FixTTMMod::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp
index 82a78d3e73..33bf636e64 100644
--- a/src/USER-MISC/fix_wall_region_ees.cpp
+++ b/src/USER-MISC/fix_wall_region_ees.cpp
@@ -149,7 +149,7 @@ void FixWallRegionEES::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegionEES::post_force(int vflag)
+void FixWallRegionEES::post_force(int /*vflag*/)
{
//sth is needed here, but I dont know what
//that is calculation of sn
@@ -246,7 +246,7 @@ void FixWallRegionEES::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 11bf2ae01e..3bba690e19 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -246,7 +246,7 @@ void PairAGNI::allocate()
global settings
------------------------------------------------------------------------- */
-void PairAGNI::settings(int narg, char **arg)
+void PairAGNI::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index 457d75bc77..61d32892fc 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -391,8 +391,8 @@ void PairBuckMDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBuckMDF::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBuckMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index 3f07df3d98..0154e89731 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -326,7 +326,7 @@ void PairCoulDiel::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulDiel::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r, rarg,forcedielec,phidielec;
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index deec7da81f..11df975c19 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -341,7 +341,7 @@ void PairCoulShield::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulShield::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r, rarg,Vc,fvc,forcecoul,phishieldec;
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 2976d7ad73..4716e271d7 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -621,7 +621,7 @@ void PairEDIP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEDIP::settings(int narg, char **arg)
+void PairEDIP::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index 6be57eee74..fc76aadb0b 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -516,7 +516,7 @@ void PairEDIPMulti::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEDIPMulti::settings(int narg, char **arg)
+void PairEDIPMulti::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index 5a8cdf2884..49c562471f 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -442,7 +442,7 @@ void PairExTeP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairExTeP::settings(int narg, char **arg)
+void PairExTeP::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 85f7c02887..a000eff028 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -374,8 +374,8 @@ void PairGaussCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGaussCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r, rexp,ugauss,phigauss;
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 30ee2e7a5a..2aecbe5d19 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -1010,8 +1010,8 @@ void PairILPGrapheneHBN::read_file(char *filename)
/* ---------------------------------------------------------------------- */
-double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,r2inv,r6inv,r8inv,forcelj,philj,fpair;
@@ -1047,7 +1047,7 @@ double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq
/* ---------------------------------------------------------------------- */
int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m,id,ip,l;
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index be0e81d48d..4c1f36c640 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -1015,8 +1015,8 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
/* ---------------------------------------------------------------------- */
-double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,r2inv,r6inv,r8inv,forcelj,philj;
@@ -1050,7 +1050,7 @@ double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, doub
/* ---------------------------------------------------------------------- */
int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m,l,ip,id;
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index f6e7f7f56b..45d0da4d83 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -352,9 +352,9 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJ_AB_MDF::single(int i, int j, int itype, int jtype,
+double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index d43a6c3086..891239016b 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -352,9 +352,9 @@ void PairLJMDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJMDF::single(int i, int j, int itype, int jtype,
+double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 750f6ac5bb..1305891b33 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -360,7 +360,7 @@ void PairMEAMSpline::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMSpline::settings(int narg, char **arg)
+void PairMEAMSpline::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -592,7 +592,7 @@ void PairMEAMSpline::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMSpline::init_one(int i, int j)
+double PairMEAMSpline::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
@@ -600,7 +600,7 @@ double PairMEAMSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -618,14 +618,14 @@ void PairMEAMSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSpline::pack_reverse_comm(int n, int first, double *buf)
+int PairMEAMSpline::pack_reverse_comm(int /*n*/, int /*first*/, double */*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSpline::unpack_reverse_comm(int n, int *list, double *buf)
+void PairMEAMSpline::unpack_reverse_comm(int /*n*/, int */*list*/, double */*buf*/)
{
}
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index f6b7212f9c..be0ac1c35b 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -372,7 +372,7 @@ void PairMEAMSWSpline::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMSWSpline::settings(int narg, char **arg)
+void PairMEAMSWSpline::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -552,7 +552,7 @@ void PairMEAMSWSpline::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMSWSpline::init_one(int i, int j)
+double PairMEAMSWSpline::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
@@ -560,7 +560,7 @@ double PairMEAMSWSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -578,14 +578,14 @@ void PairMEAMSWSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSWSpline::pack_reverse_comm(int n, int first, double *buf)
+int PairMEAMSWSpline::pack_reverse_comm(int /*n*/, int /*first*/, double */*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSWSpline::unpack_reverse_comm(int n, int *list, double *buf)
+void PairMEAMSWSpline::unpack_reverse_comm(int /*n*/, int */*list*/, double */*buf*/)
{
}
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 12a40bb08b..927181ebf6 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -365,8 +365,8 @@ void PairMomb::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMomb::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMomb::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 8a9c89cf69..328c1bd27b 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -337,8 +337,8 @@ void PairMorseSmoothLinear::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorseSmoothLinear::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorseSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index c2362b8de9..d7e28a1e40 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -719,7 +719,7 @@ void PairTersoffTable::allocate()
global settings
------------------------------------------------------------------------- */
-void PairTersoffTable::settings(int narg, char **arg)
+void PairTersoffTable::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index b5800db2be..352c28be4d 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -309,7 +309,7 @@ void AngleCosineBuck6d::init_style()
/* ---------------------------------------------------------------------- */
-double AngleCosineBuck6d::equilibrium_angle(int i)
+double AngleCosineBuck6d::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index 3a37c67a38..cdbe4068bc 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -299,7 +299,7 @@ void FixPhonon::init()
/* ---------------------------------------------------------------------- */
-void FixPhonon::setup(int flag)
+void FixPhonon::setup(int /*flag*/)
{
// initialize accumulating variables
for (int i = 0; i < sysdim; ++i) TempSum[i] = 0.;
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index fa5ee75bcb..e8a4f85eaa 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -424,7 +424,7 @@ void FixQBMSST::init()
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixQBMSST::setup(int vflag)
+void FixQBMSST::setup(int /*vflag*/)
{
lagrangian_position = 0.0;
@@ -507,7 +507,7 @@ void FixQBMSST::setup(int vflag)
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixQBMSST::initial_integrate(int vflag)
+void FixQBMSST::initial_integrate(int /*vflag*/)
{
int sd;
sd = direction;
@@ -1157,7 +1157,7 @@ void FixQBMSST::grow_arrays(int nmax)
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixQBMSST::copy_arrays(int i, int j, int delflag)
+void FixQBMSST::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2*N_f; m++) {
random_array_0[j][m] = random_array_0[i][m];
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index 7f9a6510be..015f953b8e 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -239,7 +239,7 @@ void FixQTB::setup(int vflag)
/* ----------------------------------------------------------------------
post_force
------------------------------------------------------------------------- */
-void FixQTB::post_force(int vflag)
+void FixQTB::post_force(int /*vflag*/)
{
double gamma1,gamma3;
@@ -334,7 +334,7 @@ void FixQTB::post_force(int vflag)
/* ----------------------------------------------------------------------
post_force_respa
------------------------------------------------------------------------- */
-void FixQTB::post_force_respa(int vflag, int ilevel, int iloop)
+void FixQTB::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -392,7 +392,7 @@ void FixQTB::grow_arrays(int nmax)
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixQTB::copy_arrays(int i, int j, int delflag)
+void FixQTB::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2*N_f; m++) {
random_array_0[j][m] = random_array_0[i][m];
diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp
index 0c00a5ef59..6f5040d037 100644
--- a/src/USER-QUIP/pair_quip.cpp
+++ b/src/USER-QUIP/pair_quip.cpp
@@ -212,7 +212,7 @@ void PairQUIP::compute(int eflag, int vflag)
global settings
------------------------------------------------------------------------- */
-void PairQUIP::settings(int narg, char **arg)
+void PairQUIP::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid") == 0)
@@ -315,7 +315,7 @@ void PairQUIP::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairQUIP::init_one(int i, int j)
+double PairQUIP::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index a2f4d3d0e9..a6e59f7620 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -381,7 +381,7 @@ void FixQEqReax::init()
/* ---------------------------------------------------------------------- */
-void FixQEqReax::init_list(int id, NeighList *ptr)
+void FixQEqReax::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -485,7 +485,7 @@ void FixQEqReax::init_storage()
/* ---------------------------------------------------------------------- */
-void FixQEqReax::pre_force(int vflag)
+void FixQEqReax::pre_force(int /*vflag*/)
{
double t_start, t_end;
@@ -518,7 +518,7 @@ void FixQEqReax::pre_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEqReax::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixQEqReax::pre_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) pre_force(vflag);
}
@@ -833,7 +833,7 @@ void FixQEqReax::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEqReax::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int m;
@@ -952,7 +952,7 @@ void FixQEqReax::grow_arrays(int nmax)
copy values within fictitious charge arrays
------------------------------------------------------------------------- */
-void FixQEqReax::copy_arrays(int i, int j, int delflag)
+void FixQEqReax::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp
index df06217993..df1d7db085 100644
--- a/src/USER-REAXC/fix_reaxc.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -105,7 +105,7 @@ void FixReaxC::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixReaxC::copy_arrays(int i, int j, int delflag)
+void FixReaxC::copy_arrays(int i, int j, int /*delflag*/)
{
num_bonds[j] = num_bonds[i];
num_hbonds[j] = num_hbonds[i];
@@ -136,7 +136,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixReaxC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index b38d137412..f3e592a682 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -112,7 +112,7 @@ int FixReaxCBonds::setmask()
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::setup(int vflag)
+void FixReaxCBonds::setup(int /*vflag*/)
{
end_of_step();
}
@@ -137,7 +137,7 @@ void FixReaxCBonds::end_of_step()
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
+void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE */*fp*/)
{
int i, j;
@@ -185,7 +185,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::FindBond(struct _reax_list *lists, int &numbonds)
+void FixReaxCBonds::FindBond(struct _reax_list */*lists*/, int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj;
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 61b4cebf96..abb8708d8d 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -281,7 +281,7 @@ int FixReaxCSpecies::setmask()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::setup(int vflag)
+void FixReaxCSpecies::setup(int /*vflag*/)
{
ntotal = static_cast<int> (atom->natoms);
if (Name == NULL)
@@ -427,7 +427,7 @@ void FixReaxCSpecies::create_fix()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::init_list(int id, NeighList *ptr)
+void FixReaxCSpecies::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -442,7 +442,7 @@ void FixReaxCSpecies::post_integrate()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
+void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE */*fp*/)
{
int Nmole, Nspec;
@@ -946,7 +946,7 @@ int FixReaxCSpecies::nint(const double &r)
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 7f77d875bc..378d20952c 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -751,7 +751,7 @@ int PairReaxC::write_reax_lists()
/* ---------------------------------------------------------------------- */
-void PairReaxC::read_reax_forces(int vflag)
+void PairReaxC::read_reax_forces(int /*vflag*/)
{
for( int i = 0; i < system->N; ++i ) {
system->my_atoms[i].f[0] = workspace->f[i][0];
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index a07f090f92..14906a2a9c 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -39,8 +39,8 @@
important: we cannot know the exact number of atoms that will fall into a
process's box throughout the whole simulation. therefore
we need to make upper bound estimates for various data structures */
-int PreAllocate_Space( reax_system *system, control_params *control,
- storage *workspace, MPI_Comm comm )
+int PreAllocate_Space( reax_system *system, control_params */*control*/,
+ storage */*workspace*/, MPI_Comm comm )
{
int mincap = system->mincap;
double safezone = system->safezone;
@@ -68,8 +68,8 @@ int PreAllocate_Space( reax_system *system, control_params *control,
/************* system *************/
-int Allocate_System( reax_system *system, int local_cap, int total_cap,
- char *msg )
+int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap,
+ char */*msg*/ )
{
system->my_atoms = (reax_atom*)
realloc( system->my_atoms, total_cap*sizeof(reax_atom) );
@@ -116,7 +116,7 @@ void DeAllocate_System( reax_system *system )
/************* workspace *************/
-void DeAllocate_Workspace( control_params *control, storage *workspace )
+void DeAllocate_Workspace( control_params */*control*/, storage *workspace )
{
int i;
@@ -204,9 +204,9 @@ void DeAllocate_Workspace( control_params *control, storage *workspace )
}
-int Allocate_Workspace( reax_system *system, control_params *control,
+int Allocate_Workspace( reax_system */*system*/, control_params */*control*/,
storage *workspace, int local_cap, int total_cap,
- MPI_Comm comm, char *msg )
+ MPI_Comm comm, char */*msg*/ )
{
int i, total_real, total_rvec, local_rvec;
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 468164a2c0..02df9ec518 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -359,8 +359,8 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut,
}
-void BO( reax_system *system, control_params *control, simulation_data *data,
- storage *workspace, reax_list **lists, output_controls *out_control )
+void BO( reax_system *system, control_params */*control*/, simulation_data */*data*/,
+ storage *workspace, reax_list **lists, output_controls */*out_control*/ )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index;
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 9678addd6b..a26f70c543 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -31,9 +31,9 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-void Bonds( reax_system *system, control_params *control,
+void Bonds( reax_system *system, control_params */*control*/,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+ output_controls */*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index 00b29824ea..56501eeda0 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -41,9 +41,9 @@
interaction_function Interaction_Functions[NUM_INTRS];
-void Dummy_Interaction( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Dummy_Interaction( reax_system */*system*/, control_params */*control*/,
+ simulation_data */*data*/, storage */*workspace*/,
+ reax_list **/*lists*/, output_controls */*out_control*/ )
{
}
@@ -68,7 +68,7 @@ void Init_Force_Functions( control_params *control )
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+ MPI_Comm /*comm*/ )
{
int i;
@@ -83,7 +83,7 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+ MPI_Comm /*comm*/ )
{
/* van der Waals and Coulomb interactions */
@@ -98,7 +98,7 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, mpi_datatypes *mpi_data )
+ reax_list **lists, mpi_datatypes */*mpi_data*/ )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
@@ -114,8 +114,8 @@ void Compute_Total_Force( reax_system *system, control_params *control,
}
-void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
- int step, int n, int N, int numH, MPI_Comm comm )
+void Validate_Lists( reax_system *system, storage */*workspace*/, reax_list **lists,
+ int step, int /*n*/, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
@@ -173,7 +173,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
+ reax_list **lists, output_controls */*out_control*/,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
@@ -317,7 +317,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
- int *bond_top, int *num_3body, MPI_Comm comm )
+ int *bond_top, int *num_3body, MPI_Comm /*comm*/ )
{
int i, j, pj;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index cb516b24f7..c0b3121a40 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -33,7 +33,7 @@
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls */*out_control*/ )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index 4af21284f2..33614c7c68 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -36,7 +36,7 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-int Init_System( reax_system *system, control_params *control, char *msg )
+int Init_System( reax_system *system, control_params *control, char */*msg*/ )
{
int i;
reax_atom *atom;
@@ -66,7 +66,7 @@ int Init_System( reax_system *system, control_params *control, char *msg )
int Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, char *msg )
+ simulation_data *data, char */*msg*/ )
{
Reset_Simulation_Data( data, control->virial );
@@ -139,8 +139,8 @@ int Init_Workspace( reax_system *system, control_params *control,
/************** setup communication data structures **************/
-int Init_MPI_Datatypes( reax_system *system, storage *workspace,
- mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
+int Init_MPI_Datatypes( reax_system *system, storage */*workspace*/,
+ mpi_datatypes *mpi_data, MPI_Comm comm, char */*msg*/ )
{
/* setup the world */
@@ -151,8 +151,8 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
}
int Init_Lists( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- mpi_datatypes *mpi_data, char *msg )
+ simulation_data */*data*/, storage */*workspace*/, reax_list **lists,
+ mpi_datatypes *mpi_data, char */*msg*/ )
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 4d58f7514d..030912d4b7 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -88,7 +88,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
/************************ close output files ************************/
int Close_Output_Files( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+ output_controls *out_control, mpi_datatypes */*mpi_data*/ )
{
if( out_control->write_steps > 0 )
End_Traj( system->my_rank, out_control );
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 9db8b7b9f6..8cc1555c59 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -151,7 +151,7 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double
int Init_Lookup_Tables( reax_system *system, control_params *control,
- storage *workspace, mpi_datatypes *mpi_data, char *msg )
+ storage *workspace, mpi_datatypes *mpi_data, char */*msg*/ )
{
int i, j, r;
int num_atom_types;
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index ce5b966529..e599a3d86e 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -32,7 +32,7 @@
void Atom_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+ output_controls */*out_control*/ )
{
int i, j, pj, type_i, type_j;
double Delta_lpcorr, dfvl;
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index 9c223428a6..731b1602e9 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -33,7 +33,7 @@
void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls */*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i, flag;
@@ -206,7 +206,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
- output_controls *out_control )
+ output_controls */*out_control*/ )
{
int i, j, pj, r, natoms;
int type_i, type_j, tmin, tmax;
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index 4ec744e7b1..1b16f10aee 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -87,7 +87,7 @@ void Reset_Pressures( simulation_data *data )
}
-void Reset_Simulation_Data( simulation_data* data, int virial )
+void Reset_Simulation_Data( simulation_data* data, int /*virial*/ )
{
Reset_Energies( &data->my_en );
Reset_Energies( &data->sys_en );
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index c5a7f23b30..d6f38d3765 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -41,7 +41,7 @@ double Calculate_Omega( rvec dvec_ij, double r_ij,
three_body_interaction_data *p_jkl,
rvec dcos_omega_di, rvec dcos_omega_dj,
rvec dcos_omega_dk, rvec dcos_omega_dl,
- output_controls *out_control )
+ output_controls */*out_control*/ )
{
double unnorm_cos_omega, unnorm_sin_omega, omega;
double sin_ijk, cos_ijk, sin_jkl, cos_jkl;
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index ae2bba2150..f980120a59 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -48,7 +48,7 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
}
-void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data,
+void Write_Skip_Line( output_controls *out_control, mpi_datatypes */*mpi_data*/,
int my_rank, int skip, int num_section )
{
if( my_rank == MASTER_NODE )
@@ -259,7 +259,7 @@ int Write_Header( reax_system *system, control_params *control,
}
-int Write_Init_Desc( reax_system *system, control_params *control,
+int Write_Init_Desc( reax_system *system, control_params */*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, cnt, buffer_len, buffer_req;
@@ -482,7 +482,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
-int Write_Atoms( reax_system *system, control_params *control,
+int Write_Atoms( reax_system *system, control_params */*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, line_len, buffer_len, buffer_req, cnt;
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index c92996e56b..35342c9173 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -76,7 +76,7 @@ void Calculate_dCos_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk,
void Valence_Angles( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls */*out_control*/ )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index e99f3c5169..97a2fb0349 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -208,7 +208,7 @@ void AtomVecSMD::copy(int i, int j, int delflag) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int AtomVecSMD::pack_comm(int /*n*/, int */*list*/, double */*buf*/, int /*pbc_flag*/, int */*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -333,7 +333,7 @@ int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_comm(int n, int first, double *buf) {
+void AtomVecSMD::unpack_comm(int /*n*/, int /*first*/, double */*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -441,7 +441,7 @@ int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int AtomVecSMD::pack_border(int /*n*/, int */*list*/, double */*buf*/, int /*pbc_flag*/, int */*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -633,7 +633,7 @@ int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_border(int n, int first, double *buf) {
+void AtomVecSMD::unpack_border(int /*n*/, int /*first*/, double */*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -1098,7 +1098,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
-int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
+int AtomVecSMD::data_atom_hybrid(int /*nlocal*/, char **/*values*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1120,7 +1120,7 @@ void AtomVecSMD::data_vel(int m, char **values) {
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
-int AtomVecSMD::data_vel_hybrid(int m, char **values) {
+int AtomVecSMD::data_vel_hybrid(int /*m*/, char **/*values*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1158,7 +1158,7 @@ void AtomVecSMD::pack_data(double **buf) {
pack hybrid atom info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
+int AtomVecSMD::pack_data_hybrid(int /*i*/, double */*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1180,7 +1180,7 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
write hybrid atom info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
+int AtomVecSMD::write_data_hybrid(FILE */*fp*/, double */*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1203,7 +1203,7 @@ void AtomVecSMD::pack_vel(double **buf) {
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
+int AtomVecSMD::pack_vel_hybrid(int /*i*/, double */*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1222,7 +1222,7 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
write hybrid velocity info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
+int AtomVecSMD::write_vel_hybrid(FILE */*fp*/, double */*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 3;
}
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index 3685248d5e..f015c6c4df 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -86,13 +86,13 @@ void FixSMDTlsphDtReset::init() {
/* ---------------------------------------------------------------------- */
-void FixSMDTlsphDtReset::setup(int vflag) {
+void FixSMDTlsphDtReset::setup(int /*vflag*/) {
end_of_step();
}
/* ---------------------------------------------------------------------- */
-void FixSMDTlsphDtReset::initial_integrate(int vflag) {
+void FixSMDTlsphDtReset::initial_integrate(int /*vflag*/) {
//printf("in adjust_dt: dt = %20.10f\n", update->dt);
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index 4668e673fc..1eae45161f 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -125,7 +125,7 @@ void FixSMDIntegrateTlsph::init() {
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
-void FixSMDIntegrateTlsph::initial_integrate(int vflag) {
+void FixSMDIntegrateTlsph::initial_integrate(int /*vflag*/) {
double dtfm, vsq, scale;
// update v and x of atoms in group
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index a145deeb61..685d6af5a8 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -158,7 +158,7 @@ void FixSMDIntegrateUlsph::init() {
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixSMDIntegrateUlsph::initial_integrate(int vflag) {
+void FixSMDIntegrateUlsph::initial_integrate(int /*vflag*/) {
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index d4afbe0535..1515849c53 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -248,7 +248,7 @@ void FixSMDMoveTriSurf::init() {
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
-void FixSMDMoveTriSurf::initial_integrate(int vflag) {
+void FixSMDMoveTriSurf::initial_integrate(int /*vflag*/) {
double **x = atom->x;
double **x0 = atom->x0;
double **v = atom->v;
@@ -461,7 +461,7 @@ void FixSMDMoveTriSurf::reset_dt() {
/* ---------------------------------------------------------------------- */
-int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
int i, j, m;
double **x0 = atom->x0;
double **smd_data_9 = atom->smd_data_9;
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 5e7cdbad38..4bc8b5127b 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -231,7 +231,7 @@ void FixSMDSetVel::min_setup(int vflag) {
/* ---------------------------------------------------------------------- */
//void FixSMDSetVel::initial_integrate(int vflag) {
-void FixSMDSetVel::post_force(int vflag) {
+void FixSMDSetVel::post_force(int /*vflag*/) {
double **x = atom->x;
double **f = atom->f;
double **v = atom->v;
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 3e2812aa12..eba094da53 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -199,7 +199,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
so can be migrated or stored with atoms
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
+void FixSMD_TLSPH_ReferenceConfiguration::setup(int /*vflag*/) {
int i, j, ii, jj, n, inum, jnum;
int *ilist, *jlist, *numneigh, **firstneigh;
double r, h, wf, wfd;
@@ -386,7 +386,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) {
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int delflag) {
+void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int /*delflag*/) {
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
@@ -470,7 +470,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) {
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) {
+void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int /*nlocal*/, int /*nth*/) {
// ipage = NULL if being called from granular pair style init()
// skip to Nth set of extra values
@@ -512,7 +512,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) {
/* ---------------------------------------------------------------------- */
-int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
int i, j, m;
double *radius = atom->radius;
double *vfrac = atom->vfrac;
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 97c2ead5fc..4dd415f53e 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -110,7 +110,7 @@ void FixSMDWallSurface::min_setup(int vflag) {
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
-void FixSMDWallSurface::setup(int vflag) {
+void FixSMDWallSurface::setup(int /*vflag*/) {
if (!first)
return;
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index 815db4a450..13f48e995e 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -373,7 +373,7 @@ double PairHertz::memory_usage() {
return 0.0;
}
-void *PairHertz::extract(const char *str, int &i) {
+void *PairHertz::extract(const char *str, int &/*i*/) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 4dd16c4d83..f9922ef222 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -1802,7 +1802,7 @@ double PairTlsph::memory_usage() {
extract method to provide access to this class' data structures
------------------------------------------------------------------------- */
-void *PairTlsph::extract(const char *str, int &i) {
+void *PairTlsph::extract(const char *str, int &/*i*/) {
//printf("in PairTlsph::extract\n");
if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) {
return (void *) Fincr;
@@ -1839,7 +1839,7 @@ void *PairTlsph::extract(const char *str, int &i) {
/* ---------------------------------------------------------------------- */
-int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
int i, j, m;
tagint *mol = atom->molecule;
double *damage = atom->damage;
@@ -1928,7 +1928,7 @@ void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
------------------------------------------------------------------------- */
void PairTlsph::effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate,
- const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) {
+ const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double /*damage*/, double &K_eff, double &mu_eff, double &M_eff) {
double M0; // initial longitudinal modulus
double shear_rate_sq;
@@ -2094,7 +2094,7 @@ void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_d
/* ----------------------------------------------------------------------
Compute damage. Called from AssembleStress().
------------------------------------------------------------------------- */
-void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &stress_damaged) {
+void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &/*stress_damaged*/) {
double *eff_plastic_strain = atom->eff_plastic_strain;
double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
double *radius = atom->radius;
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index b8bff7e799..e40c876ec3 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -834,7 +834,7 @@ double PairTriSurf::clamp(const double a, const double min, const double max) {
}
}
-void *PairTriSurf::extract(const char *str, int &i) {
+void *PairTriSurf::extract(const char *str, int &/*i*/) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index 96eb912fae..aa88e125d6 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -1487,7 +1487,7 @@ double PairULSPH::memory_usage() {
/* ---------------------------------------------------------------------- */
-int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
double *vfrac = atom->vfrac;
double *eff_plastic_strain = atom->eff_plastic_strain;
int i, j, m;
@@ -1562,7 +1562,7 @@ void PairULSPH::unpack_forward_comm(int n, int first, double *buf) {
* EXTRACT
*/
-void *PairULSPH::extract(const char *str, int &i) {
+void *PairULSPH::extract(const char *str, int &/*i*/) {
//printf("in extract\n");
if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) {
return (void *) smoothVel;
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index e3deb199b6..4213428872 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -97,7 +97,7 @@ void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S,
final pressure pFinal
------------------------------------------------------------------------- */
-void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6,
+void polynomialEOS(double rho, double rho0, double /*e*/, double C0, double C1, double C2, double C3, double /*C4*/, double /*C5*/, double /*C6*/,
double pInitial, double dt, double &pFinal, double &p_rate) {
double mu = rho / rho0 - 1.0;
@@ -307,7 +307,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri
output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate.
------------------------------------------------------------------------- */
void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a,
- const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
+ const double C, const double epdot0, const double T0, const double Tmelt, const double /*M*/, const double dt, const double ep,
const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 1028d8a897..9eee7d0728 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -242,7 +242,7 @@ void PairSMTBQ::allocate()
global settings
------------------------------------------------------------------------- */
-void PairSMTBQ::settings(int narg, char **arg)
+void PairSMTBQ::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -1592,7 +1592,7 @@ void PairSMTBQ::tabqeq()
/* ---------------------------------------------------------------------*/
void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
- double &fforce, int eflag, double &eng)
+ double &fforce, int /*eflag*/, double &eng)
{
/* ===================================================================
@@ -1840,7 +1840,7 @@ void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot)
-------------------------------------------------------------------- */
void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
- int eflag, double &eng)
+ int /*eflag*/, double &eng)
{
double r,tmp_exp,tmp;
double A = intparam->abuck ;
@@ -1858,7 +1858,7 @@ void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce,
- int eflag, double &eng)
+ int /*eflag*/, double &eng)
{
double r,tmp_exp;
double aOO = intparam->aOO ;
@@ -1980,8 +1980,8 @@ void PairSMTBQ::tabsm()
/* -------------------------------------------------------------- */
-void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
- double &fforce, int eflag, double &eng)
+void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int /*i*/, int /*j*/,
+ double &fforce, int /*eflag*/, double &eng)
{
/* ================================================
@@ -2031,7 +2031,7 @@ void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
void PairSMTBQ::attractive(Intparam *intparam, double rsq,
- int eflag, int i, double iq, int j, double jq)
+ int /*eflag*/, int i, double /*iq*/, int /*j*/, double /*jq*/)
{
int itype,l;
double r,t1,t2,xi,sds;
@@ -3334,7 +3334,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
/* ---------------------------------------------------------------------- */
-void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
+void PairSMTBQ::Init_charge(int */*nQEq*/, int */*nQEqa*/, int */*nQEqc*/)
{
int ii,i,gp,itype;
int *ilist,test[nteam],init[nteam];
@@ -3391,7 +3391,7 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
* COMMUNICATION
* ---------------------------------------------------------------------- */
-int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
{
int i,j,m;
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index d7a5d81517..b688eccfea 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -64,7 +64,7 @@ void FixMeso::init() {
dtf = 0.5 * update->dt * force->ftm2v;
}
-void FixMeso::setup_pre_force(int vflag)
+void FixMeso::setup_pre_force(int /*vflag*/)
{
// set vest equal to v
double **v = atom->v;
@@ -87,7 +87,7 @@ void FixMeso::setup_pre_force(int vflag)
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMeso::initial_integrate(int vflag) {
+void FixMeso::initial_integrate(int /*vflag*/) {
// update v and x and rho and e of atoms in group
double **x = atom->x;
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index f5fc306320..29e8a1554c 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -67,7 +67,7 @@ void FixMesoStationary::init() {
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMesoStationary::initial_integrate(int vflag) {
+void FixMesoStationary::initial_integrate(int /*vflag*/) {
double *rho = atom->rho;
double *drho = atom->drho;
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
index 6f0cf7eca2..4a8990d6fd 100644
--- a/src/USER-SPH/pair_sph_heatconduction.cpp
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -155,7 +155,7 @@ void PairSPHHeatConduction::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHHeatConduction::settings(int narg, char **arg) {
+void PairSPHHeatConduction::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/heatconduction");
@@ -211,8 +211,8 @@ double PairSPHHeatConduction::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHHeatConduction::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHHeatConduction::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
index 99fba05917..32b3e61233 100644
--- a/src/USER-SPH/pair_sph_idealgas.cpp
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -197,7 +197,7 @@ void PairSPHIdealGas::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHIdealGas::settings(int narg, char **arg) {
+void PairSPHIdealGas::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/idealgas");
@@ -252,8 +252,8 @@ double PairSPHIdealGas::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHIdealGas::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHIdealGas::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
index 5cefdf87c4..c382833baf 100644
--- a/src/USER-SPH/pair_sph_lj.cpp
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -204,7 +204,7 @@ void PairSPHLJ::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHLJ::settings(int narg, char **arg) {
+void PairSPHLJ::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/lj");
@@ -261,8 +261,8 @@ double PairSPHLJ::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHLJ::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHLJ::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 605187d3a7..9b5a535288 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -278,8 +278,8 @@ double PairSPHRhoSum::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce) {
+double PairSPHRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
+ double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
@@ -288,7 +288,7 @@ double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc) {
+ int /*pbc_flag*/, int */*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
index 00500b940d..42b318f2c9 100644
--- a/src/USER-SPH/pair_sph_taitwater.cpp
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -225,7 +225,7 @@ void PairSPHTaitwater::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHTaitwater::settings(int narg, char **arg) {
+void PairSPHTaitwater::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/taitwater");
@@ -293,8 +293,8 @@ double PairSPHTaitwater::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHTaitwater::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHTaitwater::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
index 80607cb333..8012895af8 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.cpp
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -225,7 +225,7 @@ void PairSPHTaitwaterMorris::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHTaitwaterMorris::settings(int narg, char **arg) {
+void PairSPHTaitwaterMorris::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/taitwater/morris");
@@ -289,8 +289,8 @@ double PairSPHTaitwaterMorris::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHTaitwaterMorris::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHTaitwaterMorris::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index bfa4549286..bffcd7849f 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -348,7 +348,7 @@ void FixNHUef::final_integrate()
* at outer level: call this->final_integrate()
* at other levels: rotate -> 2nd verlet step -> rotate back
* ---------------------------------------------------------------------- */
-void FixNHUef::final_integrate_respa(int ilevel, int iloop)
+void FixNHUef::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
--
GitLab
From 735ec9de0babfc4fd9d781ac1e1dedbddcd66eb1 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 24 Aug 2018 10:53:05 -0600
Subject: [PATCH 170/332] more general MD c/s protocol
---
src/MESSAGE/fix_client_md.cpp | 43 ++++++++++++++----
src/MESSAGE/server_md.cpp | 86 +++++++++++++++++++++++++----------
src/MESSAGE/server_md.h | 4 ++
3 files changed, 100 insertions(+), 33 deletions(-)
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 9c270ac2c9..c4ee24d344 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -28,9 +28,9 @@ using namespace LAMMPS_NS;
using namespace CSLIB_NS;
using namespace FixConst;
-enum{REAL,METAL}
+enum{OTHER,REAL,METAL}
enum{SETUP=1,STEP};
-enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
/* ---------------------------------------------------------------------- */
@@ -47,7 +47,7 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(update->unit_style,"real") == 0) units = REAL;
else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
- else error->all(FLERR,"Units must be real or metal for fix client/md");
+ else units = OTHER;
scalar_flag = 1;
global_freq = 1;
@@ -55,18 +55,19 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
virial_flag = 1;
thermo_virial = 1;
+ inv_nprocs = 1.0 / comm->nprocs;
if (domain->dimension == 2)
box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0;
maxatom = 0;
xpbc = NULL;
- // unit conversion factors
-
- double inv_nprocs = 1.0 / comm->nprocs;
+ // unit conversion factors for REAL
+ // otherwise not needed
fconvert = econvert = vconvert = 1.0;
if (units == REAL) {
+ // NOTE: still need to set these
fconvert = 1.0;
econvert = 1.0;
vconvert = 1.0;
@@ -120,10 +121,12 @@ void FixClientMD::setup(int vflag)
{
CSlib *cs = (CSlib *) lmp->cslib;
+ // SETUP send at beginning of each run
// required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
// optional fields: others in enum above
int nfields = 8;
+ if (units == OTHER) nfields++;
if (atom->q_flag) nfields++;
cs->send(SETUP,nfields);
@@ -142,12 +145,20 @@ void FixClientMD::setup(int vflag)
pack_coords();
cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+ if (units == OTHER) cs->pack_string(UNITS,update->unit_style);
+
if (atom->q_flag)
cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
// receive initial forces, energy, virial
receive_fev(vflag);
+
+ if (server_error) {
+ str = char[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
}
/* ---------------------------------------------------------------------- */
@@ -168,6 +179,7 @@ void FixClientMD::post_force(int vflag)
if (vflag) v_setup(vflag);
else evflag = 0;
+ // STEP send every step
// required fields: COORDS
// optional fields: ORIGIN, BOX
@@ -189,9 +201,15 @@ void FixClientMD::post_force(int vflag)
cs->pack(BOX,4,9,&box[0][0]);
}
- // recv forces, energy, virial
+ // receive forces, energy, virial
receive_fev(vflag);
+
+ if (server_error) {
+ str = char[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
}
/* ---------------------------------------------------------------------- */
@@ -202,7 +220,7 @@ void FixClientMD::min_post_force(int vflag)
}
/* ----------------------------------------------------------------------
- potential energy from QM code
+ potential energy from server
------------------------------------------------------------------------- */
double FixClientMD::compute_scalar()
@@ -255,7 +273,9 @@ void FixClientMD::pack_box()
}
/* ----------------------------------------------------------------------
- receive message from server with forces, energy, virial
+ receive message from server
+ required fields: FORCES, ENERGY, VIRIAL
+ optional field: ERROR
------------------------------------------------------------------------- */
void FixClientMD::receive_fev(int vflag)
@@ -291,4 +311,9 @@ void FixClientMD::receive_fev(int vflag)
for (int i = 0; i < 6; i++)
virial[i] = inv_nprocs * vconvert * v[i];
}
+
+ // error return
+
+ server_error = 0;
+ if (nfield == 4) server_error = cs->unpack_int(ERROR);
}
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index af93c3b4b0..98ce71638d 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -33,21 +33,11 @@
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
-enum{REAL,METAL}
+enum{OTHER,REAL,METAL}
enum{SETUP=1,STEP};
-enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
-// NOTE: features that could be added to this interface
-// allow client to set periodicity vs shrink-wrap
-// currently just assume server is same as client
-// test that triclinic boxes actually work
-// send new box size/shape every step, for NPT client
-// unit check between client/server with unit conversion if needed
-// option for client to send other per-atom quantities, e.g. rmass
-// more precise request of energy/virial (global or peratom) by client
-// maybe Verlet should have a single(eflag,vflag) method to more easily comply
-
/* ---------------------------------------------------------------------- */
ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
@@ -61,7 +51,27 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
if (strcmp(update->unit_style,"real") == 0) units = REAL;
else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
- else error->all(FLERR,"Units must be real or metal for server md");
+ else units = OTHER;
+
+ // unit conversion factors for REAL
+ // otherwise not needed
+
+ fconvert = econvert = vconvert = 1.0;
+ if (units == REAL) {
+ // NOTE: still need to set these
+ fconvert = 1.0;
+ econvert = 1.0;
+ vconvert = 1.0;
+ }
+
+ fcopy = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::~ServerMD();
+{
+ memory->destroy(fcopy);
}
/* ---------------------------------------------------------------------- */
@@ -89,8 +99,9 @@ void ServerMD::loop()
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID < 0) break;
- // SETUP call at beginning of each run
- // required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
+ // SETUP receive at beginning of each run
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ // NATOMS, NTYPES, TYPES, COORDS
// optional fields: others in enum above
if (msgID == SETUP) {
@@ -103,6 +114,7 @@ void ServerMD::loop()
double *box = NULL;
int *types = NULL;
double *coords = NULL;
+ char *units = NULL;
double *charge = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
@@ -132,6 +144,9 @@ void ServerMD::loop()
types = (int *) cs->unpack(TYPES);
} else if (fieldID[ifield] == COORDS) {
coords = (double *) cs->unpack(COORDS);
+
+ } else if (fieldID[ifield] == UNITS) {
+ units = (char *) cs->unpack(UNITS);
} else if (fieldID[ifield] == CHARGE) {
charge = (double *) cs->unpack(CHARGE);
} else error->all(FLERR,"Server md setup field unknown");
@@ -141,6 +156,9 @@ void ServerMD::loop()
natoms < 0 || ntypes < 0 || !types || !coords)
error->all(FLERR,"Required server md setup field not received");
+ if (units && strcmp(units,update->unit_style) != 0)
+ error->all(FLERR,"Server md does not match client units");
+
if (charge && atom->q_flag == 0)
error->all(FLERR,"Server md does not define atom attribute q");
@@ -183,6 +201,13 @@ void ServerMD::loop()
atom->map_set();
atom->natoms = natoms;
+ // allocate fcopy if needed
+
+ if (units == REAL) {
+ memory->destroy(fcopy);
+ memory->create(fcopy,atom->nlocal,3,"server/md:fcopy");
+ }
+
// perform system setup() for dynamics
// also OK for minimization, since client runs minimizer
// return forces, energy, virial to client
@@ -195,7 +220,7 @@ void ServerMD::loop()
send_fev(msgID);
- // STEP call at each timestep of run or minimization
+ // STEP receive at each timestep of run or minimization
// required fields: COORDS
// optional fields: BOXLO, BOXHI, BOXTILT
@@ -309,13 +334,13 @@ void ServerMD::box_change(double *origin, double *box)
domain->xy = box[3];
domain->xz = box[6];
domain->yz = box[7];
-
-
}
/* ----------------------------------------------------------------------
- send return message with forces, energy, pressure tensor
- pressure tensor should be just pair style virial
+ return message with forces, energy, pressure tensor
+ pressure tensor should be just pair and KSpace contributions
+ required fields: FORCES, ENERGY, VIRIAL
+ optional field: ERROR (not ever sending)
------------------------------------------------------------------------- */
void ServerMD::send_fev(int msgID)
@@ -325,12 +350,25 @@ void ServerMD::send_fev(int msgID)
cs->send(msgID,3);
double *forces = NULL;
- if (atom->nlocal) forces = &atom->f[0][0];
+ if (atom->nlocal) {
+ if (units != REAL) forces = &atom->f[0][0];
+ else {
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ for (i = 0; i < nlocal; i++) {
+ fcopy[i][0] = fconvert*f[i][0];
+ fcopy[i][1] = fconvert*f[i][1];
+ fcopy[i][2] = fconvert*f[i][2];
+ }
+ forces = &fcopy[0][0];
+ }
+ }
cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces);
-
+
double eng = force->pair->eng_vdwl + force->pair->eng_coul;
double engall;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
+ engall *= econvert;
cs->pack_double(ENERGY,engall);
double v[6],vall[6];
@@ -339,8 +377,8 @@ void ServerMD::send_fev(int msgID)
if (force->kspace)
for (int i = 0; i < 6; i++)
v[i] += force->kspace->virial[i];
-
+
+ for (int i = 0; i < 6; i++) v[i] *= vconvert;
MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
cs->pack(VIRIAL,4,6,vall);
}
-
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
index 70134cbff9..ecc713a4e8 100644
--- a/src/MESSAGE/server_md.h
+++ b/src/MESSAGE/server_md.h
@@ -21,9 +21,13 @@ namespace LAMMPS_NS {
class ServerMD : protected Pointers {
public:
ServerMD(class LAMMPS *);
+ ~ServerMD();
void loop();
private:
+ int units;
+ double **fcopy;
+
void box_change(double *, double *, double *);
void send_fev(int);
};
--
GitLab
From d8b087aeb4a3ab82974cb047dbeedfd9f352e4eb Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 24 Aug 2018 11:11:34 -0600
Subject: [PATCH 171/332] docs for MD protocol enhancements
---
doc/src/server_mc.txt | 18 +++++++++---------
doc/src/server_md.txt | 35 ++++++++++++++++++-----------------
src/MESSAGE/fix_client_md.cpp | 2 +-
src/MESSAGE/fix_client_md.h | 1 -
src/MESSAGE/server_md.cpp | 2 +-
5 files changed, 29 insertions(+), 29 deletions(-)
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index 3c658187da..3f7b3b8893 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -71,26 +71,26 @@ cs->send(NATOMS,0) # msgID = 1 with no fields :pre
cs->send(EINIT,0) # msgID = 2 with no fields :pre
cs->send(DISPLACE,2) # msgID = 3 with 2 fields
-cs->pack(1,1,ID) # 1st field = ID of atom to displace
+cs->pack_int(1,ID) # 1st field = ID of atom to displace
cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
cs->send(ACCEPT,1) # msgID = 4 with 1 field
-cs->pack(1,1,flag) # 1st field = accept/reject flag :pre
+cs->pack_int(1,flag) # 1st field = accept/reject flag :pre
cs->send(RUN,1) # msgID = 5 with 1 field
-cs->pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
+cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
[Server replies]:
cs->send(NATOMS,1) # msgID = 1 with 1 field
-cs->pack(1,1,Natoms) # 1st field = number of atoms :pre
+cs->pack_int(1,natoms) # 1st field = number of atoms :pre
-cs->send(EINIT,2) # msgID = 2 with 2 fields
-cs->pack(1,1,poteng) # 1st field = potential energy of system
-cs->pack(2,3*Natoms,x) # 2nd field = 3N coords of Natoms :pre
+cs->send(EINIT,2) # msgID = 2 with 2 fields
+cs->pack_double(1,poteng) # 1st field = potential energy of system
+cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
-cs->send(DISPLACE,1) # msgID = 3 with 1 field
-cs->pack(1,1,poteng) # 1st field = new potential energy of system :pre
+cs->send(DISPLACE,1) # msgID = 3 with 1 field
+cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
cs->send(ACCEPT,0) # msgID = 4 with no fields
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 4fe605f7a5..58dfa7f762 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -66,45 +66,46 @@ files for details on how LAMMPS uses these messages. See the
examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
a quantum code (VASP) can use use these messages.
-The following code uses these values, defined as enums in LAMMPS:
+The following pseudo-code uses these values, defined as enums.
enum{SETUP=1,STEP};
-enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL}; :pre
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,VIRIAL,ERROR}; :pre
[Client sends 2 kinds of messages]:
-# required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
-# optional fields: others in 2nd enum above :pre
+# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+# optional fields: UNITS, CHARGE :pre
cs->send(SETUP,nfields) # msgID with nfields :pre
-cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
-cs->pack_int(NATOMS,natoms) # total numer of atoms
+cs->pack_int(DIM,dim) # dimension (2,3) of simulation
+cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+cs->pack_int(NATOMS,natoms) # total number of atoms
cs->pack_int(NTYPES,ntypes) # number of atom types
-cs->pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
-cs->pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
-cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
cs->pack(TYPES,natoms,type) # vector of per-atom types
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
# required fields: COORDS
-# optional fields: BOXLO, BOXHI, BOXTILT :pre
+# optional fields: ORIGIN, BOX :pre
cs->send(STEP,nfields) # msgID with nfields :pre
-cs->pack_int(NATOMS,natoms) # total numer of atoms
-cs->pack_int(NTYPES,ntypes) # number of atom types
-cs->pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
-cs->pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :pre
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
[Server replies to either kind of message]:
-cs->send(msgID,3) # msgID = 1 with 3 fields
+cs->send(msgID,nfields) # msgID with nfields
cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
cs->pack(ENERGY,1,poteng) # total potential energy of system
-cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
+cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector)
+cs->pack(ERROR,6,virial) # server had an error (e.g. DFT non-convergence) :pre
:line
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index c4ee24d344..b85c7f8f76 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -31,7 +31,7 @@ using namespace FixConst;
enum{OTHER,REAL,METAL}
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL};
+enum{FORCES=1,ENERGY,VIRIAL,ERROR};
/* ---------------------------------------------------------------------- */
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
index b6561bce41..9c70e4c026 100644
--- a/src/MESSAGE/fix_client_md.h
+++ b/src/MESSAGE/fix_client_md.h
@@ -37,7 +37,6 @@ class FixClientMD : public Fix {
double compute_scalar();
private:
- void *cslib;
int maxatom,units;
double box[3][3];
double eng;
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index 98ce71638d..acdc06a0e9 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -36,7 +36,7 @@ using namespace CSLIB_NS;
enum{OTHER,REAL,METAL}
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL};
+enum{FORCES=1,ENERGY,VIRIAL,ERROR};
/* ---------------------------------------------------------------------- */
--
GitLab
From c01fb5f701581cdde2ae2e5d966ab048b2cdd981 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 24 Aug 2018 14:33:06 -0600
Subject: [PATCH 172/332] new loop structure in pair ATM
---
src/MANYBODY/pair_atm.cpp | 27 +++++++++++++++++++++++++--
1 file changed, 25 insertions(+), 2 deletions(-)
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index 44587dfdff..b63407dfe9 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -98,6 +98,10 @@ void PairATM::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
+ int count1 = 0;
+ int count2 = 0;
+ int count3 = 0;
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xi = x[i][0];
@@ -108,7 +112,10 @@ void PairATM::compute(int eflag, int vflag)
jnum = numneigh[i];
jnumm1 = jnum - 1;
- for (jj = 0; jj < jnumm1; jj++) {
+ // for (jj = 0; jj < jnumm1; jj++) {
+ // replace with this line:
+ for (jj = 0; jj < jnum; jj++) {
+
j = jlist[jj];
j &= NEIGHMASK;
rij[0] = x[j][0] - xi;
@@ -118,9 +125,15 @@ void PairATM::compute(int eflag, int vflag)
rij[2] = x[j][2] - zi;
if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ count1++;
if (rij2 > cutoff_squared) continue;
+ count2++;
+
+ //for (kk = jj+1; kk < jnum; kk++) {
+ // replace with these two lines:
+ for (kk = 0; kk < jnum; kk++) {
+ if (kk == jj) continue;
- for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
@@ -145,6 +158,7 @@ void PairATM::compute(int eflag, int vflag)
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
+ count3++;
interaction_ddd(nu_local,
r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
@@ -163,6 +177,15 @@ void PairATM::compute(int eflag, int vflag)
}
}
+ int count = count1;
+ MPI_Allreduce(&count,&count1,1,MPI_INT,MPI_SUM,world);
+ count = count2;
+ MPI_Allreduce(&count,&count2,1,MPI_INT,MPI_SUM,world);
+ count = count3;
+ MPI_Allreduce(&count,&count3,1,MPI_INT,MPI_SUM,world);
+ printf("FORCE %g %d %d %d\n",cutoff_squared,count1,count2,count3);
+
+
if (vflag_fdotr) virial_fdotr_compute();
}
--
GitLab
From 0661a800a7dc4efb88b20366026f899bd316f480 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 24 Aug 2018 14:57:49 -0600
Subject: [PATCH 173/332] lammps.1: add options block
---
doc/lammps.1 | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/doc/lammps.1 b/doc/lammps.1
index 8f0ba78fdd..d49650bfaa 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -24,6 +24,10 @@ atomic, meso, or continuum scale.
See http://lammps.sandia.gov/ for documentation.
+.SH OPTIONS
+See https://lammps.sandia.gov/doc/Run_options.html for details on
+command-line options.
+
.SH COPYRIGHT
© 2003--2018 Sandia Corporation
--
GitLab
From 38a998c03cf539dfe7782329d509e501cd3d8a4b Mon Sep 17 00:00:00 2001
From: Daniel Schwen <daniel.schwen@inl.gov>
Date: Fri, 24 Aug 2018 13:09:36 -0600
Subject: [PATCH 174/332] Fix misc. warnings (#1076)
---
src/BODY/body_rounded_polyhedron.cpp | 6 ++---
src/BODY/fix_wall_body_polygon.cpp | 16 +++++-------
src/BODY/fix_wall_body_polyhedron.cpp | 15 ++++-------
src/BODY/pair_body_rounded_polygon.cpp | 11 ++++----
src/BODY/pair_body_rounded_polyhedron.cpp | 19 +++++++-------
src/RIGID/fix_rigid.cpp | 1 -
src/RIGID/fix_rigid_nh.cpp | 4 +--
src/RIGID/fix_rigid_nh_small.cpp | 2 +-
src/SNAP/compute_snav_atom.h | 1 -
src/SPIN/compute_spin.h | 1 -
src/USER-BOCS/fix_bocs.cpp | 2 --
src/USER-DPD/fix_rx.cpp | 4 +--
src/USER-INTEL/fix_intel.cpp | 2 ++
src/USER-INTEL/fix_nh_intel.cpp | 1 -
src/USER-INTEL/fix_nve_asphere_intel.cpp | 7 -----
src/USER-INTEL/intel_intrinsics_airebo.h | 2 +-
src/USER-INTEL/nbin_intel.cpp | 7 +----
src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 8 ++----
src/USER-INTEL/npair_intel.cpp | 6 ++---
src/USER-MANIFOLD/manifold_sphere.h | 2 +-
src/USER-MGPT/mgpt_linalg.cpp | 26 +++++++++----------
src/USER-MISC/fix_bond_react.cpp | 1 -
src/USER-MOFFF/angle_cosine_buck6d.cpp | 2 +-
.../improper_inversion_harmonic.cpp | 5 ++--
src/USER-SMD/fix_smd_setvel.h | 1 -
.../fix_smd_tlsph_reference_configuration.cpp | 2 +-
src/fix_halt.cpp | 2 +-
src/library.cpp | 2 +-
28 files changed, 63 insertions(+), 95 deletions(-)
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 5ba4bce8e8..0e2ebbed83 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -96,7 +96,7 @@ int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus)
{
int nvertices = bonus->ivalue[0];
int nedges = bonus->ivalue[1];
- int nfaces = bonus->ivalue[2];
+ //int nfaces = bonus->ivalue[2];
if (nvertices == 1) return 0;
else if (nvertices == 2) return 1;
return nedges; //(nvertices+nfaces-2); // Euler's polyon formula: V-E+F=2
@@ -463,7 +463,7 @@ void BodyRoundedPolyhedron::output(int ibonus, int m, double *values)
int BodyRoundedPolyhedron::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
- int j, nelements;
+ int nelements;
double p[3][3];
double *x, rrad;
@@ -488,7 +488,7 @@ int BodyRoundedPolyhedron::image(int ibonus, double flag1, double /*flag2*/,
nelements = nvertices;
} else {
- int nfaces = bonus->ivalue[2];
+ //int nfaces = bonus->ivalue[2];
int nedges = bonus->ivalue[1]; //nvertices + nfaces - 2;
if (nvertices == 2) nedges = 1; // special case: rods
double* edge_ends = &bonus->dvalue[3*nvertices];
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index f217db774e..3f8c08b6bd 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -310,9 +310,6 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) continue;
- double r = sqrt(rsq);
- double rsqinv = 1.0 / rsq;
-
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
@@ -478,9 +475,8 @@ int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
Contact* contact_list, int &num_contacts, double* /*facc*/)
{
int ni, npi, ifirst, interact;
- double xpi[3], xpj[3], dist, eradi, rradi;
- double fx, fy, fz, rx, ry, rz;
- int nlocal = atom->nlocal;
+ double xpi[3], eradi, rradi;
+ double fx, fy, fz;
npi = dnum[i];
ifirst = dfirst[i];
@@ -499,9 +495,9 @@ int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
xpi[1] = x[i][1] + discrete[ifirst+ni][1];
xpi[2] = x[i][2] + discrete[ifirst+ni][2];
- int mode, contact, p2vertex;
- double d, R, hi[3], t, delx, dely, delz, fpair, shift;
- double xj[3], rij;
+ int mode, contact;
+ double d, R, hi[3], delx, dely, delz, fpair;
+ double rij;
// compute the distance from the vertex xpi to the wall
@@ -671,7 +667,7 @@ void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
double** torque, double* vwall, double* facc)
{
- int ibody,ibonus,ifirst, jefirst, ni;
+ int ibody,ibonus,ifirst, ni;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double fn[3],ft[3],vi[3];
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index b90731acf6..5a066b88bb 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -213,7 +213,7 @@ void FixWallBodyPolyhedron::setup(int vflag)
void FixWallBodyPolyhedron::post_force(int /*vflag*/)
{
- double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
+ double vwall[3],dx,dy,dz,del1,del2,rsq,eradi,rradi,wall_pos;
int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side;
double facc[3];
@@ -325,9 +325,6 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) continue;
- double r = sqrt(rsq);
- double rsqinv = 1.0 / rsq;
-
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
@@ -359,8 +356,7 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
edge[iefirst+ni][5] = 0;
}
- int interact, num_contacts, done;
- double delta_a, delta_ua, j_a;
+ int interact, num_contacts;
Contact contact_list[MAX_CONTACTS];
num_contacts = 0;
@@ -550,7 +546,6 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
{
int ni, nei, mode, contact;
double rradi;
- int nlocal = atom->nlocal;
nei = ednum[i];
rradi = rounded_radius[i];
@@ -702,10 +697,10 @@ void FixWallBodyPolyhedron::contact_forces(int ibody,
double fx, double fy, double fz, double** x, double** v, double** angmom,
double** f, double** torque, double* vwall)
{
- int ibonus,jbonus;
+ int ibonus;
double fxt,fyt,fzt,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
- double fn[3],ft[3],vi[3],vj[3];
+ double fn[3],ft[3],vi[3];
double *quat, *inertia;
AtomVecBody::Bonus *bonus;
@@ -787,7 +782,7 @@ void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
double** torque, double* vwall, double* facc)
{
- int ibody,ibonus,ifirst, jefirst, ni;
+ int ibody,ibonus,ifirst,ni;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double fn[3],ft[3],vi[3];
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 97d3ad5606..6a176f1083 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -105,10 +105,9 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype;
int ni,nj,npi,npj,ifirst,jfirst;
int nei,nej,iefirst,jefirst;
- double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fx,fy,fz;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl;
double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij;
- double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3],facc[3];
- double *dxi,*dxj;
+ double xi[3],xj[3],facc[3];
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@@ -709,9 +708,8 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
int ni, npi, ifirst, nei, iefirst;
int nj, npj, jfirst, nej, jefirst;
double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj;
- double fx, fy, fz, rx, ry, rz, energy;
+ double fx, fy, fz, energy;
int interact;
- int nlocal = atom->nlocal;
npi = dnum[i];
ifirst = dfirst[i];
@@ -758,7 +756,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
int mode, contact, p2vertex;
double d, R, hi[3], t, delx, dely, delz, fpair, shift;
- double xj[3], rij;
+ double rij;
// loop through body j's edges
@@ -781,6 +779,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
if (mode == VERTEXI) p2vertex = edge[jefirst+nj][0];
else if (mode == VERTEXJ) p2vertex = edge[jefirst+nj][1];
+ // double xj[3];
// p2.body2space(p2vertex, xj);
xpj[0] = x[j][0] + discrete[jfirst+p2vertex][0];
xpj[1] = x[j][1] + discrete[jfirst+p2vertex][1];
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 051be762e5..eea2aa3724 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -603,7 +603,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
{
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
- double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy;
+ double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,energy;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -685,7 +685,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
{
int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
- double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -835,7 +835,7 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
{
int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp;
double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d;
- double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -988,7 +988,7 @@ int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
- int ni,nei,nj,nej,contact,interact;
+ int ni,nei,nj,nej,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
@@ -1045,7 +1045,7 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
- int ni,nei,nj,nfj,contact,interact;
+ int ni,nei,nj,nfj,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
@@ -1118,7 +1118,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact;
double xi1[3],xi2[3],xpj1[3],xpj2[3];
double r,t1,t2,h1[3],h2[3];
- double contact_dist, shift;
+ double contact_dist;
double** x = atom->x;
double** v = atom->v;
@@ -1314,7 +1314,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
// determine the intersection of the edge to the face
- double hi1[3], hi2[3], d1, d2, contact_dist, shift;
+ double hi1[3], hi2[3], d1, d2, contact_dist;
int inside1 = 0;
int inside2 = 0;
@@ -2345,9 +2345,8 @@ void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
void PairBodyRoundedPolyhedron::sanity_check()
{
- double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b,u[3],v[3],n[3];
+ double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b;
double a[3],b[3],t_a,t_b;
- int inside_a, inside_b;
x1[0] = 0; x1[1] = 3; x1[2] = 0;
x2[0] = 3; x2[1] = 0; x2[2] = 0;
@@ -2364,9 +2363,11 @@ void PairBodyRoundedPolyhedron::sanity_check()
h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a, d_b);
*/
/*
+ int inside_a, inside_b;
int mode = edge_face_intersect(x1, x2, x3, a, b, h_a, h_b, d_a, d_b,
inside_a, inside_b);
+ double u[3],v[3],n[3];
MathExtra::sub3(x2, x1, u);
MathExtra::sub3(x3, x1, v);
MathExtra::cross3(u, v, n);
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index c0f33346bb..c15a909ada 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -1030,7 +1030,6 @@ void FixRigid::enforce2d()
void FixRigid::compute_forces_and_torques()
{
int i,ibody;
- double dtfm;
// sum over atoms to get force and torque on rigid body
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 96c44d15b5..4dceb1b8b4 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -591,9 +591,9 @@ void FixRigidNH::initial_integrate(int vflag)
void FixRigidNH::final_integrate()
{
- int i,ibody;
+ int ibody;
double tmp,scale_t[3],scale_r;
- double dtfm,xy,xz,yz;
+ double dtfm;
double mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 135a1fb4bd..5016d3f168 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -618,7 +618,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
void FixRigidNHSmall::final_integrate()
{
- int i,ibody;
+ int ibody;
double tmp,scale_t[3],scale_r;
double dtfm;
double mbody[3],tbody[3],fquat[4];
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 2eb9fb804f..7d39786ef9 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -45,7 +45,6 @@ class ComputeSNAVAtom : public Compute {
double *radelem;
double *wjelem;
class SNA** snaptr;
- double cutmax;
int quadraticflag;
};
diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h
index 59f0ce2876..b57876b7a0 100644
--- a/src/SPIN/compute_spin.h
+++ b/src/SPIN/compute_spin.h
@@ -33,7 +33,6 @@ class ComputeSpin : public Compute {
private:
double kb,hbar;
- int usecenter;
void allocate();
};
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index eacfc83b40..03fc94ae58 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -625,11 +625,9 @@ void FixBocs::init()
// NJD MRD 2 functions
int FixBocs::read_F_table( char *filename, int p_basis_type )
{
- char separator = ',';
FILE *fpi;
int N_columns = 2, n_entries = 0, i;
float f1, f2;
- double n1, n2;
int test_sscanf;
double **data = (double **) calloc(N_columns,sizeof(double *));
char * line = (char *) calloc(200,sizeof(char));
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 4dae89b491..4a78bb30d2 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -729,7 +729,7 @@ void FixRX::setup_pre_force(int /*vflag*/)
void FixRX::pre_force(int /*vflag*/)
{
- TimerType timer_start = getTimeStamp();
+ //TimerType timer_start = getTimeStamp();
int nlocal = atom->nlocal;
int nghost = atom->nghost;
@@ -808,7 +808,7 @@ void FixRX::pre_force(int /*vflag*/)
comm->forward_comm_fix(this);
if(localTempFlag) delete [] dpdThetaLocal;
- TimerType timer_stop = getTimeStamp();
+ //TimerType timer_stop = getTimeStamp();
double time_ODE = getElapsedTime(timer_localTemperature, timer_ODE);
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 4c703da833..3a67b60632 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -724,11 +724,13 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset;
if (atom->torque) {
if (f_in[1].w)
+ {
if (f_in[1].w == 1)
error->all(FLERR,"Bad matrix inversion in mldivide3");
else
error->all(FLERR,
"Sphere particles not yet supported for gayberne/intel");
+ }
}
int packthreads;
diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp
index 44253e8bb0..bf4764f104 100644
--- a/src/USER-INTEL/fix_nh_intel.cpp
+++ b/src/USER-INTEL/fix_nh_intel.cpp
@@ -464,7 +464,6 @@ void FixNHIntel::nve_x()
{
double * _noalias const x = atom->x[0];
double * _noalias const v = atom->v[0];
- const double * _noalias const f = atom->f[0];
// x update by full step only for atoms in group
diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp
index a83306def5..7eeb8a1635 100644
--- a/src/USER-INTEL/fix_nve_asphere_intel.cpp
+++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp
@@ -81,10 +81,6 @@ void FixNVEAsphereIntel::setup(int vflag)
void FixNVEAsphereIntel::initial_integrate(int /*vflag*/)
{
- double dtfm;
- double inertia[3],omega[3];
- double *shape,*quat;
-
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double * _noalias const x = atom->x[0];
@@ -94,7 +90,6 @@ void FixNVEAsphereIntel::initial_integrate(int /*vflag*/)
double **angmom = atom->angmom;
double **torque = atom->torque;
- double *rmass = atom->rmass;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@@ -143,8 +138,6 @@ void FixNVEAsphereIntel::final_integrate()
{
if (neighbor->ago == 0) reset_dt();
- double dtfm;
-
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
double * _noalias const angmom = atom->angmom[0];
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index 2c86ad3520..b20f9c8ad1 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -2243,7 +2243,7 @@ public:
FVEC_BINOP(*, mul)
FVEC_BINOP(/, div)
- VEC_INLINE static void gather_prefetch0(const ivec &idx, const void * mem) {}
+ VEC_INLINE static void gather_prefetch0(const ivec & /*idx*/, const void * /*mem*/) {}
};
class avec {
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index e071b141fe..789fa35b42 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -192,15 +192,10 @@ void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
// ---------- Bin Atoms -------------
_fix->start_watch(TIME_HOST_NEIGHBOR);
- const ATOM_T * _noalias const x = buffers->get_x();
+ //const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const atombin = this->_atombin;
int * _noalias const binpacked = this->_binpacked;
-
- const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx;
- const double sboxlo1 = bboxlo[1] + mbinylo/bininvy;
- const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz;
-
int i, ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index 8be2165deb..74a04f0e7d 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -115,7 +115,6 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
int nall_t = nall;
const int aend = nall;
- const int pack_width = _fix->nbor_pack_width();
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const firstneigh = buffers->firstneigh(list);
const int e_nall = nall_t;
@@ -155,9 +154,6 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
tagint * const molecule = atom->molecule;
#endif
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
int moltemplate;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
@@ -167,8 +163,8 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
int tnum;
int *overflow;
- double *timer_compute;
#ifdef _LMP_INTEL_OFFLOAD
+ double *timer_compute;
if (offload) {
timer_compute = _fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
@@ -311,7 +307,7 @@ void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
int * _noalias const ttag = ncachetag + toffs;
// loop over all atoms in other bins in stencil, store every pair
- int istart, icount, ncount, oldbin = -9999999, lane, max_chunk;
+ int ncount, oldbin = -9999999;
for (int i = ifrom; i < ito; i++) {
const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index d59cd2304a..6d4529752a 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -109,8 +109,8 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list,
int tnum;
int *overflow;
- double *timer_compute;
#ifdef _LMP_INTEL_OFFLOAD
+ double *timer_compute;
if (offload) {
timer_compute = _fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
@@ -265,8 +265,9 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list,
int * _noalias itjtype;
// loop over all atoms in other bins in stencil, store every pair
- int istart, icount, ncount, oldbin = -9999999, lane, max_chunk;
+ int istart, icount, ncount, oldbin = -9999999;
#ifdef LMP_INTEL_3BODY_FAST
+ int lane, max_chunk;
if (THREE) {
lane = 0;
max_chunk = 0;
@@ -579,7 +580,6 @@ void NPairIntel::bin_newton(const int /*offload*/, NeighList *list,
int ns;
if (THREE) {
- int alln = n;
ns = n - pack_offset;
atombin[i] = ns;
ns += n2 - pack_offset - maxnbors;
diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/USER-MANIFOLD/manifold_sphere.h
index 5d4ae55fda..d9cd46c9c3 100644
--- a/src/USER-MANIFOLD/manifold_sphere.h
+++ b/src/USER-MANIFOLD/manifold_sphere.h
@@ -40,7 +40,7 @@ namespace user_manifold {
nn[2] = 2*x[2];
}
- virtual void H( double *x, double h[3][3] )
+ virtual void H( double * /*x*/, double h[3][3] )
{
h[0][1] = h[0][2] = h[1][0] = h[1][2] = h[2][0] = h[2][1] = 0.0;
h[0][0] = h[1][1] = h[2][2] = 2.0;
diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp
index 94a4e21ea6..68701037f4 100644
--- a/src/USER-MGPT/mgpt_linalg.cpp
+++ b/src/USER-MGPT/mgpt_linalg.cpp
@@ -81,8 +81,8 @@
#define const
#endif
static void transprod_generic(const double * restrict A,
- const double * restrict B,
- double * restrict C) {
+ const double * restrict B,
+ double * restrict C) {
const int lda = 8,n = mgpt_linalg::matrix_size;
int i,j,k;
double s;
@@ -90,15 +90,15 @@ static void transprod_generic(const double * restrict A,
for(j = 0; j<n; j++) {
s = 0.0;
for(k = 1; k<=n; k++)
- s = s + A[i*lda+k]*B[j*lda+k];
+ s = s + A[i*lda+k]*B[j*lda+k];
C[i*lda+(j+1)] = s;
}
}
static void transtrace3_generic(const double * restrict A,
- const double * restrict B0,double * restrict tout0,
- const double * restrict B1,double * restrict tout1,
- const double * restrict B2,double * restrict tout2) {
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
const int lda = 8,n = mgpt_linalg::matrix_size;
double t0 = 0.0,t1 = 0.0,t2 = 0.0;
int i,j;
@@ -116,16 +116,16 @@ static void transtrace3_generic(const double * restrict A,
*tout2 = t2;
}
-static void transprod_error(const double * restrict A,
- const double * restrict B,
- double * restrict C) {
+static void transprod_error(const double * restrict /*A*/,
+ const double * restrict /*B*/,
+ double * restrict /*C*/) {
printf("Linear algebra subroutines not initialized (transprod).\n");
exit(1);
}
-static void transtrace3_error(const double * restrict A,
- const double * restrict B0,double * restrict tout0,
- const double * restrict B1,double * restrict tout1,
- const double * restrict B2,double * restrict tout2) {
+static void transtrace3_error(const double * restrict /*A*/,
+ const double * restrict /*B0*/,double * restrict /*tout0*/,
+ const double * restrict /*B1*/,double * restrict /*tout1*/,
+ const double * restrict /*B2*/,double * restrict /*tout2*/) {
printf("Linear algebra subroutines not initialized (transtrace3).\n");
exit(1);
}
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index cd7918f4dd..8a05a304f1 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1558,7 +1558,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
for (int i = 0; i < twomol->natoms; i++) {
if (landlocked_atoms[i][myrxn] == 0) {
- int twomol_atomi = i+1;
for (int j = 0; j < twomol->num_bond[i]; j++) {
int twomol_atomj = twomol->bond_atom[i][j];
if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 352c28be4d..3f87aeb757 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -56,7 +56,7 @@ AngleCosineBuck6d::~AngleCosineBuck6d()
void AngleCosineBuck6d::compute(int eflag, int vflag)
{
- int i,i1,i2,i3,n,type,itype,jtype;
+ int i1,i2,i3,n,type,itype,jtype;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 53a7b4729a..9608d58054 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -139,7 +139,6 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
double upx,upy,upz,upn,rup,umx,umy,umz,umn,rum,wwr;
double rucb,rudb,rvcb,rvdb,rupupn,rumumn;
- double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -242,7 +241,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
f[i4][2] += f4[2];
}
- double rb1x, rb1y, rb1z, rb2x, rb2y, rb2z, rb3x, rb3y, rb3z;
+ double rb3x, rb3y, rb3z;
if (evflag)
rb3x = vb1x - vb2x;
@@ -253,7 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
vb3x,vb3y,vb3z,
vb2x,vb2y,vb2z,
rb3x,rb3y,rb3z);
- }
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h
index b987a56f6c..a3e650e682 100644
--- a/src/USER-SMD/fix_smd_setvel.h
+++ b/src/USER-SMD/fix_smd_setvel.h
@@ -56,7 +56,6 @@ class FixSMDSetVel : public Fix {
int xvar,yvar,zvar,xstyle,ystyle,zstyle;
double foriginal[3],foriginal_all[3];
int force_flag;
- int nlevels_respa;
int maxatom;
double **sforce;
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index eba094da53..8af12acd99 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -149,7 +149,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
if (updateFlag > 0) {
if (comm->me == 0) {
- printf("**** updating ref config at step: %ld\n", update->ntimestep);
+ printf("**** updating ref config at step: " BIGINT_FORMAT "\n", update->ntimestep);
}
for (i = 0; i < nlocal; i++) {
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index 7de09a0fa4..983f993ae8 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -184,7 +184,7 @@ void FixHalt::end_of_step()
// print message with ID of fix halt in case multiple instances
char str[128];
- sprintf(str,"Fix halt %s condition met on step %ld with value %g",
+ sprintf(str,"Fix halt %s condition met on step " BIGINT_FORMAT " with value %g",
id,update->ntimestep,attvalue);
if (eflag == HARD) {
diff --git a/src/library.cpp b/src/library.cpp
index 18f7005116..83e13efd08 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1515,7 +1515,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
- "invalid total atoms %ld %ld",lmp->atom->natoms,natoms_prev+n);
+ "invalid total atoms " BIGINT_FORMAT " %lld",lmp->atom->natoms,natoms_prev+n);
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,str);
}
--
GitLab
From 9ed6d0a9d1bb1c385d079e3b3c231176a6662cf6 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 24 Aug 2018 15:27:15 -0600
Subject: [PATCH 175/332] cmake: sort package in header
---
cmake/CMakeLists.txt | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 460d177c92..c684c9df23 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -1008,7 +1008,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
######################################
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n")
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+list(SORT temp_PKG_LIST)
+foreach(PKG ${temp_PKG_LIST})
if(PKG_${PKG})
set(temp "${temp} \"${PKG}\",\n")
endif()
--
GitLab
From c4771291650e032e4b67681a99416ebfc2913c1c Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 24 Aug 2018 16:17:07 -0600
Subject: [PATCH 176/332] real <-> metal unit conversion factors
---
src/MESSAGE/fix_client_md.cpp | 7 +++----
src/MESSAGE/server_md.cpp | 7 +++----
2 files changed, 6 insertions(+), 8 deletions(-)
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index b85c7f8f76..97d0436a27 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -64,13 +64,12 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
// unit conversion factors for REAL
// otherwise not needed
+ // message received in METAL units, convert to local REAL units
fconvert = econvert = vconvert = 1.0;
if (units == REAL) {
- // NOTE: still need to set these
- fconvert = 1.0;
- econvert = 1.0;
- vconvert = 1.0;
+ fconvert = econvert = 23.06035;
+ vconvert = 0.986923;
}
}
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index acdc06a0e9..340431021b 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -55,13 +55,12 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
// unit conversion factors for REAL
// otherwise not needed
+ // local computation in REAL units, send message in METAL units
fconvert = econvert = vconvert = 1.0;
if (units == REAL) {
- // NOTE: still need to set these
- fconvert = 1.0;
- econvert = 1.0;
- vconvert = 1.0;
+ fconvert = econvert = 1.0 / 23.06035;
+ vconvert = 1.0 / 0.986923;
}
fcopy = NULL;
--
GitLab
From b05aa62c49f27374281b56bd2f21330890b7e542 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Sat, 25 Aug 2018 15:46:48 -0600
Subject: [PATCH 177/332] correctly exclude atoms from simultaneous competing
reactions
---
src/USER-MISC/fix_bond_react.cpp | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 5ce1f11475..c3865ce869 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1862,13 +1862,13 @@ void FixBondReact::glove_ghostcheck()
// noteworthy: it's only relevant for parallel
// here we add glove to either local_mega_glove or ghostly_mega_glove
- int ghostly = 0;
- for (int i = 0; i < onemol->natoms; i++) {
- if (atom->map(glove[i][1]) >= atom->nlocal) {
- ghostly = 1;
- break;
- }
- }
+ int ghostly = 1;
+ //for (int i = 0; i < onemol->natoms; i++) {
+ // if (atom->map(glove[i][1]) >= atom->nlocal) {
+ // ghostly = 1;
+ // break;
+ // }
+ //}
if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
--
GitLab
From 5189bc4f4b8ba1dcc13dff36e903b296cc75f780 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@votca.org>
Date: Sun, 26 Aug 2018 07:57:49 -0600
Subject: [PATCH 178/332] cmake: fix install of potential files
Add an '/' at the end avoids the double potentials/ subdir.
---
cmake/CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 51997593db..76edcf858c 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -1130,7 +1130,7 @@ endif()
# Install potential files in data directory
###############################################################################
set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
--
GitLab
From dbc0f0eea01d7ae7d83247cc20e2a52539b05a29 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 12:17:57 -0400
Subject: [PATCH 179/332] Ensure generated style headers are sorted
---
cmake/Modules/StyleHeaderUtils.cmake | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake
index 29ea372597..2b00a81c8d 100644
--- a/cmake/Modules/StyleHeaderUtils.cmake
+++ b/cmake/Modules/StyleHeaderUtils.cmake
@@ -48,8 +48,13 @@ function(CreateStyleHeader path filename)
set(temp "")
if(ARGC GREATER 2)
list(REMOVE_AT ARGV 0 1)
+ set(header_list)
foreach(FNAME ${ARGV})
get_filename_component(FNAME ${FNAME} NAME)
+ list(APPEND header_list ${FNAME})
+ endforeach()
+ list(SORT header_list)
+ foreach(FNAME ${header_list})
set(temp "${temp}#include \"${FNAME}\"\n")
endforeach()
endif()
--
GitLab
From 31ed3f7178a349b5d47827eb8fefea90b034e7cd Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 27 Aug 2018 17:09:59 -0600
Subject: [PATCH 180/332] more changes to insure each triplet IJK computed
exactly once
---
...og.23Aug18.atm.g++.1 => log.27Aug18.g++.1} | 32 +++++------
...og.23Aug18.atm.g++.4 => log.27Aug18.g++.4} | 32 +++++------
src/MANYBODY/pair_atm.cpp | 54 ++++++++-----------
3 files changed, 53 insertions(+), 65 deletions(-)
rename examples/atm/{log.23Aug18.atm.g++.1 => log.27Aug18.g++.1} (69%)
rename examples/atm/{log.23Aug18.atm.g++.4 => log.27Aug18.g++.4} (69%)
diff --git a/examples/atm/log.23Aug18.atm.g++.1 b/examples/atm/log.27Aug18.g++.1
similarity index 69%
rename from examples/atm/log.23Aug18.atm.g++.1
rename to examples/atm/log.27Aug18.g++.1
index 3373846b31..46215e108c 100644
--- a/examples/atm/log.23Aug18.atm.g++.1
+++ b/examples/atm/log.27Aug18.g++.1
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.00126314 secs
+ Time spent = 0.00139618 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.8899813 0 -3.3408686 -4.2298176
- 5 1.0337853 -4.8928208 0 -3.3425304 -4.2233154
- 10 1.0358056 -4.8953304 0 -3.3420104 -4.1897183
- 15 1.0380938 -4.8990457 0 -3.3422942 -4.1310148
- 20 1.0389566 -4.9014345 0 -3.3433892 -4.0406616
- 25 1.0358313 -4.8989663 0 -3.3456079 -3.9093019
-Loop time of 12.2062 on 1 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms
-Performance: 353.920 tau/day, 2.048 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 270.846 tau/day, 1.567 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 12.202 | 12.202 | 12.202 | 0.0 | 99.96
+Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0015621 | 0.0015621 | 0.0015621 | 0.0 | 0.01
-Output | 0.00020814 | 0.00020814 | 0.00020814 | 0.0 | 0.00
-Modify | 0.0019698 | 0.0019698 | 0.0019698 | 0.0 | 0.02
-Other | | 0.0007734 | | | 0.01
+Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01
+Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00
+Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01
+Other | | 0.0006771 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:13
+Total wall time: 0:00:16
diff --git a/examples/atm/log.23Aug18.atm.g++.4 b/examples/atm/log.27Aug18.g++.4
similarity index 69%
rename from examples/atm/log.23Aug18.atm.g++.4
rename to examples/atm/log.27Aug18.g++.4
index d5edfe32ba..d84f17ee2b 100644
--- a/examples/atm/log.23Aug18.atm.g++.4
+++ b/examples/atm/log.27Aug18.g++.4
@@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
- Time spent = 0.000785112 secs
+ Time spent = 0.000900984 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 1.033 -4.8921547 0 -3.343042 -4.2340557
- 5 1.0337949 -4.8947881 0 -3.3444835 -4.2271456
- 10 1.0358286 -4.8973178 0 -3.3439632 -4.1935779
- 15 1.0381322 -4.9010593 0 -3.3442503 -4.134913
- 20 1.0390107 -4.9034854 0 -3.3453589 -4.0446162
- 25 1.0358988 -4.9010506 0 -3.3475908 -3.9133006
-Loop time of 3.20632 on 4 procs for 25 steps with 4000 atoms
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms
-Performance: 1347.340 tau/day, 7.797 timesteps/s
-100.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 993.935 tau/day, 5.752 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.1207 | 3.1553 | 3.1859 | 1.5 | 98.41
+Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.019466 | 0.05009 | 0.084602 | 12.0 | 1.56
-Output | 7.1049e-05 | 8.2076e-05 | 0.00011325 | 0.0 | 0.00
-Modify | 0.00056338 | 0.00057292 | 0.00058413 | 0.0 | 0.02
-Other | | 0.0003092 | | | 0.01
+Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55
+Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00
+Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02
+Other | | 0.0003656 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:03
+Total wall time: 0:00:04
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
index b63407dfe9..a6e52faeba 100644
--- a/src/MANYBODY/pair_atm.cpp
+++ b/src/MANYBODY/pair_atm.cpp
@@ -98,9 +98,15 @@ void PairATM::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- int count1 = 0;
- int count2 = 0;
- int count3 = 0;
+ // triple loop over local atoms and neighbors twice
+ // must compute each IJK triplet interaction exactly once
+ // by proc that owns the triplet atom with smallest x coord
+ // special logic to break ties if multiple atoms have same x or y coords
+ // inner two loops for jj=1,Jnum and kk=jj+1,Jnum insure
+ // the pair of other 2 non-minimum-x atoms is only considered once
+ // triplet geometry criteria for calculation:
+ // each pair distance <= cutoff
+ // produce of 3 pair distances <= cutoff_triple^3
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -112,12 +118,10 @@ void PairATM::compute(int eflag, int vflag)
jnum = numneigh[i];
jnumm1 = jnum - 1;
- // for (jj = 0; jj < jnumm1; jj++) {
- // replace with this line:
- for (jj = 0; jj < jnum; jj++) {
-
+ for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
+
rij[0] = x[j][0] - xi;
if (rij[0] < 0.0) continue;
rij[1] = x[j][1] - yi;
@@ -125,40 +129,33 @@ void PairATM::compute(int eflag, int vflag)
rij[2] = x[j][2] - zi;
if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
- count1++;
if (rij2 > cutoff_squared) continue;
- count2++;
-
- //for (kk = jj+1; kk < jnum; kk++) {
- // replace with these two lines:
- for (kk = 0; kk < jnum; kk++) {
- if (kk == jj) continue;
+ for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
- rjk[0] = x[k][0] - x[j][0];
- if (rjk[0] < 0.0) continue;
- rjk[1] = x[k][1] - x[j][1];
- if (rjk[0] == 0.0 and rjk[1] < 0.0) continue;
- rjk[2] = x[k][2] - x[j][2];
- if (rjk[0] == 0.0 and rjk[1] == 0.0 and rjk[2] < 0.0) continue;
- rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
- if (rjk2 > cutoff_squared) continue;
-
rik[0] = x[k][0] - xi;
+ if (rik[0] < 0.0) continue;
rik[1] = x[k][1] - yi;
+ if (rik[0] == 0.0 and rik[1] < 0.0) continue;
rik[2] = x[k][2] - zi;
+ if (rik[0] == 0.0 and rik[1] == 0.0 and rik[2] < 0.0) continue;
rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
if (rik2 > cutoff_squared) continue;
+ rjk[0] = x[k][0] - x[j][0];
+ rjk[1] = x[k][1] - x[j][1];
+ rjk[2] = x[k][2] - x[j][2];
+ rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ if (rjk2 > cutoff_squared) continue;
+
double r6 = rij2*rjk2*rik2;
if (r6 > cutoff_triple_sixth) continue;
nu_local = nu[type[i]][type[j]][type[k]];
if (nu_local == 0.0) continue;
- count3++;
interaction_ddd(nu_local,
r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
@@ -177,15 +174,6 @@ void PairATM::compute(int eflag, int vflag)
}
}
- int count = count1;
- MPI_Allreduce(&count,&count1,1,MPI_INT,MPI_SUM,world);
- count = count2;
- MPI_Allreduce(&count,&count2,1,MPI_INT,MPI_SUM,world);
- count = count3;
- MPI_Allreduce(&count,&count3,1,MPI_INT,MPI_SUM,world);
- printf("FORCE %g %d %d %d\n",cutoff_squared,count1,count2,count3);
-
-
if (vflag_fdotr) virial_fdotr_compute();
}
--
GitLab
From aac238503bbe70de24e3d2bc8f8544d5d178f8ca Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 21:23:47 -0400
Subject: [PATCH 181/332] Add missing LMP_USER_OMP definition with CMake
---
cmake/CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index fe904938a3..78e18e489c 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -679,6 +679,7 @@ if(PKG_USER-OMP)
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
+ add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
--
GitLab
From a103bd4de296a418247be0c87d5bd0c9f0fb6e49 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 21:25:48 -0400
Subject: [PATCH 182/332] Correct compilation error introduced by #1077
---
src/USER-REAXC/reaxc_allocate.cpp | 16 ++++++++++------
src/lmptype.h | 2 ++
2 files changed, 12 insertions(+), 6 deletions(-)
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index 14906a2a9c..c6c103b6f4 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -39,8 +39,8 @@
important: we cannot know the exact number of atoms that will fall into a
process's box throughout the whole simulation. therefore
we need to make upper bound estimates for various data structures */
-int PreAllocate_Space( reax_system *system, control_params */*control*/,
- storage */*workspace*/, MPI_Comm comm )
+int PreAllocate_Space( reax_system *system, control_params * /*control*/,
+ storage * workspace, MPI_Comm comm )
{
int mincap = system->mincap;
double safezone = system->safezone;
@@ -60,6 +60,8 @@ int PreAllocate_Space( reax_system *system, control_params */*control*/,
workspace->forceReduction = NULL;
workspace->valence_angle_atom_myoffset = NULL;
workspace->my_ext_pressReduction = NULL;
+#else
+ LMP_UNUSED_PARAM(workspace);
#endif
return SUCCESS;
@@ -69,7 +71,7 @@ int PreAllocate_Space( reax_system *system, control_params */*control*/,
/************* system *************/
int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap,
- char */*msg*/ )
+ char * /*msg*/ )
{
system->my_atoms = (reax_atom*)
realloc( system->my_atoms, total_cap*sizeof(reax_atom) );
@@ -116,7 +118,7 @@ void DeAllocate_System( reax_system *system )
/************* workspace *************/
-void DeAllocate_Workspace( control_params */*control*/, storage *workspace )
+void DeAllocate_Workspace( control_params * /*control*/, storage *workspace )
{
int i;
@@ -204,9 +206,9 @@ void DeAllocate_Workspace( control_params */*control*/, storage *workspace )
}
-int Allocate_Workspace( reax_system */*system*/, control_params */*control*/,
+int Allocate_Workspace( reax_system * /*system*/, control_params * control,
storage *workspace, int local_cap, int total_cap,
- MPI_Comm comm, char */*msg*/ )
+ MPI_Comm comm, char * /*msg*/ )
{
int i, total_real, total_rvec, local_rvec;
@@ -307,6 +309,8 @@ int Allocate_Workspace( reax_system */*system*/, control_params */*control*/,
workspace->valence_angle_atom_myoffset = (int *) scalloc(sizeof(int), total_cap, "valence_angle_atom_myoffset", comm);
workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads);
+#else
+ LMP_UNUSED_PARAM(control);
#endif
return SUCCESS;
diff --git a/src/lmptype.h b/src/lmptype.h
index 7e359d2abe..e5c202aa87 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -213,4 +213,6 @@ typedef int bigint;
#include "lmpwindows.h"
#endif
+#define LMP_UNUSED_PARAM(x) (void)x
+
#endif
--
GitLab
From 02f131c5446a60d74bc13b33fb03ccdd3caeb3b7 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 22:11:15 -0400
Subject: [PATCH 183/332] Fix USER-OMP compilation with CMake
---
cmake/CMakeLists.txt | 3 +-
src/accelerator_omp.h | 88 +------------------------------------------
2 files changed, 4 insertions(+), 87 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 78e18e489c..b1287661c0 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -678,7 +678,8 @@ if(PKG_USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
- ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
+ ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h
index 6caa0826fe..25910ae800 100644
--- a/src/accelerator_omp.h
+++ b/src/accelerator_omp.h
@@ -17,47 +17,6 @@
// true interface to USER-OMP
-// this part is used inside the neighbor.h header file to
-// add functions to the Neighbor class definition
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
-
- void half_nsq_no_newton_omp(class NeighList *);
- void half_nsq_no_newton_ghost_omp(class NeighList *);
- void half_nsq_newton_omp(class NeighList *);
-
- void half_bin_no_newton_omp(class NeighList *);
- void half_bin_no_newton_ghost_omp(class NeighList *);
- void half_bin_newton_omp(class NeighList *);
- void half_bin_newton_tri_omp(class NeighList *);
-
- void half_multi_no_newton_omp(class NeighList *);
- void half_multi_newton_omp(class NeighList *);
- void half_multi_newton_tri_omp(class NeighList *);
-
- void full_nsq_omp(class NeighList *);
- void full_nsq_ghost_omp(class NeighList *);
- void full_bin_omp(class NeighList *);
- void full_bin_ghost_omp(class NeighList *);
- void full_multi_omp(class NeighList *);
-
- void half_from_full_no_newton_omp(class NeighList *);
- void half_from_full_newton_omp(class NeighList *);
-
- void granular_nsq_no_newton_omp(class NeighList *);
- void granular_nsq_newton_omp(class NeighList *);
- void granular_bin_no_newton_omp(class NeighList *);
- void granular_bin_newton_omp(class NeighList *);
- void granular_bin_newton_tri_omp(class NeighList *);
-
- void respa_nsq_no_newton_omp(class NeighList *);
- void respa_nsq_newton_omp(class NeighList *);
- void respa_bin_no_newton_omp(class NeighList *);
- void respa_bin_newton_omp(class NeighList *);
- void respa_bin_newton_tri_omp(class NeighList *);
-
-#else /* !LMP_INSIDE_NEIGHBOR_H */
-
// provide a DomainOMP class with some overrides for Domain
#include "domain.h"
@@ -68,8 +27,8 @@ namespace LAMMPS_NS {
class DomainOMP : public Domain {
public:
- DomainOMP(class LAMMPS *lmp) : Domain(lmp) {};
- virtual ~DomainOMP() {};
+ DomainOMP(class LAMMPS *lmp) : Domain(lmp) {}
+ virtual ~DomainOMP() {}
// multi-threaded versions
virtual void pbc();
@@ -81,48 +40,5 @@ class DomainOMP : public Domain {
}
#endif /* LMP_DOMAIN_OMP_H */
-#endif /* !LMP_INSIDE_NEIGHBOR_H */
-
-#else /* !LMP_USER_OMP */
-
-// dummy interface to USER-OMP
-// needed for compiling when USER-OMP is not installed
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
-
- void half_nsq_no_newton_omp(class NeighList *) {}
- void half_nsq_no_newton_ghost_omp(class NeighList *) {}
- void half_nsq_newton_omp(class NeighList *) {}
-
- void half_bin_no_newton_omp(class NeighList *) {}
- void half_bin_no_newton_ghost_omp(class NeighList *) {}
- void half_bin_newton_omp(class NeighList *) {}
- void half_bin_newton_tri_omp(class NeighList *) {}
-
- void half_multi_no_newton_omp(class NeighList *) {}
- void half_multi_newton_omp(class NeighList *) {}
- void half_multi_newton_tri_omp(class NeighList *) {}
-
- void full_nsq_omp(class NeighList *) {}
- void full_nsq_ghost_omp(class NeighList *) {}
- void full_bin_omp(class NeighList *) {}
- void full_bin_ghost_omp(class NeighList *) {}
- void full_multi_omp(class NeighList *) {}
-
- void half_from_full_no_newton_omp(class NeighList *) {}
- void half_from_full_newton_omp(class NeighList *) {}
-
- void granular_nsq_no_newton_omp(class NeighList *) {}
- void granular_nsq_newton_omp(class NeighList *) {}
- void granular_bin_no_newton_omp(class NeighList *) {}
- void granular_bin_newton_omp(class NeighList *) {}
- void granular_bin_newton_tri_omp(class NeighList *) {}
-
- void respa_nsq_no_newton_omp(class NeighList *) {}
- void respa_nsq_newton_omp(class NeighList *) {}
- void respa_bin_no_newton_omp(class NeighList *) {}
- void respa_bin_newton_omp(class NeighList *) {}
- void respa_bin_newton_tri_omp(class NeighList *) {}
-#endif
#endif /* !LMP_USER_OMP */
--
GitLab
From 71bc72ec13e579da37c1c156fceed7230193477c Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 22:13:43 -0400
Subject: [PATCH 184/332] formatting: add additional space to avoid bad syntax
highlights
---
src/BODY/fix_wall_body_polyhedron.cpp | 2 +-
src/COLLOID/pair_lubricate.cpp | 2 +-
src/COLLOID/pair_lubricateU.cpp | 2 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 2 +-
src/LATTE/fix_latte.cpp | 2 +-
src/MANYBODY/fix_qeq_comb.cpp | 2 +-
src/MANYBODY/pair_adp.cpp | 2 +-
src/MANYBODY/pair_comb.cpp | 2 +-
src/MANYBODY/pair_comb3.cpp | 4 +--
src/MANYBODY/pair_eam.cpp | 2 +-
src/MANYBODY/pair_eam_cd.cpp | 2 +-
src/MANYBODY/pair_eim.cpp | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +-
src/MC/fix_atom_swap.cpp | 2 +-
src/MC/fix_bond_break.cpp | 2 +-
src/MC/fix_bond_create.cpp | 2 +-
src/MEAM/pair_meam.cpp | 2 +-
src/MISC/fix_orient_bcc.cpp | 2 +-
src/MISC/fix_orient_fcc.cpp | 2 +-
src/MISC/xdr_compat.cpp | 2 +-
src/MOLECULE/fix_cmap.cpp | 2 +-
src/PERI/fix_peri_neigh.cpp | 2 +-
src/PERI/pair_peri_eps.cpp | 2 +-
src/PERI/pair_peri_lps.cpp | 2 +-
src/PERI/pair_peri_ves.cpp | 2 +-
src/QEQ/fix_qeq.cpp | 2 +-
src/QEQ/fix_qeq_dynamic.cpp | 2 +-
src/QEQ/fix_qeq_fire.cpp | 2 +-
src/RIGID/fix_rigid_small.cpp | 2 +-
src/RIGID/fix_shake.cpp | 2 +-
src/SRD/fix_srd.cpp | 8 +++---
src/USER-DPD/fix_eos_table_rx.cpp | 2 +-
src/USER-DPD/fix_rx.cpp | 2 +-
src/USER-DPD/fix_shardlow.cpp | 2 +-
src/USER-DPD/pair_multi_lucy.cpp | 2 +-
src/USER-DPD/pair_multi_lucy_rx.cpp | 2 +-
src/USER-INTEL/angle_charmm_intel.cpp | 2 +-
src/USER-INTEL/angle_harmonic_intel.cpp | 2 +-
src/USER-INTEL/bond_fene_intel.cpp | 2 +-
src/USER-INTEL/bond_harmonic_intel.cpp | 2 +-
src/USER-INTEL/dihedral_fourier_intel.cpp | 2 +-
src/USER-INTEL/dihedral_harmonic_intel.cpp | 2 +-
src/USER-INTEL/dihedral_opls_intel.cpp | 2 +-
src/USER-INTEL/improper_cvff_intel.cpp | 2 +-
src/USER-INTEL/improper_harmonic_intel.cpp | 2 +-
src/USER-INTEL/intel_buffers.cpp | 2 +-
src/USER-INTEL/intel_buffers.h | 4 +--
src/USER-INTEL/pair_eam_intel.cpp | 2 +-
src/USER-INTEL/pppm_disp_intel.cpp | 26 +++++++++----------
src/USER-MANIFOLD/manifold_plane.cpp | 2 +-
src/USER-MANIFOLD/manifold_thylakoid.cpp | 2 +-
src/USER-MEAMC/pair_meamc.cpp | 2 +-
src/USER-MESO/pair_mdpd_rhosum.cpp | 2 +-
src/USER-MISC/fix_bond_react.cpp | 2 +-
src/USER-MISC/fix_filter_corotate.cpp | 2 +-
src/USER-MISC/fix_pimd.cpp | 2 +-
src/USER-MISC/pair_ilp_graphene_hbn.cpp | 2 +-
src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 2 +-
src/USER-MISC/pair_meam_spline.cpp | 6 ++---
src/USER-MISC/pair_meam_sw_spline.cpp | 6 ++---
src/USER-REAXC/fix_qeq_reax.cpp | 2 +-
src/USER-REAXC/fix_reaxc.cpp | 2 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 4 +--
src/USER-REAXC/fix_reaxc_species.cpp | 4 +--
src/USER-REAXC/reaxc_bond_orders.cpp | 4 +--
src/USER-REAXC/reaxc_bonds.cpp | 4 +--
src/USER-REAXC/reaxc_forces.cpp | 12 ++++-----
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 2 +-
src/USER-REAXC/reaxc_init_md.cpp | 12 ++++-----
src/USER-REAXC/reaxc_io_tools.cpp | 2 +-
src/USER-REAXC/reaxc_lookup.cpp | 2 +-
src/USER-REAXC/reaxc_multi_body.cpp | 2 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 4 +--
src/USER-REAXC/reaxc_torsion_angles.cpp | 2 +-
src/USER-REAXC/reaxc_traj.cpp | 6 ++---
src/USER-REAXC/reaxc_valence_angles.cpp | 2 +-
src/USER-SMD/atom_vec_smd.cpp | 16 ++++++------
.../fix_smd_move_triangulated_surface.cpp | 2 +-
.../fix_smd_tlsph_reference_configuration.cpp | 2 +-
src/USER-SMD/pair_smd_tlsph.cpp | 2 +-
src/USER-SMD/pair_smd_ulsph.cpp | 2 +-
src/USER-SMTBQ/pair_smtbq.cpp | 4 +--
src/USER-SPH/pair_sph_rhosum.cpp | 2 +-
src/fix_property_atom.cpp | 2 +-
src/improper_zero.cpp | 4 +--
src/library.cpp | 2 +-
src/rcb.cpp | 4 +--
87 files changed, 135 insertions(+), 135 deletions(-)
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 5a066b88bb..9504e256b4 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -693,7 +693,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
------------------------------------------------------------------------- */
void FixWallBodyPolyhedron::contact_forces(int ibody,
- double j_a, double *xi, double */*xj*/, double delx, double dely, double delz,
+ double j_a, double *xi, double * /*xj*/, double delx, double dely, double delz,
double fx, double fy, double fz, double** x, double** v, double** angmom,
double** f, double** torque, double* vwall)
{
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index fc1fa7acc5..de53d91818 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -749,7 +749,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
int PairLubricate::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 2d51f2e2b6..35fe33c84e 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -2010,7 +2010,7 @@ void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
/* ---------------------------------------------------------------------- */
int PairLubricateU::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index e74d7a0ea5..c014510fca 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -746,7 +746,7 @@ double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
/* ---------------------------------------------------------------------- */
int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index c9dd0465f8..a89be57bed 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -189,7 +189,7 @@ void FixLatte::init()
/* ---------------------------------------------------------------------- */
-void FixLatte::init_list(int /*id*/, NeighList */*ptr*/)
+void FixLatte::init_list(int /*id*/, NeighList * /*ptr*/)
{
// list = ptr;
}
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index 61bf9bf11c..e46da9bfe7 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -293,7 +293,7 @@ double FixQEQComb::memory_usage()
/* ---------------------------------------------------------------------- */
int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index fd496fcae6..831f1d0efa 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -935,7 +935,7 @@ void PairADP::grab(FILE *fp, int n, double *list)
/* ---------------------------------------------------------------------- */
int PairADP::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index b205fc46d3..e7b0d27b6e 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -2002,7 +2002,7 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
/* ---------------------------------------------------------------------- */
int PairComb::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 54fd13029b..72360be5f0 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -2109,7 +2109,7 @@ void PairComb3::coord(Param *param, double r, int i,
void PairComb3::cntri_int(int tri_flag, double xval, double yval,
double zval, int ixmin, int iymin, int izmin, double &vval,
- double &dvalx, double &dvaly, double &dvalz, Param */*param*/)
+ double &dvalx, double &dvaly, double &dvalz, Param * /*param*/)
{
double x;
vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0;
@@ -3863,7 +3863,7 @@ double PairComb3::switching_d(double rr)
/* ---------------------------------------------------------------------- */
int PairComb3::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index a861f33824..87bcebb111 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -829,7 +829,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairEAM::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
index 9b8fd29465..5b8b241b45 100644
--- a/src/MANYBODY/pair_eam_cd.cpp
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -539,7 +539,7 @@ void PairEAMCD::read_h_coeff(char *filename)
/* ---------------------------------------------------------------------- */
int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index cc35004778..6703e159e6 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -1087,7 +1087,7 @@ double PairEIM::funccoul(int i, int j, double r)
/* ---------------------------------------------------------------------- */
int PairEIM::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index a09f8a23e6..01718d14cd 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -454,7 +454,7 @@ void PairNb3bHarmonic::setup_params()
/* ---------------------------------------------------------------------- */
-void PairNb3bHarmonic::threebody(Param */*paramij*/, Param */*paramik*/,
+void PairNb3bHarmonic::threebody(Param * /*paramij*/, Param * /*paramik*/,
Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index b795b71273..3e981c5609 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -695,7 +695,7 @@ void FixAtomSwap::update_swap_atoms_list()
/* ---------------------------------------------------------------------- */
-int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 203d6b589b..a1c9bb3ab0 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -701,7 +701,7 @@ void FixBondBreak::post_integrate_respa(int ilevel, int /*iloop*/)
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 17ea7fb3f2..e1dd18cb5b 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -1214,7 +1214,7 @@ void FixBondCreate::post_integrate_respa(int ilevel, int /*iloop*/)
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index 41f1f4ce37..5aa13ab02e 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -734,7 +734,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index 9b22e571fe..c614577933 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -488,7 +488,7 @@ double FixOrientBCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientBCC::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index b061627fd8..5b394adde7 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -486,7 +486,7 @@ double FixOrientFCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientFCC::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp
index c67925d92a..0f4d73cdd9 100644
--- a/src/MISC/xdr_compat.cpp
+++ b/src/MISC/xdr_compat.cpp
@@ -650,7 +650,7 @@ xdrstdio_setpos (XDR *xdrs, unsigned int pos)
}
static xdr_int32_t *
-xdrstdio_inline (XDR */*xdrs*/, int /*len*/)
+xdrstdio_inline (XDR * /*xdrs*/, int /*len*/)
{
/*
* Must do some work to implement this: must insure
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index 2acb20de60..b527eef020 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -1163,7 +1163,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf,
/* ---------------------------------------------------------------------- */
-bigint FixCMAP::read_data_skip_lines(char */*keyword*/)
+bigint FixCMAP::read_data_skip_lines(char * /*keyword*/)
{
return ncmap;
}
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 2f5d4ac694..66137e6a01 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -514,7 +514,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index fe2041d802..76267426c6 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -799,7 +799,7 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
---------------------------------------------------------------------- */
int PairPeriEPS::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 0ff0423801..383b91c6f5 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -631,7 +631,7 @@ void PairPeriLPS::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriLPS::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index a41d55b593..7590077f0e 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -697,7 +697,7 @@ void PairPeriVES::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriVES::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index f6f41f57bd..0fe041209f 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -471,7 +471,7 @@ void FixQEq::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEq::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m;
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index 82112c5c11..f496c7e6c0 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -247,7 +247,7 @@ double FixQEqDynamic::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m=0;
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index d1683aa020..83c9907f1b 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -311,7 +311,7 @@ double FixQEqFire::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqFire::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m = 0;
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index b2dbd27c46..d5d3d36083 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -2999,7 +2999,7 @@ int FixRigidSmall::unpack_exchange(int nlocal, double *buf)
------------------------------------------------------------------------- */
int FixRigidSmall::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 5c0139737c..e0d1bf132b 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -2528,7 +2528,7 @@ void FixShake::update_arrays(int i, int atom_offset)
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
- double */*xgeom*/, double */*vcm*/, double */*quat*/)
+ double * /*xgeom*/, double * /*vcm*/, double * /*quat*/)
{
int m,flag;
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index d6053f4aa4..186f51e06a 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -2168,8 +2168,8 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_line_exact(double */*xs*/, double */*xb*/,
- double */*vs*/, double */*vb*/, Big */*big*/,
+double FixSRD::collision_line_exact(double * /*xs*/, double * /*xb*/,
+ double * /*vs*/, double * /*vb*/, Big * /*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
@@ -2197,8 +2197,8 @@ double FixSRD::collision_line_exact(double */*xs*/, double */*xb*/,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_tri_exact(double */*xs*/, double */*xb*/,
- double */*vs*/, double */*vb*/, Big */*big*/,
+double FixSRD::collision_tri_exact(double * /*xs*/, double * /*xb*/,
+ double * /*vs*/, double * /*vb*/, Big * /*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 0bb96d7664..181c7dccfa 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -803,7 +803,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
/* ---------------------------------------------------------------------- */
-int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double *uChem = atom->uChem;
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 4a78bb30d2..1a9c43704d 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -1885,7 +1885,7 @@ void FixRX::computeLocalTemperature()
/* ---------------------------------------------------------------------- */
-int FixRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int FixRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double tmp;
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 9e8ee41533..4e133480ad 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -646,7 +646,7 @@ fprintf(stdout, "\n%6d %6d,%6d %6d: "
/* ---------------------------------------------------------------------- */
-int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double **v = atom->v;
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index a7701f4d93..f911d8299e 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -781,7 +781,7 @@ void PairMultiLucy::computeLocalDensity()
}
/* ---------------------------------------------------------------------- */
-int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 744c1ff64d..13c838fe01 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -1019,7 +1019,7 @@ void PairMultiLucyRX::getMixingWeights(int id, double &mixWtSite1old, double &mi
/* ---------------------------------------------------------------------- */
-int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp
index eddef5bce8..f2542fc0c7 100644
--- a/src/USER-INTEL/angle_charmm_intel.cpp
+++ b/src/USER-INTEL/angle_charmm_intel.cpp
@@ -332,7 +332,7 @@ void AngleCharmmIntel::init_style()
template <class flt_t, class acc_t>
void AngleCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp
index 077825332c..5777dad947 100644
--- a/src/USER-INTEL/angle_harmonic_intel.cpp
+++ b/src/USER-INTEL/angle_harmonic_intel.cpp
@@ -314,7 +314,7 @@ void AngleHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void AngleHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp
index 88fa65f555..9d54269c05 100644
--- a/src/USER-INTEL/bond_fene_intel.cpp
+++ b/src/USER-INTEL/bond_fene_intel.cpp
@@ -291,7 +291,7 @@ void BondFENEIntel::init_style()
template <class flt_t, class acc_t>
void BondFENEIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp
index f4ab991b1c..65894efa05 100644
--- a/src/USER-INTEL/bond_harmonic_intel.cpp
+++ b/src/USER-INTEL/bond_harmonic_intel.cpp
@@ -262,7 +262,7 @@ void BondHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void BondHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 7494fef3bf..6ccc165c61 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -401,7 +401,7 @@ void DihedralFourierIntel::init_style()
template <class flt_t, class acc_t>
void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1, setflag, nterms, memory);
diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp
index 57361b9527..ae5eb914e7 100644
--- a/src/USER-INTEL/dihedral_harmonic_intel.cpp
+++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp
@@ -396,7 +396,7 @@ void DihedralHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void DihedralHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index ae2810f662..ef95cc75bb 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -416,7 +416,7 @@ void DihedralOPLSIntel::init_style()
template <class flt_t, class acc_t>
void DihedralOPLSIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp
index 025206dc67..c20c004657 100644
--- a/src/USER-INTEL/improper_cvff_intel.cpp
+++ b/src/USER-INTEL/improper_cvff_intel.cpp
@@ -428,7 +428,7 @@ void ImproperCvffIntel::init_style()
template <class flt_t, class acc_t>
void ImproperCvffIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp
index dde67e1d76..167095150e 100644
--- a/src/USER-INTEL/improper_harmonic_intel.cpp
+++ b/src/USER-INTEL/improper_harmonic_intel.cpp
@@ -384,7 +384,7 @@ void ImproperHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void ImproperHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index ada70a18a4..05176e1fd1 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -310,7 +310,7 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList */*list*/,
+void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList * /*list*/,
const int nlocal,
const int nthreads,
const int /*offload_end*/,
diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h
index 397fa77a7e..e8225a4a30 100644
--- a/src/USER-INTEL/intel_buffers.h
+++ b/src/USER-INTEL/intel_buffers.h
@@ -135,8 +135,8 @@ class IntelBuffers {
void set_ntypes(const int ntypes, const int use_ghost_cut = 0);
- inline int * firstneigh(const NeighList */*list*/) { return _list_alloc; }
- inline int * cnumneigh(const NeighList */*list*/) { return _cnumneigh; }
+ inline int * firstneigh(const NeighList * /*list*/) { return _list_alloc; }
+ inline int * cnumneigh(const NeighList * /*list*/) { return _cnumneigh; }
inline int * get_atombin() { return _atombin; }
inline int * get_binpacked() { return _binpacked; }
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index 11ae442c0e..ce9ede69d6 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -784,7 +784,7 @@ void PairEAMIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
/* ---------------------------------------------------------------------- */
int PairEAMIntel::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
return pack_forward_comm(n, list, buf, fp);
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index c7edc15a49..3b05658278 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -723,7 +723,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
double sft, int** p2g, int nup, int nlow,
int nxlo, int nylo, int nzlo,
int nxhi, int nyhi, int nzhi,
- IntelBuffers<flt_t,acc_t> */*buffers*/)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
int nlocal = atom->nlocal;
int nthr = comm->nthreads;
@@ -790,7 +790,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -940,7 +940,7 @@ void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -1091,7 +1091,7 @@ void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -1225,7 +1225,7 @@ void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
FFT_SCALAR * _noalias global_density = &(density_brick_none[0][nzlo_out_6][nylo_out_6][nxlo_out_6]);
@@ -1373,7 +1373,7 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1520,7 +1520,7 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1725,7 +1725,7 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1869,7 +1869,7 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2069,7 +2069,7 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2282,7 +2282,7 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2594,7 +2594,7 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2755,7 +2755,7 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> */*buffers*/)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> */*buffers*/)
+void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/USER-MANIFOLD/manifold_plane.cpp
index 45a1f4b46e..6c3f17393a 100644
--- a/src/USER-MANIFOLD/manifold_plane.cpp
+++ b/src/USER-MANIFOLD/manifold_plane.cpp
@@ -16,7 +16,7 @@ double manifold_plane::g( const double *x )
}
-void manifold_plane::n( const double */*x*/, double *n )
+void manifold_plane::n( const double * /*x*/, double *n )
{
n[0] = params[0];
n[1] = params[1];
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp
index 16c4e696d5..93cf60ad03 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp
@@ -117,7 +117,7 @@ void manifold_thylakoid::n( const double *x, double *n )
}
}
-thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int */*err_flag*/, std::size_t *idx )
+thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_flag*/, std::size_t *idx )
{
for( std::size_t i = 0; i < parts.size(); ++i ){
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index da0e4c1d28..eca1040c9c 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -598,7 +598,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAMC::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index d705285584..806a63f898 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -246,7 +246,7 @@ double PairMDPDRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/
/* ---------------------------------------------------------------------- */
int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/) {
+ int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 8a05a304f1..a4377e4ce8 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -2628,7 +2628,7 @@ void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/)
/* ---------------------------------------------------------------------- */
int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index 4a6b3226d4..56ab2b3df9 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -1699,7 +1699,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
}
int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double**f = atom->f;
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index 506590f02c..eba8ed5d0c 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -686,7 +686,7 @@ void FixPIMD::comm_exec(double **ptr)
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 2aecbe5d19..7e11cdff4f 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -1047,7 +1047,7 @@ double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, do
/* ---------------------------------------------------------------------- */
int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m,id,ip,l;
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index 4c1f36c640..bc3bfaeba9 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -1050,7 +1050,7 @@ double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jty
/* ---------------------------------------------------------------------- */
int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m,l,ip,id;
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 1305891b33..e6ea6c2ae4 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -600,7 +600,7 @@ double PairMEAMSpline::init_one(int /*i*/, int /*j*/)
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -618,14 +618,14 @@ void PairMEAMSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSpline::pack_reverse_comm(int /*n*/, int /*first*/, double */*buf*/)
+int PairMEAMSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSpline::unpack_reverse_comm(int /*n*/, int */*list*/, double */*buf*/)
+void PairMEAMSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/)
{
}
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index be0ac1c35b..891913ccfc 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -560,7 +560,7 @@ double PairMEAMSWSpline::init_one(int /*i*/, int /*j*/)
/* ---------------------------------------------------------------------- */
int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -578,14 +578,14 @@ void PairMEAMSWSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSWSpline::pack_reverse_comm(int /*n*/, int /*first*/, double */*buf*/)
+int PairMEAMSWSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSWSpline::unpack_reverse_comm(int /*n*/, int */*list*/, double */*buf*/)
+void PairMEAMSWSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/)
{
}
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index a6e59f7620..6f0b93235f 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -833,7 +833,7 @@ void FixQEqReax::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEqReax::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m;
diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp
index df1d7db085..c470173663 100644
--- a/src/USER-REAXC/fix_reaxc.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -136,7 +136,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixReaxC::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index f3e592a682..fb40b2042e 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -137,7 +137,7 @@ void FixReaxCBonds::end_of_step()
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE */*fp*/)
+void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/)
{
int i, j;
@@ -185,7 +185,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE */*fp*/)
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::FindBond(struct _reax_list */*lists*/, int &numbonds)
+void FixReaxCBonds::FindBond(struct _reax_list * /*lists*/, int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj;
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index abb8708d8d..8ec7f4174f 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -442,7 +442,7 @@ void FixReaxCSpecies::post_integrate()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE */*fp*/)
+void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/)
{
int Nmole, Nspec;
@@ -946,7 +946,7 @@ int FixReaxCSpecies::nint(const double &r)
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 02df9ec518..572d27526c 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -359,8 +359,8 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut,
}
-void BO( reax_system *system, control_params */*control*/, simulation_data */*data*/,
- storage *workspace, reax_list **lists, output_controls */*out_control*/ )
+void BO( reax_system *system, control_params * /*control*/, simulation_data * /*data*/,
+ storage *workspace, reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index;
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index a26f70c543..6fde18e5c2 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -31,9 +31,9 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-void Bonds( reax_system *system, control_params */*control*/,
+void Bonds( reax_system *system, control_params * /*control*/,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls */*out_control*/ )
+ output_controls * /*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index 56501eeda0..dfcc9fd4ae 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -41,9 +41,9 @@
interaction_function Interaction_Functions[NUM_INTRS];
-void Dummy_Interaction( reax_system */*system*/, control_params */*control*/,
- simulation_data */*data*/, storage */*workspace*/,
- reax_list **/*lists*/, output_controls */*out_control*/ )
+void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/,
+ simulation_data * /*data*/, storage * /*workspace*/,
+ reax_list **/*lists*/, output_controls * /*out_control*/ )
{
}
@@ -98,7 +98,7 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, mpi_datatypes */*mpi_data*/ )
+ reax_list **lists, mpi_datatypes * /*mpi_data*/ )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
@@ -114,7 +114,7 @@ void Compute_Total_Force( reax_system *system, control_params *control,
}
-void Validate_Lists( reax_system *system, storage */*workspace*/, reax_list **lists,
+void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists,
int step, int /*n*/, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
@@ -173,7 +173,7 @@ void Validate_Lists( reax_system *system, storage */*workspace*/, reax_list **li
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls */*out_control*/,
+ reax_list **lists, output_controls * /*out_control*/,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index c0b3121a40..6442dd47e9 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -33,7 +33,7 @@
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls */*out_control*/ )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index 33614c7c68..88fb9cf17f 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -36,7 +36,7 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-int Init_System( reax_system *system, control_params *control, char */*msg*/ )
+int Init_System( reax_system *system, control_params *control, char * /*msg*/ )
{
int i;
reax_atom *atom;
@@ -66,7 +66,7 @@ int Init_System( reax_system *system, control_params *control, char */*msg*/ )
int Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, char */*msg*/ )
+ simulation_data *data, char * /*msg*/ )
{
Reset_Simulation_Data( data, control->virial );
@@ -139,8 +139,8 @@ int Init_Workspace( reax_system *system, control_params *control,
/************** setup communication data structures **************/
-int Init_MPI_Datatypes( reax_system *system, storage */*workspace*/,
- mpi_datatypes *mpi_data, MPI_Comm comm, char */*msg*/ )
+int Init_MPI_Datatypes( reax_system *system, storage * /*workspace*/,
+ mpi_datatypes *mpi_data, MPI_Comm comm, char * /*msg*/ )
{
/* setup the world */
@@ -151,8 +151,8 @@ int Init_MPI_Datatypes( reax_system *system, storage */*workspace*/,
}
int Init_Lists( reax_system *system, control_params *control,
- simulation_data */*data*/, storage */*workspace*/, reax_list **lists,
- mpi_datatypes *mpi_data, char */*msg*/ )
+ simulation_data * /*data*/, storage * /*workspace*/, reax_list **lists,
+ mpi_datatypes *mpi_data, char * /*msg*/ )
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 030912d4b7..b63fee2309 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -88,7 +88,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
/************************ close output files ************************/
int Close_Output_Files( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes */*mpi_data*/ )
+ output_controls *out_control, mpi_datatypes * /*mpi_data*/ )
{
if( out_control->write_steps > 0 )
End_Traj( system->my_rank, out_control );
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 8cc1555c59..918099a631 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -151,7 +151,7 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double
int Init_Lookup_Tables( reax_system *system, control_params *control,
- storage *workspace, mpi_datatypes *mpi_data, char */*msg*/ )
+ storage *workspace, mpi_datatypes *mpi_data, char * /*msg*/ )
{
int i, j, r;
int num_atom_types;
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index e599a3d86e..360a9431cf 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -32,7 +32,7 @@
void Atom_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls */*out_control*/ )
+ output_controls * /*out_control*/ )
{
int i, j, pj, type_i, type_j;
double Delta_lpcorr, dfvl;
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index 731b1602e9..b44632ec29 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -33,7 +33,7 @@
void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls */*out_control*/ )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i, flag;
@@ -206,7 +206,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
- output_controls */*out_control*/ )
+ output_controls * /*out_control*/ )
{
int i, j, pj, r, natoms;
int type_i, type_j, tmin, tmax;
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index d6f38d3765..2abfbde61d 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -41,7 +41,7 @@ double Calculate_Omega( rvec dvec_ij, double r_ij,
three_body_interaction_data *p_jkl,
rvec dcos_omega_di, rvec dcos_omega_dj,
rvec dcos_omega_dk, rvec dcos_omega_dl,
- output_controls */*out_control*/ )
+ output_controls * /*out_control*/ )
{
double unnorm_cos_omega, unnorm_sin_omega, omega;
double sin_ijk, cos_ijk, sin_jkl, cos_jkl;
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index f980120a59..c1f3e8ae8f 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -48,7 +48,7 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
}
-void Write_Skip_Line( output_controls *out_control, mpi_datatypes */*mpi_data*/,
+void Write_Skip_Line( output_controls *out_control, mpi_datatypes * /*mpi_data*/,
int my_rank, int skip, int num_section )
{
if( my_rank == MASTER_NODE )
@@ -259,7 +259,7 @@ int Write_Header( reax_system *system, control_params *control,
}
-int Write_Init_Desc( reax_system *system, control_params */*control*/,
+int Write_Init_Desc( reax_system *system, control_params * /*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, cnt, buffer_len, buffer_req;
@@ -482,7 +482,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
-int Write_Atoms( reax_system *system, control_params */*control*/,
+int Write_Atoms( reax_system *system, control_params * /*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, line_len, buffer_len, buffer_req, cnt;
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index 35342c9173..118735fbbd 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -76,7 +76,7 @@ void Calculate_dCos_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk,
void Valence_Angles( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls */*out_control*/ )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 97a2fb0349..020284312b 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -208,7 +208,7 @@ void AtomVecSMD::copy(int i, int j, int delflag) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_comm(int /*n*/, int */*list*/, double */*buf*/, int /*pbc_flag*/, int */*pbc*/) {
+int AtomVecSMD::pack_comm(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -333,7 +333,7 @@ int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_comm(int /*n*/, int /*first*/, double */*buf*/) {
+void AtomVecSMD::unpack_comm(int /*n*/, int /*first*/, double * /*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -441,7 +441,7 @@ int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_border(int /*n*/, int */*list*/, double */*buf*/, int /*pbc_flag*/, int */*pbc*/) {
+int AtomVecSMD::pack_border(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -633,7 +633,7 @@ int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_border(int /*n*/, int /*first*/, double */*buf*/) {
+void AtomVecSMD::unpack_border(int /*n*/, int /*first*/, double * /*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -1158,7 +1158,7 @@ void AtomVecSMD::pack_data(double **buf) {
pack hybrid atom info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_data_hybrid(int /*i*/, double */*buf*/) {
+int AtomVecSMD::pack_data_hybrid(int /*i*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1180,7 +1180,7 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
write hybrid atom info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_data_hybrid(FILE */*fp*/, double */*buf*/) {
+int AtomVecSMD::write_data_hybrid(FILE * /*fp*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1203,7 +1203,7 @@ void AtomVecSMD::pack_vel(double **buf) {
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_vel_hybrid(int /*i*/, double */*buf*/) {
+int AtomVecSMD::pack_vel_hybrid(int /*i*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1222,7 +1222,7 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
write hybrid velocity info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_vel_hybrid(FILE */*fp*/, double */*buf*/) {
+int AtomVecSMD::write_vel_hybrid(FILE * /*fp*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 3;
}
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index 1515849c53..b0944f1186 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -461,7 +461,7 @@ void FixSMDMoveTriSurf::reset_dt() {
/* ---------------------------------------------------------------------- */
-int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
+int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double **x0 = atom->x0;
double **smd_data_9 = atom->smd_data_9;
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 8af12acd99..a2813cc3ca 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -512,7 +512,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) {
/* ---------------------------------------------------------------------- */
-int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
+int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *radius = atom->radius;
double *vfrac = atom->vfrac;
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index f9922ef222..09fe3b1180 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -1839,7 +1839,7 @@ void *PairTlsph::extract(const char *str, int &/*i*/) {
/* ---------------------------------------------------------------------- */
-int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
+int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
tagint *mol = atom->molecule;
double *damage = atom->damage;
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index aa88e125d6..ff3720b2ff 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -1487,7 +1487,7 @@ double PairULSPH::memory_usage() {
/* ---------------------------------------------------------------------- */
-int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
+int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
double *vfrac = atom->vfrac;
double *eff_plastic_strain = atom->eff_plastic_strain;
int i, j, m;
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 9eee7d0728..a8cce49749 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -3334,7 +3334,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
/* ---------------------------------------------------------------------- */
-void PairSMTBQ::Init_charge(int */*nQEq*/, int */*nQEqa*/, int */*nQEqc*/)
+void PairSMTBQ::Init_charge(int * /*nQEq*/, int * /*nQEqa*/, int * /*nQEqc*/)
{
int ii,i,gp,itype;
int *ilist,test[nteam],init[nteam];
@@ -3391,7 +3391,7 @@ void PairSMTBQ::Init_charge(int */*nQEq*/, int */*nQEqa*/, int */*nQEqc*/)
* COMMUNICATION
* ---------------------------------------------------------------------- */
-int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/)
+int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 9b5a535288..7a3c78efd0 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -288,7 +288,7 @@ double PairSPHRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
/* ---------------------------------------------------------------------- */
int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int */*pbc*/) {
+ int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index fc99137c3d..5b12b6def2 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -292,7 +292,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
return # of lines in section of data file labeled by keyword
------------------------------------------------------------------------- */
-bigint FixPropertyAtom::read_data_skip_lines(char */*keyword*/)
+bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/)
{
return atom->natoms;
}
diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp
index 86c724e17d..8a1fa529c6 100644
--- a/src/improper_zero.cpp
+++ b/src/improper_zero.cpp
@@ -99,13 +99,13 @@ void ImproperZero::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
-void ImproperZero::write_restart(FILE */*fp*/) {}
+void ImproperZero::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
-void ImproperZero::read_restart(FILE */*fp*/)
+void ImproperZero::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
diff --git a/src/library.cpp b/src/library.cpp
index 83e13efd08..245ae7ba84 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -336,7 +336,7 @@ void lammps_free(void *ptr)
customize by adding names
------------------------------------------------------------------------- */
-int lammps_extract_setting(void */*ptr*/, char *name)
+int lammps_extract_setting(void * /*ptr*/, char *name)
{
if (strcmp(name,"bigint") == 0) return sizeof(bigint);
if (strcmp(name,"tagint") == 0) return sizeof(tagint);
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 644f879c73..630cef309a 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -1108,7 +1108,7 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
merge of each component of an RCB bounding box
------------------------------------------------------------------------- */
-void box_merge(void *in, void *inout, int */*len*/, MPI_Datatype */*dptr*/)
+void box_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/)
{
RCB::BBox *box1 = (RCB::BBox *) in;
@@ -1138,7 +1138,7 @@ void box_merge(void *in, void *inout, int */*len*/, MPI_Datatype */*dptr*/)
all procs must get same proclo,prochi
------------------------------------------------------------------------- */
-void median_merge(void *in, void *inout, int */*len*/, MPI_Datatype */*dptr*/)
+void median_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/)
{
RCB::Median *med1 = (RCB::Median *) in;
--
GitLab
From a404da02d54d0c537a5c532eb545972ecb531f1a Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 27 Aug 2018 22:36:38 -0400
Subject: [PATCH 185/332] Use LMP_UNUSED_PARAM macro instead of existing
workarounds
---
src/image.cpp | 6 ++++--
src/lmptype.h | 4 +++-
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/src/image.cpp b/src/image.cpp
index 1e428921a2..3df167bbf6 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -992,7 +992,6 @@ void Image::compute_SSAO()
void Image::write_JPG(FILE *fp)
{
- (void)(fp); // suppress unused parameter warning
#ifdef LAMMPS_JPEG
struct jpeg_compress_struct cinfo;
struct jpeg_error_mgr jerr;
@@ -1018,6 +1017,8 @@ void Image::write_JPG(FILE *fp)
jpeg_finish_compress(&cinfo);
jpeg_destroy_compress(&cinfo);
+#else
+ LMP_UNUSED_PARAM(fp);
#endif
}
@@ -1025,7 +1026,6 @@ void Image::write_JPG(FILE *fp)
void Image::write_PNG(FILE *fp)
{
- (void)(fp); // suppress unused parameter warning
#ifdef LAMMPS_PNG
png_structp png_ptr;
png_infop info_ptr;
@@ -1076,6 +1076,8 @@ void Image::write_PNG(FILE *fp)
png_destroy_write_struct(&png_ptr, &info_ptr);
delete[] row_pointers;
+#else
+ LMP_UNUSED_PARAM(fp);
#endif
}
diff --git a/src/lmptype.h b/src/lmptype.h
index e5c202aa87..7c3dbc1c3d 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -213,6 +213,8 @@ typedef int bigint;
#include "lmpwindows.h"
#endif
-#define LMP_UNUSED_PARAM(x) (void)x
+// suppress unused parameter warning
+
+#define LMP_UNUSED_PARAM(x) (void)(x)
#endif
--
GitLab
From cb318f55e95e2cd237d4830ea7b3552d509b87ad Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 28 Aug 2018 10:11:16 -0400
Subject: [PATCH 186/332] Add missing or lost cmake changes
---
cmake/CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 076f1025dc..b0da29db26 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -195,7 +195,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ)
+set(OTHER_PACKAGES CORESHELL QEQ MESSAGE)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
@@ -1198,7 +1198,7 @@ endif()
###############################################################################
# Print package summary
###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
--
GitLab
From eb850c53264d83a5b11f79cd13f0d5ece2c34482 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 28 Aug 2018 15:17:31 -0400
Subject: [PATCH 187/332] silence compiler warning about unused static function
in shared include file
---
src/USER-CGSDK/lj_sdk_common.h | 2 ++
src/USER-CGSDK/pair_lj_sdk.cpp | 1 +
src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 1 +
3 files changed, 4 insertions(+)
diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h
index c1f2cf215a..055d6228fc 100644
--- a/src/USER-CGSDK/lj_sdk_common.h
+++ b/src/USER-CGSDK/lj_sdk_common.h
@@ -27,6 +27,7 @@ namespace LJSDKParms {
// LJ type flags. list of supported LJ exponent combinations
enum {LJ_NOT_SET=0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES};
+#if defined(LMP_NEED_FIND_SDK_LJ_TYPE)
static int find_lj_type(const char *label,
const char * const * const list) {
for (int i=0; i < NUM_LJ_TYPES; ++i)
@@ -34,6 +35,7 @@ namespace LJSDKParms {
return LJ_NOT_SET;
}
+#endif
static const char * const lj_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6"};
static const double lj_prefact[] = {0.0, 6.75, 2.59807621135332, 4.0};
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index cbcba7f6b2..d6e755aaab 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -33,6 +33,7 @@
#include "memory.h"
#include "error.h"
+#define LMP_NEED_FIND_SDK_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index 1d93363e20..e1be18c6a8 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -34,6 +34,7 @@
#include "memory.h"
#include "error.h"
+#define LMP_NEED_FIND_SDK_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
--
GitLab
From 03654b2b7f108064625961b41049c8f6ee24dcce Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 28 Aug 2018 15:19:07 -0400
Subject: [PATCH 188/332] rename define to better fit LAMMPS' logic
---
src/USER-CGSDK/lj_sdk_common.h | 2 +-
src/USER-CGSDK/pair_lj_sdk.cpp | 2 +-
src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h
index 055d6228fc..51dcb4c2b7 100644
--- a/src/USER-CGSDK/lj_sdk_common.h
+++ b/src/USER-CGSDK/lj_sdk_common.h
@@ -27,7 +27,7 @@ namespace LJSDKParms {
// LJ type flags. list of supported LJ exponent combinations
enum {LJ_NOT_SET=0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES};
-#if defined(LMP_NEED_FIND_SDK_LJ_TYPE)
+#if defined(LMP_NEED_SDK_FIND_LJ_TYPE)
static int find_lj_type(const char *label,
const char * const * const list) {
for (int i=0; i < NUM_LJ_TYPES; ++i)
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index d6e755aaab..3404beb58a 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -33,7 +33,7 @@
#include "memory.h"
#include "error.h"
-#define LMP_NEED_FIND_SDK_LJ_TYPE 1
+#define LMP_NEED_SDK_FIND_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index e1be18c6a8..c51235518b 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -34,7 +34,7 @@
#include "memory.h"
#include "error.h"
-#define LMP_NEED_FIND_SDK_LJ_TYPE 1
+#define LMP_NEED_SDK_FIND_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
--
GitLab
From 30d45e6773e5eca5065c76c25ad8e0090b9a2cfd Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 28 Aug 2018 15:22:43 -0400
Subject: [PATCH 189/332] Ensure MESSAGE files are added to CMake compilation
---
cmake/CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index b0da29db26..f22df48afe 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -188,14 +188,14 @@ if(ENABLE_TESTING)
endif(ENABLE_TESTING)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
+ KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ MESSAGE)
+set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
--
GitLab
From 83d453e78bb6fdf52ab47d61a6e411c6e480b156 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Tue, 28 Aug 2018 17:08:52 -0600
Subject: [PATCH 190/332] updates to MD protocol and examples
---
examples/COUPLE/lammps_mc/README | 20 +--
...Jul18.zmq.g++.1 => log.28Aug18.file.g++.1} | 40 +++---
...ul18.file.g++.4 => log.28Aug18.file.g++.4} | 40 +++---
...Jul18.file.g++.1 => log.28Aug18.zmq.g++.1} | 24 ++--
...3Jul18.zmq.g++.4 => log.28Aug18.zmq.g++.4} | 36 ++---
examples/COUPLE/lammps_mc/mc.cpp | 7 +-
examples/COUPLE/lammps_mc/mc.h | 4 +-
examples/COUPLE/lammps_vasp/README | 3 +-
examples/COUPLE/lammps_vasp/vasp_wrap.py | 117 ++++++++++++----
examples/message/README | 17 ++-
examples/message/Script.sh | 55 ++++++++
examples/message/in.message | 2 +
examples/message/in.message.client | 3 +
examples/message/in.message.tilt | 30 ++++
examples/message/in.message.tilt.client | 42 ++++++
examples/message/in.message.tilt.server | 31 +++++
... => log.28Aug18.message.client.file.g++.1} | 21 +--
... => log.28Aug18.message.client.file.g++.2} | 23 ++--
...> log.28Aug18.message.client.mpione.g++.1} | 21 +--
...> log.28Aug18.message.client.mpione.g++.2} | 23 ++--
...> log.28Aug18.message.client.mpitwo.g++.1} | 25 ++--
...> log.28Aug18.message.client.mpitwo.g++.2} | 25 ++--
...1 => log.28Aug18.message.client.zmq.g++.1} | 25 ++--
...2 => log.28Aug18.message.client.zmq.g++.2} | 25 ++--
...essage.g++.1 => log.28Aug18.message.g++.1} | 24 ++--
...essage.g++.4 => log.28Aug18.message.g++.4} | 24 ++--
... => log.28Aug18.message.server.file.g++.1} | 2 +-
... => log.28Aug18.message.server.file.g++.4} | 2 +-
...> log.28Aug18.message.server.mpione.g++.1} | 2 +-
...> log.28Aug18.message.server.mpione.g++.4} | 2 +-
...> log.28Aug18.message.server.mpitwo.g++.1} | 2 +-
...> log.28Aug18.message.server.mpitwo.g++.4} | 2 +-
...1 => log.28Aug18.message.server.zmq.g++.1} | 2 +-
...4 => log.28Aug18.message.server.zmq.g++.4} | 2 +-
...g.28Aug18.message.tilt.client.mpione.g++.1 | 130 ++++++++++++++++++
...g.28Aug18.message.tilt.client.mpione.g++.2 | 130 ++++++++++++++++++
...g.28Aug18.message.tilt.client.mpitwo.g++.1 | 130 ++++++++++++++++++
...g.28Aug18.message.tilt.client.mpitwo.g++.2 | 130 ++++++++++++++++++
.../log.28Aug18.message.tilt.client.zmq.g++.1 | 130 ++++++++++++++++++
.../log.28Aug18.message.tilt.client.zmq.g++.2 | 130 ++++++++++++++++++
.../message/log.28Aug18.message.tilt.g++.1 | 129 +++++++++++++++++
.../message/log.28Aug18.message.tilt.g++.4 | 129 +++++++++++++++++
...g.28Aug18.message.tilt.server.mpione.g++.1 | 48 +++++++
...g.28Aug18.message.tilt.server.mpione.g++.4 | 48 +++++++
...g.28Aug18.message.tilt.server.mpitwo.g++.1 | 48 +++++++
...g.28Aug18.message.tilt.server.mpitwo.g++.4 | 48 +++++++
.../log.28Aug18.message.tilt.server.zmq.g++.1 | 48 +++++++
.../log.28Aug18.message.tilt.server.zmq.g++.4 | 48 +++++++
src/MESSAGE/fix_client_md.cpp | 7 +-
src/MESSAGE/fix_client_md.h | 10 +-
src/MESSAGE/server_md.cpp | 17 +--
src/MESSAGE/server_md.h | 3 +-
52 files changed, 1847 insertions(+), 239 deletions(-)
rename examples/COUPLE/lammps_mc/{log.23Jul18.zmq.g++.1 => log.28Aug18.file.g++.1} (91%)
rename examples/COUPLE/lammps_mc/{log.23Jul18.file.g++.4 => log.28Aug18.file.g++.4} (88%)
rename examples/COUPLE/lammps_mc/{log.23Jul18.file.g++.1 => log.28Aug18.zmq.g++.1} (95%)
rename examples/COUPLE/lammps_mc/{log.23Jul18.zmq.g++.4 => log.28Aug18.zmq.g++.4} (90%)
create mode 100644 examples/message/Script.sh
create mode 100644 examples/message/in.message.tilt
create mode 100644 examples/message/in.message.tilt.client
create mode 100644 examples/message/in.message.tilt.server
rename examples/message/{log.23Jul18.message.client.file.g++.1 => log.28Aug18.message.client.file.g++.1} (81%)
rename examples/message/{log.23Jul18.message.client.file.g++.2 => log.28Aug18.message.client.file.g++.2} (78%)
rename examples/message/{log.23Jul18.message.client.mpione.g++.1 => log.28Aug18.message.client.mpione.g++.1} (79%)
rename examples/message/{log.23Jul18.message.client.mpione.g++.2 => log.28Aug18.message.client.mpione.g++.2} (77%)
rename examples/message/{log.23Jul18.message.client.mpitwo.g++.1 => log.28Aug18.message.client.mpitwo.g++.1} (77%)
rename examples/message/{log.23Jul18.message.client.mpitwo.g++.2 => log.28Aug18.message.client.mpitwo.g++.2} (76%)
rename examples/message/{log.23Jul18.message.client.zmq.g++.1 => log.28Aug18.message.client.zmq.g++.1} (76%)
rename examples/message/{log.23Jul18.message.client.zmq.g++.2 => log.28Aug18.message.client.zmq.g++.2} (76%)
rename examples/message/{log.23Jul18.message.g++.1 => log.28Aug18.message.g++.1} (76%)
rename examples/message/{log.23Jul18.message.g++.4 => log.28Aug18.message.g++.4} (76%)
rename examples/message/{log.23Jul18.message.server.file.g++.1 => log.28Aug18.message.server.file.g++.1} (98%)
rename examples/message/{log.23Jul18.message.server.file.g++.4 => log.28Aug18.message.server.file.g++.4} (98%)
rename examples/message/{log.23Jul18.message.server.mpione.g++.1 => log.28Aug18.message.server.mpione.g++.1} (98%)
rename examples/message/{log.23Jul18.message.server.mpione.g++.4 => log.28Aug18.message.server.mpione.g++.4} (98%)
rename examples/message/{log.23Jul18.message.server.mpitwo.g++.1 => log.28Aug18.message.server.mpitwo.g++.1} (98%)
rename examples/message/{log.23Jul18.message.server.mpitwo.g++.4 => log.28Aug18.message.server.mpitwo.g++.4} (98%)
rename examples/message/{log.23Jul18.message.server.zmq.g++.1 => log.28Aug18.message.server.zmq.g++.1} (98%)
rename examples/message/{log.23Jul18.message.server.zmq.g++.4 => log.28Aug18.message.server.zmq.g++.4} (98%)
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README
index 512f7304de..af4d86f92f 100644
--- a/examples/COUPLE/lammps_mc/README
+++ b/examples/COUPLE/lammps_mc/README
@@ -26,21 +26,25 @@ Build LAMMPS and the MC client code
First, build LAMMPS with its MESSAGE package installed:
-cd lammps/lib/message
-python Install.py -m -z # build CSlib with MPI and ZMQ support
-cd lammps/src
-make yes-message
-make mpi
+% cd lammps/lib/message
+% python Install.py -m -z # build CSlib with MPI and ZMQ support
+% python Install.py -s -z # also build serial lib and ZMQ support
+% cd lammps/src
+% make yes-message
+% make mpi
You can leave off the -z if you do not have ZMQ on your system.
-Next build the MC client code:
+Next build the MC client code, which will link with the serial CSlib.
First edit the Makefile in this dir. The CSLIB variable should be the
path to where the LAMMPS lib/message dir is on your system. If you
built the CSlib without ZMQ support you will also need to
-comment/uncomment two lines. Then you can just type "make" and you
-should get an "mc" executable.
+comment/uncomment two lines. Then you can just type
+
+% make
+
+and you should get an "mc" executable.
----------------
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
similarity index 91%
rename from examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1
rename to examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
index 18af66d587..0d67c89cf1 100644
--- a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.1
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
@@ -1,10 +1,10 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
-message server mc zmq *:5555
+message server mc file tmp.couple
variable x index 5
variable y index 5
variable z index 5
@@ -24,7 +24,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000612974 secs
+ Time spent = 0.000649929 secs
mass 1 1.0
pair_style lj/cut 2.5
@@ -58,7 +58,7 @@ Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
-46.6% CPU use with 1 MPI tasks x no OpenMP threads
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -85,9 +85,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
-Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
-157.3% CPU use with 1 MPI tasks x no OpenMP threads
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -97,7 +97,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 1.907e-06 | | |100.00
+Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -119,9 +119,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
-Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
-209.7% CPU use with 1 MPI tasks x no OpenMP threads
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -131,7 +131,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 9.537e-07 | | |100.00
+Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -153,9 +153,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
-Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
-209.7% CPU use with 1 MPI tasks x no OpenMP threads
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 9.537e-07 | | |100.00
+Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -187,9 +187,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
-Loop time of 0 on 1 procs for 0 steps with 500 atoms
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
-0.0% CPU use with 1 MPI tasks x no OpenMP threads
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -199,7 +199,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0 | | | 0.00
+Other | | 2.146e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -221,9 +221,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
-Loop time of 0 on 1 procs for 0 steps with 500 atoms
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
-0.0% CPU use with 1 MPI tasks x no OpenMP threads
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -233,7 +233,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0 | | | 0.00
+Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -251,4 +251,4 @@ Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
-Total wall time: 0:00:00
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
similarity index 88%
rename from examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4
rename to examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
index 3b73e52595..2ae51d2461 100644
--- a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.4
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
@@ -24,7 +24,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000604868 secs
+ Time spent = 0.000592947 secs
mass 1 1.0
pair_style lj/cut 2.5
@@ -56,9 +56,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
-Loop time of 3.09944e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
-72.6% CPU use with 4 MPI tasks x no OpenMP threads
+59.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -68,7 +68,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.099e-06 | | |100.00
+Other | | 3.815e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -85,9 +85,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
-Loop time of 3.33786e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
-119.8% CPU use with 4 MPI tasks x no OpenMP threads
+106.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -97,7 +97,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.338e-06 | | |100.00
+Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -119,9 +119,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
-Loop time of 3.51667e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
-113.7% CPU use with 4 MPI tasks x no OpenMP threads
+113.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -131,7 +131,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.517e-06 | | |100.00
+Other | | 3.755e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -153,9 +153,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
-Loop time of 2.92063e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
-119.8% CPU use with 4 MPI tasks x no OpenMP threads
+117.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 2.921e-06 | | |100.00
+Other | | 2.563e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@@ -187,9 +187,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
-Loop time of 3.39746e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
-117.7% CPU use with 4 MPI tasks x no OpenMP threads
+93.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -199,7 +199,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.397e-06 | | |100.00
+Other | | 3.994e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
@@ -221,9 +221,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
-Loop time of 3.39746e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
-117.7% CPU use with 4 MPI tasks x no OpenMP threads
+111.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -233,7 +233,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.397e-06 | | |100.00
+Other | | 3.576e-06 | | |100.00
Nlocal: 125 ave 132 max 118 min
Histogram: 1 0 0 0 0 2 0 0 0 1
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
similarity index 95%
rename from examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1
rename to examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
index 34e016e0c1..0565487bc6 100644
--- a/examples/COUPLE/lammps_mc/log.23Jul18.file.g++.1
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
@@ -1,10 +1,10 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
-message server mc file tmp.couple
+message server mc zmq *:5555
variable x index 5
variable y index 5
variable z index 5
@@ -24,7 +24,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000633001 secs
+ Time spent = 0.000741005 secs
mass 1 1.0
pair_style lj/cut 2.5
@@ -85,9 +85,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
-Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
-46.6% CPU use with 1 MPI tasks x no OpenMP threads
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -97,7 +97,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 2.146e-06 | | |100.00
+Other | | 1.907e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -119,9 +119,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
-Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
-157.3% CPU use with 1 MPI tasks x no OpenMP threads
+83.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -131,7 +131,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 1.907e-06 | | |100.00
+Other | | 1.192e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -189,7 +189,7 @@ Step Temp E_pair E_mol TotEng Press
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
-314.6% CPU use with 1 MPI tasks x no OpenMP threads
+104.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -223,7 +223,7 @@ Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
-314.6% CPU use with 1 MPI tasks x no OpenMP threads
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -251,4 +251,4 @@ Step Temp E_pair E_mol TotEng Press
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
-Total wall time: 0:00:02
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
similarity index 90%
rename from examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4
rename to examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
index 480566635f..e74d03235d 100644
--- a/examples/COUPLE/lammps_mc/log.23Jul18.zmq.g++.4
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones Monte Carlo server script
variable mode index file
@@ -24,7 +24,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000566006 secs
+ Time spent = 0.000576019 secs
mass 1 1.0
pair_style lj/cut 2.5
@@ -56,9 +56,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
-Loop time of 4.29153e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
-99.0% CPU use with 4 MPI tasks x no OpenMP threads
+89.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -68,7 +68,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 4.292e-06 | | |100.00
+Other | | 4.768e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -85,9 +85,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7723127 0 -4.6166327 -5.015531
-Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
-97.9% CPU use with 4 MPI tasks x no OpenMP threads
+94.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -97,7 +97,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.576e-06 | | |100.00
+Other | | 3.457e-06 | | |100.00
Nlocal: 125 ave 125 max 125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -119,9 +119,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
-Loop time of 3.09944e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
-121.0% CPU use with 4 MPI tasks x no OpenMP threads
+115.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -131,7 +131,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 3.099e-06 | | |100.00
+Other | | 3.04e-06 | | |100.00
Nlocal: 125 ave 126 max 124 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@@ -153,9 +153,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
-Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
-139.8% CPU use with 4 MPI tasks x no OpenMP threads
+125.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 2.146e-06 | | |100.00
+Other | | 2.384e-06 | | |100.00
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@@ -187,9 +187,9 @@ run 0
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
Step Temp E_pair E_mol TotEng Press
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
-Loop time of 1.90735e-06 on 4 procs for 0 steps with 500 atoms
+Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
-157.3% CPU use with 4 MPI tasks x no OpenMP threads
+112.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@@ -199,7 +199,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 1.907e-06 | | |100.00
+Other | | 2.444e-06 | | |100.00
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 0 1 0 1 0 1
@@ -223,7 +223,7 @@ Step Temp E_pair E_mol TotEng Press
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
-151.5% CPU use with 4 MPI tasks x no OpenMP threads
+139.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp
index e62a786ac8..7c2e2ce039 100644
--- a/examples/COUPLE/lammps_mc/mc.cpp
+++ b/examples/COUPLE/lammps_mc/mc.cpp
@@ -92,9 +92,10 @@ CSlib *cs_create(char *mode, char *arg)
// MC class
// ----------------------------------------------------------------------
-MC::MC(char *mcfile, CSlib *cs_caller)
+MC::MC(char *mcfile, void *cs_caller)
+//MC::MC(char *mcfile, CSlib *cs_caller)
{
- cs = cs_caller;
+ cs_void = cs_caller;
// setup MC params
@@ -125,6 +126,8 @@ void MC::run()
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+ CSlib *cs = (CSlib *) cs_void;
+
// one-time request for atom count from MD
// allocate 1d coord buffer
diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h
index afeb3d06ab..e9d88523fc 100644
--- a/examples/COUPLE/lammps_mc/mc.h
+++ b/examples/COUPLE/lammps_mc/mc.h
@@ -14,7 +14,7 @@ class MC {
int naccept; // # of accepted MC events
int nattempt; // # of attempted MC events
- MC(char *, class CSlib *);
+ MC(char *, void *);
~MC();
void run();
@@ -32,7 +32,7 @@ class MC {
int seed; // RNG seed
class RanPark *random;
- class CSlib *cs; // messaging library
+ void *cs_void; // messaging library
void options(char *);
};
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
index 91a85975e6..b301bd779f 100644
--- a/examples/COUPLE/lammps_vasp/README
+++ b/examples/COUPLE/lammps_vasp/README
@@ -40,7 +40,8 @@ You can run the vasp_wrap.py script as-is to test that the coupling
between it and LAMMPS is functional. This will use the included
vasprun.xml file output by a previous VASP run.
-But the as-is version of vasp_wrap.py will not attempt to run VASP.
+But note that the as-is version of vasp_wrap.py will not attempt to
+run VASP.
To do this, you must edit the 1st vaspcmd line at the top of
vasp_wrapper.py to be the launch command needed to run VASP on your
diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py
index 30d449e31c..1e2c52aa46 100644
--- a/examples/COUPLE/lammps_vasp/vasp_wrap.py
+++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py
@@ -13,18 +13,25 @@
# creates VASP inputs
# invokes VASP to calculate self-consistent energy of that config
# reads VASP outputs
-# sends message with energy, forces, virial to client
+# sends message with energy, forces, pressure to client
# NOTES:
# check to insure basic VASP input files are in place?
-# worry about archiving VASP input/output in special filenames or dirs?
-# how to get ordering (by type) of VASP atoms vs LAMMPS atoms
-# create one initial permutation vector?
+# could archive VASP input/output in special filenames or dirs?
+# need to check that POTCAR file is consistent with atom ordering?
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
+# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
-import sys,subprocess
-import xml.etree.ElementTree as ET
+from __future__ import print_function
+import sys
+
+version = sys.version_info[0]
+if version == 3:
+ sys.exit("The CSlib python wrapper does not yet support python 3")
+
+import subprocess
+import xml.etree.ElementTree as ET
from cslib import CSlib
# comment out 2nd line once 1st line is correct for your system
@@ -36,8 +43,8 @@ vaspcmd = "touch tmp"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
-UNITS,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE = range(1,10+1)
-FORCES,ENERGY,VIRIAL = range(1,3+1)
+DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
+FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
# -------------------------------------
# functions
@@ -45,7 +52,7 @@ FORCES,ENERGY,VIRIAL = range(1,3+1)
# error message and exit
def error(txt):
- print "ERROR:",txt
+ print("ERROR:",txt)
sys.exit(1)
# -------------------------------------
@@ -88,9 +95,9 @@ def poscar_write(poscar,natoms,ntypes,types,coords,box):
psnew.write(psold[0])
psnew.write(psold[1])
- psnew.write("%g 0.0 0.0\n" % box[0])
- psnew.write("0.0 %g 0.0\n" % box[1])
- psnew.write("0.0 0.0 %g\n" % box[2])
+ psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
+ psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
+ psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
psnew.write(psold[5])
psnew.write(psold[6])
@@ -149,6 +156,7 @@ def vasprun_read():
sxx = stensor[0][0]
syy = stensor[1][1]
szz = stensor[2][2]
+ # symmetrize off-diagonal components
sxy = 0.5 * (stensor[0][1] + stensor[1][0])
sxz = 0.5 * (stensor[0][2] + stensor[2][0])
syz = 0.5 * (stensor[1][2] + stensor[2][1])
@@ -164,7 +172,7 @@ def vasprun_read():
# command-line args
if len(sys.argv) != 3:
- print "Syntax: python vasp_wrap.py file/zmq POSCARfile"
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
mode = sys.argv[1]
@@ -173,7 +181,7 @@ poscar_template = sys.argv[2]
if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
else:
- print "Syntax: python vasp_wrap.py file/zmq POSCARfile"
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
sys.exit(1)
natoms,ntypes,box = vasp_setup(poscar_template)
@@ -196,30 +204,87 @@ while 1:
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
if msgID < 0: break
- # could generalize this to be more like ServerMD class
- # allow for box size, atom types, natoms, etc
+ # SETUP receive at beginning of each run
+ # required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ # NATOMS, NTYPES, TYPES, COORDS
+ # optional fields: others in enum above, but VASP ignores them
+
+ if msgID == SETUP:
+
+ origin = []
+ box = []
+ natoms_recv = ntypes_recv = 0
+ types = []
+ coords = []
+
+ for field in fieldID:
+ if field == DIM:
+ dim = cs.unpack_int(DIM)
+ if dim != 3: error("VASP only performs 3d simulations")
+ elif field == PERIODICITY:
+ periodicity = cs.unpack(PERIODICITY,1)
+ if not periodicity[0] or not periodicity[1] or not periodicity[2]:
+ error("VASP wrapper only currently supports fully periodic systems")
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+ elif field == NATOMS:
+ natoms_recv = cs.unpack_int(NATOMS)
+ if natoms != natoms_recv:
+ error("VASP wrapper mis-match in number of atoms")
+ elif field == NTYPES:
+ ntypes_recv = cs.unpack_int(NTYPES)
+ if ntypes != ntypes_recv:
+ error("VASP wrapper mis-match in number of atom types")
+ elif field == TYPES:
+ types = cs.unpack(TYPES,1)
+ elif field == COORDS:
+ coords = cs.unpack(COORDS,1)
+
+ if not origin or not box or not natoms or not ntypes or \
+ not types or not coords:
+ error("Required VASP wrapper setup field not received");
+
+ # STEP receive at each timestep of run or minimization
+ # required fields: COORDS
+ # optional fields: ORIGIN, BOX
+
+ elif msgID == STEP:
+
+ coords = []
+
+ for field in fieldID:
+ if field == COORDS:
+ coords = cs.unpack(COORDS,1)
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+
+ if not coords: error("Required VASP wrapper step field not received");
+
+ else: error("VASP wrapper received unrecognized message")
- # unpack coords from client
- # create VASP input
- # NOTE: generalize this for general list of atom types
+ # create POSCAR file
- coords = cs.unpack(COORDS,1)
- #types = cs.unpack(2);
- types = 2*[1]
-
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
# invoke VASP
- print "\nLaunching VASP ..."
- print vaspcmd
+ print("\nLaunching VASP ...")
+ print(vaspcmd)
subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
# process VASP output
energy,forces,virial = vasprun_read()
- # return forces, energy, virial to client
+ # convert VASP kilobars to bars
+
+ for i,value in enumerate(virial): virial[i] *= 1000.0
+
+ # return forces, energy, pressure to client
cs.send(msgID,3);
cs.pack(FORCES,4,3*natoms,forces)
diff --git a/examples/message/README b/examples/message/README
index 617a4249a5..34a5794e7a 100644
--- a/examples/message/README
+++ b/examples/message/README
@@ -26,6 +26,9 @@ lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
This applies to either in.message or in.message.client
+You can also run the in.message scripts with an NPT integrator
+instead of NVE, if you comment/uncomment the correct lines.
+
The client and server script define a "mode" variable
which can be set to file, zmq, mpi/one, or mpi/two,
as illustrated below.
@@ -38,6 +41,8 @@ do one of these:
% lmp_serial < in.message
% mpirun -np 4 lmp_mpi < in.message
+Or run with in.message.tilt.
+
--------------
To run in client/server mode:
@@ -75,6 +80,11 @@ processes together to exchange MPI messages between them.
--------------
+NOTE: the Script.sh file has comands to perform all the
+runs listed below.
+
+--------------
+
File or ZMQ or mpi/two modes of messaging:
% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
@@ -86,13 +96,18 @@ File or ZMQ or mpi/two modes of messaging:
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
+Or run with in.message.tilt.client/server.
+Don't run the tilt files with the "file" mode; they run too slow.
+
--------------
Mpi/one mode of messaging:
Launch LAMMPS twice in a single mpirun command:
-mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.server
+% mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.server
+
+Or run with in.message.tilt.client/server.
The two -np values determine how many procs the client and the server
run on.
diff --git a/examples/message/Script.sh b/examples/message/Script.sh
new file mode 100644
index 0000000000..0125bdd500
--- /dev/null
+++ b/examples/message/Script.sh
@@ -0,0 +1,55 @@
+# sample launch script
+
+# message on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message
+
+mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
+
+# message on 2/4 procs each
+
+mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message
+
+mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
+
+# message.tilt on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -mpi 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -mpi 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
+
+# message.tilt on 2/4 procs each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -mpi 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -mpi 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
diff --git a/examples/message/in.message b/examples/message/in.message
index 951ff95e3b..7fbbffc355 100644
--- a/examples/message/in.message
+++ b/examples/message/in.message
@@ -22,6 +22,8 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
thermo 10
run 50
diff --git a/examples/message/in.message.client b/examples/message/in.message.client
index 0c548ef2e5..f1ec644a80 100644
--- a/examples/message/in.message.client
+++ b/examples/message/in.message.client
@@ -31,6 +31,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
diff --git a/examples/message/in.message.tilt b/examples/message/in.message.tilt
new file mode 100644
index 0000000000..51126eae1e
--- /dev/null
+++ b/examples/message/in.message.tilt
@@ -0,0 +1,30 @@
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client
new file mode 100644
index 0000000000..b55bc6585b
--- /dev/null
+++ b/examples/message/in.message.tilt.client
@@ -0,0 +1,42 @@
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.server b/examples/message/in.message.tilt.server
new file mode 100644
index 0000000000..ba211ed15f
--- /dev/null
+++ b/examples/message/in.message.tilt.server
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/log.23Jul18.message.client.file.g++.1 b/examples/message/log.28Aug18.message.client.file.g++.1
similarity index 81%
rename from examples/message/log.23Jul18.message.client.file.g++.1
rename to examples/message/log.28Aug18.message.client.file.g++.1
index 0e05f6dfd5..bca1d37dd5 100644
--- a/examples/message/log.23Jul18.message.client.file.g++.1
+++ b/examples/message/log.28Aug18.message.client.file.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.00067687 secs
+ Time spent = 0.000752926 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,9 +50,9 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 5.12413 on 1 procs for 50 steps with 500 atoms
+Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms
-Performance: 4215.352 tau/day, 9.758 timesteps/s
+Performance: 4298.421 tau/day, 9.950 timesteps/s
0.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
@@ -57,10 +60,10 @@ Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
-Comm | 0.0001719 | 0.0001719 | 0.0001719 | 0.0 | 0.00
-Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00
-Modify | 5.1232 | 5.1232 | 5.1232 | 0.0 | 99.98
-Other | | 0.0004876 | | | 0.01
+Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00
+Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
+Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98
+Other | | 0.0004668 | | | 0.01
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:19
+Total wall time: 0:00:05
diff --git a/examples/message/log.23Jul18.message.client.file.g++.2 b/examples/message/log.28Aug18.message.client.file.g++.2
similarity index 78%
rename from examples/message/log.23Jul18.message.client.file.g++.2
rename to examples/message/log.28Aug18.message.client.file.g++.2
index 959c85439e..1c868dde37 100644
--- a/examples/message/log.23Jul18.message.client.file.g++.2
+++ b/examples/message/log.28Aug18.message.client.file.g++.2
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000554085 secs
+ Time spent = 0.000613928 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 5.07392 on 2 procs for 50 steps with 500 atoms
+Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms
-Performance: 4257.065 tau/day, 9.854 timesteps/s
+Performance: 4299.499 tau/day, 9.953 timesteps/s
50.1% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.00
-Comm | 0.00022864 | 0.00023806 | 0.00024748 | 0.0 | 0.00
-Output | 0.00020814 | 0.00051165 | 0.00081515 | 0.0 | 0.01
-Modify | 5.0659 | 5.0695 | 5.073 | 0.2 | 99.91
-Other | | 0.003713 | | | 0.07
+Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00
+Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00
+Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01
+Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92
+Other | | 0.003203 | | | 0.06
Nlocal: 250 ave 255 max 245 min
Histogram: 1 0 0 0 0 0 0 0 0 1
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:07
+Total wall time: 0:00:05
diff --git a/examples/message/log.23Jul18.message.client.mpione.g++.1 b/examples/message/log.28Aug18.message.client.mpione.g++.1
similarity index 79%
rename from examples/message/log.23Jul18.message.client.mpione.g++.1
rename to examples/message/log.28Aug18.message.client.mpione.g++.1
index 95a3f99ef5..78bee72fdf 100644
--- a/examples/message/log.23Jul18.message.client.mpione.g++.1
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000674009 secs
+ Time spent = 0.000540018 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.0424271 on 1 procs for 50 steps with 500 atoms
+Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms
-Performance: 509109.009 tau/day, 1178.493 timesteps/s
+Performance: 534798.272 tau/day, 1237.959 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.02
-Comm | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.19
-Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.26
-Modify | 0.042014 | 0.042014 | 0.042014 | 0.0 | 99.03
-Other | | 0.0002129 | | | 0.50
+Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01
+Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16
+Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24
+Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17
+Other | | 0.0001726 | | | 0.43
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/message/log.23Jul18.message.client.mpione.g++.2 b/examples/message/log.28Aug18.message.client.mpione.g++.2
similarity index 77%
rename from examples/message/log.23Jul18.message.client.mpione.g++.2
rename to examples/message/log.28Aug18.message.client.mpione.g++.2
index 6ba653a2be..7d7af866e3 100644
--- a/examples/message/log.23Jul18.message.client.mpione.g++.2
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.2
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000527859 secs
+ Time spent = 0.000475883 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.027467 on 2 procs for 50 steps with 500 atoms
+Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms
-Performance: 786397.868 tau/day, 1820.365 timesteps/s
-99.9% CPU use with 2 MPI tasks x no OpenMP threads
+Performance: 1035997.740 tau/day, 2398.143 timesteps/s
+99.1% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 4.0531e-06 | 4.1723e-06 | 4.2915e-06 | 0.0 | 0.02
-Comm | 0.00017691 | 0.00018024 | 0.00018358 | 0.0 | 0.66
-Output | 9.3222e-05 | 0.00012612 | 0.00015903 | 0.0 | 0.46
-Modify | 0.026678 | 0.02676 | 0.026841 | 0.0 | 97.42
-Other | | 0.0003968 | | | 1.44
+Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02
+Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60
+Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38
+Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15
+Other | | 0.0001761 | | | 0.84
Nlocal: 250 ave 255 max 245 min
Histogram: 1 0 0 0 0 0 0 0 0 1
diff --git a/examples/message/log.23Jul18.message.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
similarity index 77%
rename from examples/message/log.23Jul18.message.client.mpitwo.g++.1
rename to examples/message/log.28Aug18.message.client.mpitwo.g++.1
index 3822a0eb35..ee97e7bd1a 100644
--- a/examples/message/log.23Jul18.message.client.mpitwo.g++.1
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000490904 secs
+ Time spent = 0.000603914 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.0624809 on 1 procs for 50 steps with 500 atoms
+Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms
-Performance: 345705.501 tau/day, 800.244 timesteps/s
-40.4% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 312504.627 tau/day, 723.390 timesteps/s
+42.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 7.391e-06 | 7.391e-06 | 7.391e-06 | 0.0 | 0.01
-Comm | 8.5831e-05 | 8.5831e-05 | 8.5831e-05 | 0.0 | 0.14
-Output | 0.00011873 | 0.00011873 | 0.00011873 | 0.0 | 0.19
-Modify | 0.062024 | 0.062024 | 0.062024 | 0.0 | 99.27
-Other | | 0.0002449 | | | 0.39
+Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01
+Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15
+Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20
+Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25
+Other | | 0.0002651 | | | 0.38
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:07
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
similarity index 76%
rename from examples/message/log.23Jul18.message.client.mpitwo.g++.2
rename to examples/message/log.28Aug18.message.client.mpitwo.g++.2
index 058fc9dbf7..72db0198d5 100644
--- a/examples/message/log.23Jul18.message.client.mpitwo.g++.2
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000692129 secs
+ Time spent = 0.000667095 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.0186305 on 2 procs for 50 steps with 500 atoms
+Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms
-Performance: 1159388.887 tau/day, 2683.771 timesteps/s
-50.7% CPU use with 2 MPI tasks x no OpenMP threads
+Performance: 1135563.588 tau/day, 2628.619 timesteps/s
+58.5% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 2.861e-06 | 3.8147e-06 | 4.7684e-06 | 0.0 | 0.02
-Comm | 0.00017023 | 0.00017631 | 0.00018239 | 0.0 | 0.95
-Output | 0.00010896 | 0.00013852 | 0.00016809 | 0.0 | 0.74
-Modify | 0.017709 | 0.017821 | 0.017933 | 0.1 | 95.66
-Other | | 0.0004908 | | | 2.63
+Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02
+Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95
+Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81
+Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58
+Other | | 0.0005029 | | | 2.64
Nlocal: 250 ave 255 max 245 min
Histogram: 1 0 0 0 0 0 0 0 0 1
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:05
+Total wall time: 0:00:01
diff --git a/examples/message/log.23Jul18.message.client.zmq.g++.1 b/examples/message/log.28Aug18.message.client.zmq.g++.1
similarity index 76%
rename from examples/message/log.23Jul18.message.client.zmq.g++.1
rename to examples/message/log.28Aug18.message.client.zmq.g++.1
index d895ee7556..23fa70c1be 100644
--- a/examples/message/log.23Jul18.message.client.zmq.g++.1
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000747919 secs
+ Time spent = 0.000734091 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.0769799 on 1 procs for 50 steps with 500 atoms
+Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms
-Performance: 280592.815 tau/day, 649.520 timesteps/s
-12.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 277513.222 tau/day, 642.392 timesteps/s
+11.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.01
-Comm | 9.5129e-05 | 9.5129e-05 | 9.5129e-05 | 0.0 | 0.12
-Output | 0.00011516 | 0.00011516 | 0.00011516 | 0.0 | 0.15
-Modify | 0.076471 | 0.076471 | 0.076471 | 0.0 | 99.34
-Other | | 0.0002928 | | | 0.38
+Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01
+Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11
+Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15
+Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37
+Other | | 0.0002885 | | | 0.37
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:08
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.client.zmq.g++.2 b/examples/message/log.28Aug18.message.client.zmq.g++.2
similarity index 76%
rename from examples/message/log.23Jul18.message.client.zmq.g++.2
rename to examples/message/log.28Aug18.message.client.zmq.g++.2
index 4bdb8abecc..7833befd21 100644
--- a/examples/message/log.23Jul18.message.client.zmq.g++.2
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.2
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - client script
variable mode index file
@@ -25,7 +25,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000608921 secs
+ Time spent = 0.000570059 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -34,6 +34,9 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
fix 2 all client/md
fix_modify 2 energy yes
@@ -47,20 +50,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 0 0 -4.6254647 0.49629637
40 0.69517962 0 0 -4.6253506 0.69303877
50 0.70150496 0 0 -4.6259832 0.59551518
-Loop time of 0.0453095 on 2 procs for 50 steps with 500 atoms
+Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms
-Performance: 476720.759 tau/day, 1103.520 timesteps/s
-55.6% CPU use with 2 MPI tasks x no OpenMP threads
+Performance: 518489.499 tau/day, 1200.207 timesteps/s
+56.5% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
-Neigh | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.01
-Comm | 0.0001595 | 0.00015998 | 0.00016046 | 0.0 | 0.35
-Output | 8.893e-05 | 0.00011587 | 0.00014281 | 0.0 | 0.26
-Modify | 0.044439 | 0.044582 | 0.044724 | 0.1 | 98.39
-Other | | 0.0004481 | | | 0.99
+Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01
+Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33
+Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27
+Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49
+Other | | 0.0003769 | | | 0.90
Nlocal: 250 ave 255 max 245 min
Histogram: 1 0 0 0 0 0 0 0 0 1
@@ -73,4 +76,4 @@ Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 4
Dangerous builds = 0
-Total wall time: 0:00:04
+Total wall time: 0:00:00
diff --git a/examples/message/log.23Jul18.message.g++.1 b/examples/message/log.28Aug18.message.g++.1
similarity index 76%
rename from examples/message/log.23Jul18.message.g++.1
rename to examples/message/log.28Aug18.message.g++.1
index 53457c0129..c06af4e0d1 100644
--- a/examples/message/log.23Jul18.message.g++.1
+++ b/examples/message/log.28Aug18.message.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - no client/server mode
variable x index 5
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000540972 secs
+ Time spent = 0.000682831 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -31,6 +31,8 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
thermo 10
run 50
@@ -54,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
-Loop time of 0.037292 on 1 procs for 50 steps with 500 atoms
+Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms
-Performance: 579212.643 tau/day, 1340.770 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 544341.699 tau/day, 1260.050 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.028156 | 0.028156 | 0.028156 | 0.0 | 75.50
-Neigh | 0.0069656 | 0.0069656 | 0.0069656 | 0.0 | 18.68
-Comm | 0.0011504 | 0.0011504 | 0.0011504 | 0.0 | 3.08
-Output | 0.00013399 | 0.00013399 | 0.00013399 | 0.0 | 0.36
-Modify | 0.00049257 | 0.00049257 | 0.00049257 | 0.0 | 1.32
-Other | | 0.0003934 | | | 1.05
+Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59
+Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41
+Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21
+Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32
+Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34
+Other | | 0.000448 | | | 1.13
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/message/log.23Jul18.message.g++.4 b/examples/message/log.28Aug18.message.g++.4
similarity index 76%
rename from examples/message/log.23Jul18.message.g++.4
rename to examples/message/log.28Aug18.message.g++.4
index 09bd755380..695b51f166 100644
--- a/examples/message/log.23Jul18.message.g++.4
+++ b/examples/message/log.28Aug18.message.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - no client/server mode
variable x index 5
@@ -19,7 +19,7 @@ Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
- Time spent = 0.000635862 secs
+ Time spent = 0.000656843 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@@ -31,6 +31,8 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
thermo 10
run 50
@@ -54,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
-Loop time of 0.0152688 on 4 procs for 50 steps with 500 atoms
+Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms
-Performance: 1414649.236 tau/day, 3274.651 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 1642350.242 tau/day, 3801.737 timesteps/s
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.006639 | 0.007916 | 0.0083909 | 0.8 | 51.84
-Neigh | 0.0015991 | 0.0018443 | 0.0019469 | 0.3 | 12.08
-Comm | 0.0041771 | 0.0047471 | 0.0063298 | 1.3 | 31.09
-Output | 9.6798e-05 | 0.00012475 | 0.00019407 | 0.0 | 0.82
-Modify | 0.00015974 | 0.0001967 | 0.00023103 | 0.0 | 1.29
-Other | | 0.0004399 | | | 2.88
+Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71
+Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82
+Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41
+Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98
+Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14
+Other | | 0.0003865 | | | 2.94
Nlocal: 125 ave 128 max 121 min
Histogram: 1 0 0 0 1 0 0 0 1 1
diff --git a/examples/message/log.23Jul18.message.server.file.g++.1 b/examples/message/log.28Aug18.message.server.file.g++.1
similarity index 98%
rename from examples/message/log.23Jul18.message.server.file.g++.1
rename to examples/message/log.28Aug18.message.server.file.g++.1
index 159332c2b4..cf1418d3c5 100644
--- a/examples/message/log.23Jul18.message.server.file.g++.1
+++ b/examples/message/log.28Aug18.message.server.file.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.file.g++.4 b/examples/message/log.28Aug18.message.server.file.g++.4
similarity index 98%
rename from examples/message/log.23Jul18.message.server.file.g++.4
rename to examples/message/log.28Aug18.message.server.file.g++.4
index f5ea67196f..c233bad692 100644
--- a/examples/message/log.23Jul18.message.server.file.g++.4
+++ b/examples/message/log.28Aug18.message.server.file.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.mpione.g++.1 b/examples/message/log.28Aug18.message.server.mpione.g++.1
similarity index 98%
rename from examples/message/log.23Jul18.message.server.mpione.g++.1
rename to examples/message/log.28Aug18.message.server.mpione.g++.1
index 245461d4b2..81e04aa923 100644
--- a/examples/message/log.23Jul18.message.server.mpione.g++.1
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.mpione.g++.4 b/examples/message/log.28Aug18.message.server.mpione.g++.4
similarity index 98%
rename from examples/message/log.23Jul18.message.server.mpione.g++.4
rename to examples/message/log.28Aug18.message.server.mpione.g++.4
index d4d9a98189..a185cb1c29 100644
--- a/examples/message/log.23Jul18.message.server.mpione.g++.4
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
similarity index 98%
rename from examples/message/log.23Jul18.message.server.mpitwo.g++.1
rename to examples/message/log.28Aug18.message.server.mpitwo.g++.1
index 440a03bad7..973a08eb6a 100644
--- a/examples/message/log.23Jul18.message.server.mpitwo.g++.1
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
similarity index 98%
rename from examples/message/log.23Jul18.message.server.mpitwo.g++.4
rename to examples/message/log.28Aug18.message.server.mpitwo.g++.4
index 0265bda54c..9e76e52d90 100644
--- a/examples/message/log.23Jul18.message.server.mpitwo.g++.4
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.zmq.g++.1 b/examples/message/log.28Aug18.message.server.zmq.g++.1
similarity index 98%
rename from examples/message/log.23Jul18.message.server.zmq.g++.1
rename to examples/message/log.28Aug18.message.server.zmq.g++.1
index 4fa9244bfe..ce5729878b 100644
--- a/examples/message/log.23Jul18.message.server.zmq.g++.1
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.23Jul18.message.server.zmq.g++.4 b/examples/message/log.28Aug18.message.server.zmq.g++.4
similarity index 98%
rename from examples/message/log.23Jul18.message.server.zmq.g++.4
rename to examples/message/log.28Aug18.message.server.zmq.g++.4
index f094153e83..b3201da4da 100644
--- a/examples/message/log.23Jul18.message.server.zmq.g++.4
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (22 Aug 2018)
# 3d Lennard-Jones melt - server script
variable mode index file
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
new file mode 100644
index 0000000000..a290ec307b
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000485897 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 12374053.445 tau/day, 28643.642 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12
+Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89
+Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03
+Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15
+Other | | 0.04905 | | | 2.81
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
new file mode 100644
index 0000000000..0089732355
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000453949 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 7638300.565 tau/day, 17681.251 timesteps/s
+100.0% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04
+Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89
+Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02
+Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41
+Other | | 0.07465 | | | 2.64
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
new file mode 100644
index 0000000000..814b3df1aa
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000543118 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 4497356.047 tau/day, 10410.546 timesteps/s
+50.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07
+Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70
+Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02
+Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25
+Other | | 0.09449 | | | 1.97
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
new file mode 100644
index 0000000000..7c172d3727
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000574827 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 3812643.232 tau/day, 8825.563 timesteps/s
+48.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03
+Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67
+Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01
+Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27
+Other | | 0.1146 | | | 2.02
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
new file mode 100644
index 0000000000..f5e2f220cd
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000530005 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 1666000.147 tau/day, 3856.482 timesteps/s
+23.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01
+Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16
+Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00
+Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28
+Other | | 0.07062 | | | 0.54
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
new file mode 100644
index 0000000000..8fc570f5da
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000673056 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 1586733.497 tau/day, 3672.994 timesteps/s
+59.3% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01
+Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21
+Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00
+Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04
+Other | | 0.0994 | | | 0.73
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/message/log.28Aug18.message.tilt.g++.1 b/examples/message/log.28Aug18.message.tilt.g++.1
new file mode 100644
index 0000000000..3f7cfc9da0
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.1
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000437021 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 18673426.371 tau/day, 43225.524 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66
+Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10
+Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85
+Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05
+Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42
+Other | | 0.05684 | | | 4.91
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.g++.4 b/examples/message/log.28Aug18.message.tilt.g++.4
new file mode 100644
index 0000000000..74061463f6
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.4
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000396967 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 23312793.646 tau/day, 53964.800 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26
+Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81
+Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87
+Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07
+Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98
+Other | | 0.0465 | | | 5.02
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
new file mode 100644
index 0000000000..428ff346ad
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000438929 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
new file mode 100644
index 0000000000..3da50163ed
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000455141 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
new file mode 100644
index 0000000000..fc29a6da63
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000521898 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
new file mode 100644
index 0000000000..758b84fe9d
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000378847 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
new file mode 100644
index 0000000000..78526ba748
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000557184 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
new file mode 100644
index 0000000000..b1ad768470
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000586987 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:13
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 97d0436a27..bfcca4841b 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -14,6 +14,7 @@
#include <cstdio>
#include <cstring>
#include "fix_client_md.h"
+#include "update.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
@@ -28,7 +29,7 @@ using namespace LAMMPS_NS;
using namespace CSLIB_NS;
using namespace FixConst;
-enum{OTHER,REAL,METAL}
+enum{OTHER,REAL,METAL};
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL,ERROR};
@@ -154,7 +155,7 @@ void FixClientMD::setup(int vflag)
receive_fev(vflag);
if (server_error) {
- str = char[64];
+ char str[64];
sprintf(str,"Fix client/md received server error %d\n",server_error);
error->all(FLERR,str);
}
@@ -205,7 +206,7 @@ void FixClientMD::post_force(int vflag)
receive_fev(vflag);
if (server_error) {
- str = char[64];
+ char str[64];
sprintf(str,"Fix client/md received server error %d\n",server_error);
error->all(FLERR,str);
}
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
index 9c70e4c026..262a4736ed 100644
--- a/src/MESSAGE/fix_client_md.h
+++ b/src/MESSAGE/fix_client_md.h
@@ -37,16 +37,16 @@ class FixClientMD : public Fix {
double compute_scalar();
private:
- int maxatom,units;
- double box[3][3];
+ int maxatom,units,server_error;
double eng;
- double *xpbc;
-
double inv_nprocs;
double fconvert,econvert,vconvert;
+ double box[3][3];
+ double *xpbc;
void pack_coords();
- void receive_fev(int );
+ void pack_box();
+ void receive_fev(int);
};
}
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index 340431021b..e51571e972 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -24,6 +24,7 @@
#include "neighbor.h"
#include "comm.h"
#include "domain.h"
+#include "memory.h"
#include "error.h"
// CSlib interface
@@ -33,7 +34,7 @@
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
-enum{OTHER,REAL,METAL}
+enum{OTHER,REAL,METAL};
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL,ERROR};
@@ -68,7 +69,7 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
/* ---------------------------------------------------------------------- */
-ServerMD::~ServerMD();
+ServerMD::~ServerMD()
{
memory->destroy(fcopy);
}
@@ -113,7 +114,7 @@ void ServerMD::loop()
double *box = NULL;
int *types = NULL;
double *coords = NULL;
- char *units = NULL;
+ char *unit_style = NULL;
double *charge = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
@@ -124,7 +125,7 @@ void ServerMD::loop()
} else if (fieldID[ifield] == PERIODICITY) {
periodicity = (int *) cs->unpack(PERIODICITY);
if (periodicity[0] != domain->periodicity[0] ||
- periodicity[1] != domain->periodicity[1]
+ periodicity[1] != domain->periodicity[1] ||
periodicity[2] != domain->periodicity[2])
error->all(FLERR,"Server md periodicity mis-match with client");
} else if (fieldID[ifield] == ORIGIN) {
@@ -145,7 +146,7 @@ void ServerMD::loop()
coords = (double *) cs->unpack(COORDS);
} else if (fieldID[ifield] == UNITS) {
- units = (char *) cs->unpack(UNITS);
+ unit_style = (char *) cs->unpack(UNITS);
} else if (fieldID[ifield] == CHARGE) {
charge = (double *) cs->unpack(CHARGE);
} else error->all(FLERR,"Server md setup field unknown");
@@ -155,7 +156,7 @@ void ServerMD::loop()
natoms < 0 || ntypes < 0 || !types || !coords)
error->all(FLERR,"Required server md setup field not received");
- if (units && strcmp(units,update->unit_style) != 0)
+ if (unit_style && strcmp(unit_style,update->unit_style) != 0)
error->all(FLERR,"Server md does not match client units");
if (charge && atom->q_flag == 0)
@@ -221,7 +222,7 @@ void ServerMD::loop()
// STEP receive at each timestep of run or minimization
// required fields: COORDS
- // optional fields: BOXLO, BOXHI, BOXTILT
+ // optional fields: ORIGIN, BOX
} else if (msgID == STEP) {
@@ -354,7 +355,7 @@ void ServerMD::send_fev(int msgID)
else {
double **f = atom->f;
int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++) {
+ for (int i = 0; i < nlocal; i++) {
fcopy[i][0] = fconvert*f[i][0];
fcopy[i][1] = fconvert*f[i][1];
fcopy[i][2] = fconvert*f[i][2];
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
index ecc713a4e8..35daad8df0 100644
--- a/src/MESSAGE/server_md.h
+++ b/src/MESSAGE/server_md.h
@@ -26,9 +26,10 @@ class ServerMD : protected Pointers {
private:
int units;
+ double fconvert,econvert,vconvert;
double **fcopy;
- void box_change(double *, double *, double *);
+ void box_change(double *, double *);
void send_fev(int);
};
--
GitLab
From 6ea33e3e893f4db561b50d46ebce383ff1460e48 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Aug 2018 06:51:20 -0400
Subject: [PATCH 191/332] Fix typo and use ZMQ stubs in CMake when necessary
---
cmake/CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index f22df48afe..9f6a31557f 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -500,7 +500,7 @@ if(PKG_MESSAGE)
target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
else()
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
- target_include_directories(cslib PRIVATE ${LAMMPS_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
endif()
list(APPEND LAMMPS_LINK_LIBS cslib)
--
GitLab
From 4c32a551bd62710628cfd04c8bb71c9f69555b32 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Aug 2018 07:24:38 -0400
Subject: [PATCH 192/332] Rename to libcs.a
---
cmake/CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 9f6a31557f..5541d8367e 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -486,6 +486,7 @@ if(PKG_MESSAGE)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "cs")
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
--
GitLab
From a7e9076bc08c44a582224f50dab4a895b769722e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Aug 2018 07:30:53 -0400
Subject: [PATCH 193/332] Rename to libcsmpi/libcsnompi like in Makefile
---
cmake/CMakeLists.txt | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 5541d8367e..d83289b178 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -486,12 +486,13 @@ if(PKG_MESSAGE)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
- set_target_properties(cslib PROPERTIES OUTPUT_NAME "cs")
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
if(MESSAGE_ZMQ)
--
GitLab
From 0860b9e674571d1735387dbb721b18636fc67d31 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Aug 2018 07:52:16 -0400
Subject: [PATCH 194/332] Build cslib static or as shared
---
cmake/CMakeLists.txt | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index d83289b178..c61110bb46 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -485,7 +485,12 @@ if(PKG_MESSAGE)
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
- add_library(cslib STATIC ${cslib_SOURCES})
+
+ if(BUILD_SHARED_LIBS)
+ add_library(cslib SHARED ${cslib_SOURCES})
+ else()
+ add_library(cslib STATIC ${cslib_SOURCES})
+ endif()
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
--
GitLab
From c5861307f6f3d16570eea928d62a658608b0eaa3 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Wed, 29 Aug 2018 10:58:09 -0600
Subject: [PATCH 195/332] cmake: add FindLAMMPS.cmake.in
---
cmake/CMakeLists.txt | 14 ++++++------
cmake/FindLAMMPS.cmake.in | 47 +++++++++++++++++++++++++++++++++++++++
2 files changed, 54 insertions(+), 7 deletions(-)
create mode 100644 cmake/FindLAMMPS.cmake.in
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 3ef3e8d7f4..ec33f913e0 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -1041,13 +1041,13 @@ if(BUILD_LIB)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
- if(BUILD_SHARED_LIBS)
- set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
- install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
- configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
- endif()
+ set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+ install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+ configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LIB_SUFFIX}.cmake @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
new file mode 100644
index 0000000000..e8fac703af
--- /dev/null
+++ b/cmake/FindLAMMPS.cmake.in
@@ -0,0 +1,47 @@
+# - Find liblammps
+# Find the native liblammps headers and libraries.
+#
+# The following variables will set:
+# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
+# LAMMPS_LIBRARIES - List of libraries when using lammps.
+# LAMMPS_VERSION - lammps library version
+# LAMMPS_FOUND - True if liblammps found.
+#
+# In addition a LAMMPS::LAMMPS imported target is getting created.
+#
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright (2003) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software. This software is distributed under
+# the GNU General Public License.
+#
+# See the README file in the top-level LAMMPS directory.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_LAMMPS liblammps@LIB_SUFFIX@)
+find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
+
+# TODO figure out library version from header
+set(LAMMPS_VERSION 20180822)
+
+find_library(LAMMPS_LIBRARY NAMES lammps@LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+
+set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
+set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
+
+mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
+
+if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
+ add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
+ set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION ${LAMMPS_LIBRARY} INTERFACE_INCLUDE_DIRECTORIES ${LAMMPS_INCLUDE_DIR})
+endif()
--
GitLab
From 499ffa198d0a1c4b98507e11dc92fc053e12d284 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Wed, 29 Aug 2018 11:31:28 -0600
Subject: [PATCH 196/332] cmake: change too generic LIB_SUFFIX to
LAMMPS_LIB_SUFFIX
---
cmake/CMakeLists.txt | 18 +++++++++---------
cmake/FindLAMMPS.cmake.in | 4 ++--
cmake/pkgconfig/liblammps.pc.in | 2 +-
3 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index ec33f913e0..d3d5499ca8 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -121,10 +121,10 @@ if(BUILD_LIB)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
- set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
- mark_as_advanced(LIB_SUFFIX)
- if(LIB_SUFFIX)
- set(LIB_SUFFIX "_${LIB_SUFFIX}")
+ set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
+ mark_as_advanced(LAMMPS_LIB_SUFFIX)
+ if(LAMMPS_LIB_SUFFIX)
+ set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
endif()
endif()
@@ -1040,14 +1040,14 @@ if(BUILD_LIB)
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
- set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
+ set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
- configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
- configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LIB_SUFFIX}.cmake @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
+ configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
index e8fac703af..e816f63f43 100644
--- a/cmake/FindLAMMPS.cmake.in
+++ b/cmake/FindLAMMPS.cmake.in
@@ -23,13 +23,13 @@
find_package(PkgConfig)
-pkg_check_modules(PC_LAMMPS liblammps@LIB_SUFFIX@)
+pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
# TODO figure out library version from header
set(LAMMPS_VERSION 20180822)
-find_library(LAMMPS_LIBRARY NAMES lammps@LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index 400b7593cf..41431bb54a 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
Version:
Requires:
-Libs: -L${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
--
GitLab
From 054abe280eabd73dc257941d002214674d5f52cd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 29 Aug 2018 14:55:36 -0400
Subject: [PATCH 197/332] squash some more compiler warnings
---
src/fix_tmd.cpp | 2 +-
src/library.cpp | 3 ++-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index ea448bd178..dd11dfd0c7 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -412,7 +412,7 @@ void FixTMD::readfile(char *file)
m++;
}
- MPI_Bcast(&eof,sizeof(char *)/sizeof(char),MPI_CHAR,0,world);
+ MPI_Bcast(&eof,sizeof(char *),MPI_CHAR,0,world);
MPI_Bcast(&nlines,1,MPI_INT,0,world);
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
diff --git a/src/library.cpp b/src/library.cpp
index 245ae7ba84..a46689da09 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1515,7 +1515,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
- "invalid total atoms " BIGINT_FORMAT " %lld",lmp->atom->natoms,natoms_prev+n);
+ "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT,
+ lmp->atom->natoms,natoms_prev+n);
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,str);
}
--
GitLab
From 47b8a116a67b2971cdfe72a7bb3f0d858f6868ab Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Wed, 29 Aug 2018 13:20:04 -0600
Subject: [PATCH 198/332] liblammps.pc: fixed a typo
---
cmake/pkgconfig/liblammps.pc.in | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index 41431bb54a..b9f35e9012 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
Version:
Requires:
-Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
--
GitLab
From db180209b3faec15d72abccbaaff9ec52ddf4960 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Wed, 29 Aug 2018 13:20:25 -0600
Subject: [PATCH 199/332] FindLAMMPS.cmake: add LAMMPS_API_DEFINES
---
cmake/FindLAMMPS.cmake.in | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
index e816f63f43..fc6dbb1a71 100644
--- a/cmake/FindLAMMPS.cmake.in
+++ b/cmake/FindLAMMPS.cmake.in
@@ -4,6 +4,7 @@
# The following variables will set:
# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
# LAMMPS_LIBRARIES - List of libraries when using lammps.
+# LAMMPS_API_DEFINES - lammps library api defines
# LAMMPS_VERSION - lammps library version
# LAMMPS_FOUND - True if liblammps found.
#
@@ -26,8 +27,9 @@ find_package(PkgConfig)
pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
-# TODO figure out library version from header
+# TODO figure these out library version from header
set(LAMMPS_VERSION 20180822)
+set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
@@ -43,5 +45,5 @@ mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
- set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION ${LAMMPS_LIBRARY} INTERFACE_INCLUDE_DIRECTORIES ${LAMMPS_INCLUDE_DIR})
+ set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
endif()
--
GitLab
From b0f5400d52c2cbf2c261437f20a4ab986b632b46 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Aug 2018 16:12:16 -0400
Subject: [PATCH 200/332] Add utility function to determine LAMMPS version in
CMake
---
cmake/CMakeLists.txt | 23 +++++++++++++++++++++++
cmake/FindLAMMPS.cmake.in | 3 +--
cmake/pkgconfig/liblammps.pc.in | 2 +-
3 files changed, 25 insertions(+), 3 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index d3d5499ca8..53ac20f5d9 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -43,6 +43,29 @@ function(validate_option name values)
endif()
endfunction(validate_option)
+function(get_lammps_version version_header variable)
+ file(READ ${version_header} line)
+ set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+ string(STRIP ${day} day)
+ string(STRIP ${month} month)
+ string(STRIP ${year} year)
+ list(FIND MONTHS "${month}" month)
+ string(LENGTH ${day} day_length)
+ string(LENGTH ${month} month_length)
+ if(day_length EQUAL 1)
+ set(day "0${day}")
+ endif()
+ if(month_length EQUAL 1)
+ set(month "0${month}")
+ endif()
+ set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
+
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
index fc6dbb1a71..586df83c2d 100644
--- a/cmake/FindLAMMPS.cmake.in
+++ b/cmake/FindLAMMPS.cmake.in
@@ -27,8 +27,7 @@ find_package(PkgConfig)
pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
-# TODO figure these out library version from header
-set(LAMMPS_VERSION 20180822)
+set(LAMMPS_VERSION @LAMMPS_VERSION@)
set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index b9f35e9012..445b2ab29e 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -4,7 +4,7 @@
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
--
GitLab
From 8f5512eafec70cfc11280bf705cd80978e987e9b Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 31 Aug 2018 09:49:35 -0600
Subject: [PATCH 201/332] patch 31Aug18
---
doc/src/Manual.txt | 4 ++--
src/version.h | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ad3e66a4b2..e442aa1808 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Aug 2018 version">
+<META NAME="docnumber" CONTENT="31 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-22 Aug 2018 version :c,h2
+31 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/src/version.h b/src/version.h
index 2192b25d91..fbeeabff8d 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "22 Aug 2018"
+#define LAMMPS_VERSION "31 Aug 2018"
--
GitLab
From 41f0951d0ce05d6f394f09a00972f52df837fe38 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Fri, 31 Aug 2018 10:09:03 -0600
Subject: [PATCH 202/332] liblammps.pc: add lammps version
---
cmake/pkgconfig/liblammps.pc.in | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index 445b2ab29e..7850972f3b 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -11,7 +11,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
Requires:
Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs.private: -lm
--
GitLab
From c4c5f9a32eb556ad78be55bdf188d9eae8c4e56b Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Fri, 31 Aug 2018 13:44:49 -0600
Subject: [PATCH 203/332] 2 new computes: chunk/spread/atom and reduce/chunk
---
doc/src/Commands_compute.txt | 2 +
doc/src/Howto_chunk.txt | 45 ++-
doc/src/compute.txt | 2 +
doc/src/compute_chunk_atom.txt | 11 +-
doc/src/compute_chunk_spread_atom.txt | 173 +++++++++
doc/src/compute_reduce.txt | 6 +-
doc/src/compute_reduce_chunk.txt | 177 +++++++++
doc/src/computes.txt | 2 +
doc/src/lammps.book | 2 +
src/compute_chunk_spread_atom.cpp | 352 ++++++++++++++++++
src/compute_chunk_spread_atom.h | 61 +++
src/compute_reduce.cpp | 1 +
src/compute_reduce_chunk.cpp | 512 ++++++++++++++++++++++++++
src/compute_reduce_chunk.h | 77 ++++
14 files changed, 1407 insertions(+), 16 deletions(-)
create mode 100644 doc/src/compute_chunk_spread_atom.txt
create mode 100644 doc/src/compute_reduce_chunk.txt
create mode 100644 src/compute_chunk_spread_atom.cpp
create mode 100644 src/compute_chunk_spread_atom.h
create mode 100644 src/compute_reduce_chunk.cpp
create mode 100644 src/compute_reduce_chunk.h
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 028e274c9b..6185634187 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -35,6 +35,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
+"chunk/spread/atom"_compute_chunk_spread_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"cnp/atom"_compute_cnp_atom.html,
@@ -97,6 +98,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"property/local"_compute_property_local.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
+"reduce/chunk"_compute_reduce_chunk.html,
"reduce/region"_compute_reduce.html,
"rigid/local"_compute_rigid_local.html,
"saed"_compute_saed.html,
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
index 8e52acf4b8..611b71dac7 100644
--- a/doc/src/Howto_chunk.txt
+++ b/doc/src/Howto_chunk.txt
@@ -22,7 +22,7 @@ commands, to calculate various properties of a system:
"fix ave/chunk"_fix_ave_chunk.html
any of the "compute */chunk"_compute.html commands :ul
-Here, each of the 3 kinds of chunk-related commands is briefly
+Here, each of the 4 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
@@ -83,8 +83,9 @@ chunk.
Compute */chunk commands: :h4
-Currently the following computes operate on chunks of atoms to produce
-per-chunk values.
+The following computes operate on chunks of atoms to produce per-chunk
+values. Any compute whose style name ends in "/chunk" is in this
+category:
"compute com/chunk"_compute_com_chunk.html
"compute gyration/chunk"_compute_gyration_chunk.html
@@ -111,8 +112,8 @@ of a center of mass, which requires summing mass*position over the
atoms and then dividing by summed mass.
All of these computes produce a global vector or global array as
-output, wih one or more values per chunk. They can be used
-in various ways:
+output, wih one or more values per chunk. The output can be used in
+various ways:
As input to the "fix ave/time"_fix_ave_time.html command, which can
write the values to a file and optionally time average them. :ulb,l
@@ -122,9 +123,27 @@ histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates. :l
As input to special functions of "equal-style
-variables"_variable.html, like sum() and max(). E.g. to find the
-largest cluster or fastest diffusing molecule. :l
-:ule
+variables"_variable.html, like sum() and max() and ave(). E.g. to
+find the largest cluster or fastest diffusing molecule or average
+radius-of-gyration of a set of molecules (chunks). :l :ule
+
+Other chunk commands: :h4
+
+"compute chunk/spread/atom"_compute_chunk_spread_atom.html
+"compute reduce/chunk"_compute_reduce_chunk.html :ul
+
+The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
+spreads per-chunk values to each atom in the chunk, producing per-atom
+values as its output. This can be useful for outputting per-chunk
+values to a per-atom "dump file"_dump.html. Or for using an atom's
+associated chunk value in an "atom-style variable"_variable.html.
+
+The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
+peratom value across the atoms in each chunk to produce a value per
+chunk. When used with the "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html command it can
+create peratom values that induce a new set of chunks with a second
+"compute chunk/atom"_compute_chunk_atom.html command.
Example calculations with chunks :h4
@@ -164,3 +183,13 @@ compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
+
+(6) An example of using a per-chunk value to apply per-atom forces to
+compress individual polymer chains (molecules) in a mixture, is
+explained on the "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
+
+(7) An example of using one set of per-chunk values for molecule
+chunks, to create a 2nd set of micelle-scale chunks (clustered
+molecules, due to hydrophobicity), is explained on the "compute
+chunk/reduce"_compute_reduce_chunk.html command doc page.
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 8facb4de63..72ea1c1930 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -183,6 +183,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
"bond/local"_compute_bond_local.html - distance and energy of each bond
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
+"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
"com"_compute_com.html - center-of-mass of group of atoms
@@ -225,6 +226,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
+"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
"slice"_compute_slice.html - extract values from global vector or array
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index e76b51e6ec..c29a5600a9 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/atom = style name of this compute command :l
-style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable}
+style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name
{bin/1d} args = dim origin delta
dim = {x} or {y} or {z}
origin = {lower} or {center} or {upper} or coordinate value (distance units)
@@ -40,7 +40,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
ncbin = # of concentric circle bins between rmin and rmax
{type} args = none
{molecule} args = none
- {compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args
+ c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name args = none
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@@ -85,7 +85,8 @@ compute 1 all chunk/atom bin/1d z lower 0.02 units reduced
compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5
compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes
compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes
-compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes :pre
+compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes
+compute 1 all chunk/atom c_cluster :pre
[Description:]
@@ -386,8 +387,8 @@ described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
-compute/fix/variable value) may have been > {Nc}, because of the
-compression operation.
+compute/fix/variable) may have been > {Nc}, because of the compression
+operation.
If {compress yes} is set, and the {compress} keyword comes after the
{limit} keyword, then the {limit} value of {Nc} is applied first to
diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt
new file mode 100644
index 0000000000..59662035e5
--- /dev/null
+++ b/doc/src/compute_chunk_spread_atom.txt
@@ -0,0 +1,173 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute chunk/spread/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+chunk/spread/atom = style name of this compute command :l
+chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
+one or more inputs can be listed :l
+input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l
+ c_ID = global vector calculated by a compute with ID
+ c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+ f_ID = global vector calculated by a fix with ID
+ f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre
+:ule
+
+[Examples:]
+
+compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
+
+[Description:]
+
+Define a calculation that "spreads" one or more per-chunk values to
+each atom in the chunk. This can be useful for creating a "dump
+file"_dump.html where each atom lists info about the chunk it is in,
+e.g. for post-processing purposes. It can also be used in "atom-style
+variables"_variable.html that need info about the chunk each atom is
+in. Examples are given below.
+
+In LAMMPS, chunks are collections of atoms defined by a "compute
+chunk/atom"_compute_chunk_atom.html command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the "compute
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+For inputs that are computes, they must be a compute that calculates
+per-chunk values. These are computes whose style names end in
+"/chunk".
+
+For inputs that are fixes, they should be a a fix that calculates
+per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or
+"fix ave/time"_fix_ave_time.html (assuming it is time-averaging
+per-chunk data).
+
+For each atom, this compute accesses its chunk ID from the specified
+{chunkID} compute, then accesses the per-chunk value in each input.
+Those values are copied to this compute to become the output for that
+atom.
+
+The values generated by this compute will be 0.0 for atoms not in the
+specified compute group {group-ID}. They will also be 0.0 if the atom
+is not in a chunk, as assigned by the {chunkID} compute. They will
+also be 0.0 if the current chunk ID for the atom is out-of-bounds with
+respect to the number of chunks stored by a particular input compute
+or fix.
+
+NOTE: LAMMPS does not check that a compute or fix which calculates
+per-chunk values uses the same definition of chunks as this compute.
+It's up to you to be consistent. Likewise, for a fix input, LAMMPS
+does not check that it is per-chunk data. It only checks that the fix
+produces a global vector or array.
+
+:line
+
+Each listed input is operated on independently.
+
+If a bracketed index I is used, it can be specified using a wildcard
+asterisk with the index to effectively specify multiple values. This
+takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
+columns in the array, then an asterisk with no numeric values means
+all indices from 1 to N. A leading asterisk means all indices from 1
+to n (inclusive). A trailing asterisk means all indices from n to N
+(inclusive). A middle asterisk means all indices from m to n
+(inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one. E.g. these 2 compute chunk/spread/atom
+commands are equivalent, since the "compute
+com/chunk"_compute_com_chunk.html command creates a per-atom array
+with 3 columns:
+
+compute com all com/chunk mychunk
+compute 10 all chunk/spread/atom mychunk c_com\[*\]
+compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre
+
+:line
+
+Here is an example of writing a dump file the with the center-of-mass
+(COM) for the chunk each atom is in:
+
+compute cmol all chunk/atom molecule
+compute com all com/chunk cmol
+compute comchunk all chunk/spread/atom cmol c_com[*]
+dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
+dump_modify 1 sort id :pre
+
+The same per-chunk data for each atom could be used to define per-atom
+forces for the "fix addforce"_fix_addforce.html command. In this
+example the forces act to pull atoms of an extended polymer chain
+towards its COM in an attractive manner.
+
+compute prop all property/atom xu yu zu
+variable k equal 0.1
+variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\])
+variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\])
+variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\])
+fix 3 all addforce v_fx v_fy v_fz :pre
+
+Note that "compute property/atom"_compute_property_atom.html is used
+to generate unwrapped coordinates for use in the per-atom force
+calculation, so that the effect of periodic boundaries is accounted
+for properly.
+
+Over time this applied force could shrink each polymer chain's radius
+of gyration in a polymer mixture simulation. Here is output after
+adding the above lines to the bench/in.chain script. The thermo
+output is shown for 1000 steps, where the last column is the average
+radius of gyration over all 320 chains in the 32000 atom system:
+
+compute gyr all gyration/chunk cmol
+variable ave equal ave(c_gyr)
+thermo_style custom step etotal press v_ave :pre
+
+ 0 22.394765 4.6721833 5.128278
+ 100 22.445002 4.8166709 5.0348372
+ 200 22.500128 4.8790392 4.9364875
+ 300 22.534686 4.9183766 4.8590693
+ 400 22.557196 4.9492211 4.7937849
+ 500 22.571017 4.9161853 4.7412008
+ 600 22.573944 5.0229708 4.6931243
+ 700 22.581804 5.0541301 4.6440647
+ 800 22.584683 4.9691734 4.6000016
+ 900 22.59128 5.0247538 4.5611513
+ 1000 22.586832 4.94697 4.5238362 :pre
+
+:line
+
+[Output info:]
+
+This compute calculates a per-atom vector or array, which can be
+accessed by any command that uses per-atom values from a compute as
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
+
+The output is a per-atom vector if a single input value is specified,
+otherwise a per-atom array is output. The number of columns in the
+array is the number of inputs provided. The per-atom values for the
+vector or each column of the array will be in whatever
+"units"_units.html the corresponding input value is in.
+
+The vector or array values are "intensive".
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute chunk/atom"_compute_chunk_atom.html, "fix
+ave/chunk"_fix_ave_chunk.html, "compute
+reduce/chunk"_compute_reduce_chunk.html
+
+[Default:] none
diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt
index ef3c7c6489..0bd2accf3c 100644
--- a/doc/src/compute_reduce.txt
+++ b/doc/src/compute_reduce.txt
@@ -97,9 +97,9 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html
command creates a per-atom array with 6 columns:
compute myPress all stress/atom NULL
-compute 2 all reduce min myPress\[*\]
-compute 2 all reduce min myPress\[1\] myPress\[2\] myPress\[3\] &
- myPress\[4\] myPress\[5\] myPress\[6\] :pre
+compute 2 all reduce min c_myPress\[*\]
+compute 2 all reduce min c_myPress\[1\] c_myPress\[2\] c_myPress\[3\] &
+ c_myPress\[4\] c_myPress\[5\] c_myPress\[6\] :pre
:line
diff --git a/doc/src/compute_reduce_chunk.txt b/doc/src/compute_reduce_chunk.txt
new file mode 100644
index 0000000000..3628c0f1ad
--- /dev/null
+++ b/doc/src/compute_reduce_chunk.txt
@@ -0,0 +1,177 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute reduce/chunk command :h3
+
+[Syntax:]
+
+compute ID group-ID reduce/chunk chunkID mode input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+reduce/chunk = style name of this compute command :l
+chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
+mode = {sum} or {min} or {max} :l
+one or more inputs can be listed :l
+input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_ID :l
+ c_ID = per-atom vector calculated by a compute with ID
+ c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+ f_ID = per-atom vector calculated by a fix with ID
+ f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+ v_name = per-atom vector calculated by an atom-style variable with name :pre
+:ule
+
+[Examples:]
+
+compute 1 all reduce/chunk/atom mychunk min c_cluster :pre
+
+[Description:]
+
+Define a calculation that reduces one or more per-atom vectors into
+per-chunk values. This can be useful for diagnostic output. Or when
+used in conjunction with the "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html command it can be
+used ot create per-atom values that induce a new set of chunks with a
+second "compute chunk/atom"_compute_chunk_atom.html command. An
+example is given below.
+
+In LAMMPS, chunks are collections of atoms defined by a "compute
+chunk/atom"_compute_chunk_atom.html command, which assigns each atom
+to a single chunk (or no chunk). The ID for this command is specified
+as chunkID. For example, a single chunk could be the atoms in a
+molecule or atoms in a spatial bin. See the "compute
+chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
+doc pages for details of how chunks can be defined and examples of how
+they can be used to measure properties of a system.
+
+For each atom, this compute accesses its chunk ID from the specified
+{chunkID} compute. The per-atom value from an input contributes
+to a per-chunk value corresponding the the chunk ID.
+
+The reduction operation is specified by the {mode} setting and is
+performed over all the per-atom values from the atoms in each chunk.
+The {sum} option adds the pre-atom values to a per-chunk total. The
+{min} or {max} options find the minimum or maximum value of the
+per-atom values for each chunk.
+
+Note that only atoms in the specified group contribute to the
+reduction operation. If the {chunkID} compute returns a 0 for the
+chunk ID of an atom (i.e. the atom is not in a chunk defined by the
+"compute chunk/atom"_compute_chunk_atom.html command), that atom will
+also not contribute to the reduction operation. An input that is a
+compute or fix may define its own group which affects the quantities
+it returns. For example, a compute with return a zero value for atoms
+that are not in the group specified for that compute.
+
+Each listed input is operated on independently. Each input can be the
+result of a "compute"_compute.html or "fix"_fix.html or the evaluation
+of an atom-style "variable"_variable.html.
+
+Note that for values from a compute or fix, the bracketed index I can
+be specified using a wildcard asterisk with the index to effectively
+specify multiple values. This takes the form "*" or "*n" or "n*" or
+"m*n". If N = the size of the vector (for {mode} = scalar) or the
+number of columns in the array (for {mode} = vector), then an asterisk
+with no numeric values means all indices from 1 to N. A leading
+asterisk means all indices from 1 to n (inclusive). A trailing
+asterisk means all indices from n to N (inclusive). A middle asterisk
+means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one. E.g. these 2 compute reduce/chunk
+commands are equivalent, since the "compute
+property/chunk"_compute_property_chunk.html command creates a per-atom
+array with 3 columns:
+
+compute prop all property/atom vx vy vz
+compute 10 all reduce/chunk mychunk max c_prop\[*\]
+compute 10 all reduce/chunk mychunk max c_prop\[1\] c_prop\[2\] c_prop\[3\] :pre
+
+:line
+
+Here is an example of using this compute, in conjunction with the
+compute chunk/spread/atom command to identify self-assembled micelles.
+The commands below can be added to the examples/in.micelle script.
+
+Imagine a collection of polymer chains or small molecules with
+hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
+to a group called "phobic".
+
+These commands will assign a unique cluster ID to all HP atoms within
+a specified distance of each other. A cluster will contain all HP
+atoms in a single molecule, but also the HP atoms in nearby molecules,
+e.g. molecules that have clumped to form a micelle due to the
+attraction induced by the hydrophobicity. The output of the
+chunk/reduce command will be a cluster ID per chunk (molecule).
+Molecules with the same cluster ID are in the same micelle.
+
+group phobic type 4 # specific to in.micelle model
+compute cluster phobic cluster/atom 2.0
+compute cmol all chunk/atom molecule
+compute reduce phobic reduce/chunk cmol min c_cluster :pre
+
+This per-chunk info could be output in at least two ways:
+
+fix 10 all ave/time 1000 1 1000 c_reduce file tmp.phobic mode vector :pre
+
+compute spread all chunk/spread/atom cmol c_reduce
+dump 1 all custom 1000 tmp.dump id type mol x y z c_cluster c_spread
+dump_modify 1 sort id :pre
+
+In the first case, each snapshot in the tmp.phobic file will contain
+one line per molecule. Molecules with the same value are in the same
+micelle. In the second case each dump snapshot contains all atoms,
+each with a final field with the cluster ID of the micelle that the HP
+atoms of that atom's molecule belong to.
+
+The result from compute chunk/spread/atom can be used to define a new
+set of chunks, where all the atoms in all the molecules in the same
+micelle are assigned to the same chunk, i.e. one chunk per micelle.
+
+compute micelle all chunk/atom c_spread compress yes :pre
+
+Further analysis on a per-micelle basis can now be performed using any
+of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html
+doc page. E.g. count the number of atoms in each micelle, calculate
+its center or mass, shape (moments of intertia), radius of gyration,
+etc.
+
+compute prop all property/chunk micelle count
+fix 20 all ave/time 1000 1 1000 c_prop file tmp.micelle mode vector :pre
+
+Each snapshot in the tmp.micelle file will have one line per micelle
+with its count of atoms, plus a first line for a chunk with all the
+solvent atoms. By the time 50000 steps have elapsed there are a
+handful of large micelles.
+
+:line
+
+[Output info:]
+
+This compute calculates a global vector if a single input value is
+specified, otherwise a global array is output. The number of columns
+in the array is the number of inputs provided. The length of the
+vector or the number of vector elements or array rows = the number of
+chunks {Nchunk} as calculated by the specified "compute
+chunk/atom"_compute_chunk_atom.html command. The vector or array can
+be accessed by any command that uses global values from a compute as
+input. See the "Howto output"_Howto_output.html doc page for an
+overview of LAMMPS output options.
+
+The per-atom values for the vector or each column of the array will be
+in whatever "units"_units.html the corresponding input value is in.
+The vector or array values are "intensive".
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute chunk/atom"_compute_chunk_atom.html, "compute
+reduce"_compute_reduce.html, "compute
+chunk/spread/atom"_compute_chunk_spread_atom.html
+
+[Default:] none
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 46dd30f757..6528f78e40 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -15,6 +15,7 @@ Computes :h1
compute_bond_local
compute_centro_atom
compute_chunk_atom
+ compute_chunk_spread_atom
compute_cluster_atom
compute_cna_atom
compute_cnp_atom
@@ -72,6 +73,7 @@ Computes :h1
compute_property_local
compute_rdf
compute_reduce
+ compute_reduce_chunk
compute_rigid_local
compute_saed
compute_slice
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c296ff4039..c7f0b2fddd 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -406,6 +406,7 @@ compute_bond.html
compute_bond_local.html
compute_centro_atom.html
compute_chunk_atom.html
+compute_chunk_spread_atom.html
compute_cluster_atom.html
compute_cna_atom.html
compute_cnp_atom.html
@@ -463,6 +464,7 @@ compute_property_chunk.html
compute_property_local.html
compute_rdf.html
compute_reduce.html
+compute_reduce_chunk.html
compute_rigid_local.html
compute_saed.html
compute_slice.html
diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp
new file mode 100644
index 0000000000..93a4d30a2e
--- /dev/null
+++ b/src/compute_chunk_spread_atom.cpp
@@ -0,0 +1,352 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include <cstdlib>
+#include "compute_chunk_spread_atom.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "fix.h"
+#include "compute.h"
+#include "compute_chunk_atom.h"
+#include "input.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{COMPUTE,FIX};
+
+#define INVOKED_VECTOR 2
+#define INVOKED_ARRAY 4
+#define INVOKED_PERATOM 8
+
+/* ---------------------------------------------------------------------- */
+
+ComputeChunkSpreadAtom::
+ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg),
+ which(NULL), argindex(NULL), ids(NULL), value2index(NULL), idchunk(NULL)
+{
+ if (narg < 5) error->all(FLERR,"Illegal compute chunk/spread/atom command");
+
+ // ID of compute chunk/atom
+
+ int n = strlen(arg[3]) + 1;
+ idchunk = new char[n];
+ strcpy(idchunk,arg[3]);
+ init_chunk();
+
+ // expand args if any have wildcard character "*"
+
+ int iarg = 4;
+ int expand = 0;
+ char **earg;
+ int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
+
+ if (earg != &arg[iarg]) expand = 1;
+ arg = earg;
+
+ // parse values
+
+ which = new int[nargnew];
+ argindex = new int[nargnew];
+ ids = new char*[nargnew];
+ value2index = new int[nargnew];
+ nvalues = 0;
+
+ iarg = 0;
+ while (iarg < nargnew) {
+ ids[nvalues] = NULL;
+
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0) {
+ if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+ else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+
+ int n = strlen(arg[iarg]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[iarg][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal compute chunk/spread/atom command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
+ } else argindex[nvalues] = 0;
+
+ n = strlen(suffix) + 1;
+ ids[nvalues] = new char[n];
+ strcpy(ids[nvalues],suffix);
+ nvalues++;
+ delete [] suffix;
+
+ } else error->all(FLERR,"Illegal compute chunk/spread/atom command");
+
+ iarg++;
+ }
+
+ // if wildcard expansion occurred, free earg memory from expand_args()
+
+ if (expand) {
+ for (int i = 0; i < nargnew; i++) delete [] earg[i];
+ memory->sfree(earg);
+ }
+
+ // setup and error check
+ // for compute, must calculate per-chunk values, i.e. style ends in "/chunk"
+ // for fix, assume a global vector or array is per-chunk data
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for compute chunk/spread/atom "
+ "does not exist");
+
+ char *ptr = strstr(modify->compute[icompute]->style,"/chunk");
+ if (!ptr || (ptr != modify->compute[icompute]->style +
+ strlen(modify->compute[icompute]->style) - strlen("/chunk")))
+ error->all(FLERR,"Compute for compute chunk/spread/atom "
+ "does not calculate per-chunk values");
+
+ if (argindex[i] == 0) {
+ if (!modify->compute[icompute]->vector_flag)
+ error->all(FLERR,"Compute chunk/spread/atom compute "
+ "does not calculate global vector");
+ } else {
+ if (!modify->compute[icompute]->array_flag)
+ error->all(FLERR,"Compute chunk/spread/atom compute "
+ "does not calculate global array");
+ if (argindex[i] > modify->compute[icompute]->size_array_cols)
+ error->all(FLERR,"Compute chunk/spread/atom compute array "
+ "is accessed out-of-range");
+ }
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist");
+ if (argindex[i] == 0) {
+ if (!modify->fix[ifix]->vector_flag)
+ error->all(FLERR,"Compute chunk/spread/atom fix "
+ "does not calculate global vector");
+ } else {
+ if (!modify->fix[ifix]->array_flag)
+ error->all(FLERR,"Compute chunk/spread/atom fix "
+ "does not calculate global array");
+ if (argindex[i] > modify->fix[ifix]->size_array_cols)
+ error->all(FLERR,"Compute chunk/spread/atom fix array "
+ "is accessed out-of-range");
+ }
+ }
+ }
+
+ // this compute produces a peratom vector or array
+
+ peratom_flag = 1;
+ if (nvalues == 1) size_peratom_cols = 0;
+ else size_peratom_cols = nvalues;
+
+ // per-atom vector or array
+
+ nmax = 0;
+ vector_atom = NULL;
+ array_atom = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeChunkSpreadAtom::~ComputeChunkSpreadAtom()
+{
+ delete [] idchunk;
+
+ delete [] which;
+ delete [] argindex;
+ for (int i = 0; i < nvalues; i++) delete [] ids[i];
+ delete [] ids;
+ delete [] value2index;
+
+ memory->destroy(vector_atom);
+ memory->destroy(array_atom);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeChunkSpreadAtom::init()
+{
+ init_chunk();
+
+ // set indices of all computes,fixes,variables
+
+ for (int m = 0; m < nvalues; m++) {
+ if (which[m] == COMPUTE) {
+ int icompute = modify->find_compute(ids[m]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for compute chunk/spread/atom "
+ "does not exist");
+ value2index[m] = icompute;
+
+ } else if (which[m] == FIX) {
+ int ifix = modify->find_fix(ids[m]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute chunk/spread/atom does not exist");
+ value2index[m] = ifix;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeChunkSpreadAtom::init_chunk()
+{
+ int icompute = modify->find_compute(idchunk);
+ if (icompute < 0)
+ error->all(FLERR,"Chunk/atom compute does not exist for compute chunk/spread/atom");
+ cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+ if (strcmp(cchunk->style,"chunk/atom") != 0)
+ error->all(FLERR,"Compute chunk/spread/atom does not use chunk/atom compute");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeChunkSpreadAtom::compute_peratom()
+{
+ invoked_peratom = update->ntimestep;
+
+ // grow local vector_atom or array_atom if necessary
+
+ if (atom->nmax > nmax) {
+ if (nvalues == 1) {
+ memory->destroy(vector_atom);
+ nmax = atom->nmax;
+ memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom");
+ } else {
+ memory->destroy(array_atom);
+ nmax = atom->nmax;
+ memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom");
+ }
+ }
+
+ // compute chunk/atom assigns atoms to chunk IDs
+ // extract ichunk index vector from compute
+ // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+ int nchunk = cchunk->setup_chunks();
+ cchunk->compute_ichunk();
+ int *ichunk = cchunk->ichunk;
+
+ // loop over values, access compute or fix
+ // loop over atoms, use chunk ID of each atom to store value from compute/fix
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ int i,m,n,index,nstride;
+ double *ptr;
+
+ for (m = 0; m < nvalues; m++) {
+ n = value2index[m];
+
+ // copy compute/fix values into vector_atom or array_atom
+ // nstride between values for each atom
+
+ if (nvalues == 1) {
+ ptr = vector_atom;
+ nstride = 1;
+ } else {
+ ptr = &array_atom[0][m];
+ nstride = nvalues;
+ }
+
+ // invoke compute if not previously invoked
+
+ if (which[m] == COMPUTE) {
+ Compute *compute = modify->compute[n];
+
+ if (argindex[m] == 0) {
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ double *cvector = compute->vector;
+ for (i = 0; i < nlocal; i++, ptr += nstride) {
+ *ptr = 0.0;
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0 || index >= nchunk) continue;
+ *ptr = cvector[index];
+ }
+
+ } else {
+ if (!(compute->invoked_flag & INVOKED_ARRAY)) {
+ compute->compute_array();
+ compute->invoked_flag |= INVOKED_ARRAY;
+ }
+ int icol = argindex[m]-1;
+ double **carray = compute->array;
+ for (i = 0; i < nlocal; i++, ptr += nstride) {
+ *ptr = 0.0;
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0 || index >= nchunk) continue;
+ *ptr = carray[index][icol];
+ }
+ }
+
+ // access fix data, check if fix frequency is a match
+ // are assuming the fix global vector/array is per-chunk data
+ // check if index exceeds fix output length/rows
+
+ } else if (which[m] == FIX) {
+ Fix *fix = modify->fix[n];
+ if (update->ntimestep % fix->global_freq)
+ error->all(FLERR,"Fix used in compute chunk/spread/atom not "
+ "computed at compatible time");
+
+ if (argindex[m] == 0) {
+ int nfix = fix->size_vector;
+ for (i = 0; i < nlocal; i++, ptr += nstride) {
+ *ptr = 0.0;
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0 || index >= nchunk || index >= nfix) continue;
+ *ptr = fix->compute_vector(index);
+ }
+
+ } else {
+ int icol = argindex[m]-1;
+ int nfix = fix->size_array_rows;
+ for (i = 0; i < nlocal; i++, ptr += nstride) {
+ *ptr = 0.0;
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0 || index >= nchunk || index >= nfix) continue;
+ *ptr = fix->compute_array(index,icol);
+ }
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeChunkSpreadAtom::memory_usage()
+{
+ double bytes = nmax*nvalues * sizeof(double);
+ return bytes;
+}
diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h
new file mode 100644
index 0000000000..9a4df080ca
--- /dev/null
+++ b/src/compute_chunk_spread_atom.h
@@ -0,0 +1,61 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(chunk/spread/atom,ComputeChunkSpreadAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_CHUNK_SPREAD_ATOM_H
+#define LMP_COMPUTE_CHUNK_SPREAD_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeChunkSpreadAtom : public Compute {
+ public:
+ ComputeChunkSpreadAtom(class LAMMPS *, int, char **);
+ ~ComputeChunkSpreadAtom();
+ void init();
+ void compute_peratom();
+ double memory_usage();
+
+ protected:
+ int mode,nvalues;
+ char *idchunk;
+
+ int *which,*argindex,*value2index;
+ char **ids;
+
+ int nmax;
+ class ComputeChunkAtom *cchunk;
+
+ void init_chunk();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 7c61d666b2..e3c3c5b70a 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include <mpi.h>
#include <cstring>
#include <cstdlib>
#include "compute_reduce.h"
diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp
new file mode 100644
index 0000000000..40e9dad8dd
--- /dev/null
+++ b/src/compute_reduce_chunk.cpp
@@ -0,0 +1,512 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include "compute_reduce_chunk.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "fix.h"
+#include "compute.h"
+#include "compute_chunk_atom.h"
+#include "input.h"
+#include "variable.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{SUM,MINN,MAXX};
+enum{COMPUTE,FIX,VARIABLE};
+
+#define INVOKED_PERATOM 8
+
+#define BIG 1.0e20
+
+/* ---------------------------------------------------------------------- */
+
+ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg),
+ vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL),
+ which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL)
+{
+ if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command");
+
+ // ID of compute chunk/atom
+
+ int n = strlen(arg[3]) + 1;
+ idchunk = new char[n];
+ strcpy(idchunk,arg[3]);
+ init_chunk();
+
+ // mode
+
+ if (strcmp(arg[4],"sum") == 0) mode = SUM;
+ else if (strcmp(arg[4],"min") == 0) mode = MINN;
+ else if (strcmp(arg[4],"max") == 0) mode = MAXX;
+ else error->all(FLERR,"Illegal compute reduce/chunk command");
+
+ int iarg = 5;
+
+ // expand args if any have wildcard character "*"
+
+ int expand = 0;
+ char **earg;
+ int nargnew = input->expand_args(narg-iarg,&arg[iarg],1,earg);
+
+ if (earg != &arg[iarg]) expand = 1;
+ arg = earg;
+
+ // parse values until one isn't recognized
+
+ which = new int[nargnew];
+ argindex = new int[nargnew];
+ ids = new char*[nargnew];
+ value2index = new int[nargnew];
+ nvalues = 0;
+
+ iarg = 0;
+ while (iarg < nargnew) {
+ ids[nvalues] = NULL;
+
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"v_",2) == 0) {
+ if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+ else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+ else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
+
+ int n = strlen(arg[iarg]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[iarg][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal compute reduce/chunk command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
+ } else argindex[nvalues] = 0;
+
+ n = strlen(suffix) + 1;
+ ids[nvalues] = new char[n];
+ strcpy(ids[nvalues],suffix);
+ nvalues++;
+ delete [] suffix;
+
+ } else error->all(FLERR,"Illegal compute reduce/chunk command");
+
+ iarg++;
+ }
+
+ // if wildcard expansion occurred, free earg memory from expand_args()
+
+ if (expand) {
+ for (int i = 0; i < nargnew; i++) delete [] earg[i];
+ memory->sfree(earg);
+ }
+
+ // error check
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for compute reduce/chunk does not exist");
+ if (!modify->compute[icompute]->peratom_flag)
+ error->all(FLERR,"Compute reduce/chunk compute does not "
+ "calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->compute[icompute]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute reduce/chunk compute does not "
+ "calculate a per-atom vector");
+ if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
+ error->all(FLERR,"Compute reduce/chunk compute does not "
+ "calculate a per-atom array");
+ if (argindex[i] &&
+ argindex[i] > modify->compute[icompute]->size_peratom_cols)
+ error->all(FLERR,
+ "Compute reduce/chunk compute array is accessed out-of-range");
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute reduce/chunk does not exist");
+ if (!modify->fix[ifix]->peratom_flag)
+ error->all(FLERR,"Compute reduce/chunk fix does not "
+ "calculate per-atom values");
+ if (argindex[i] == 0 &&
+ modify->fix[ifix]->size_peratom_cols != 0)
+ error->all(FLERR,"Compute reduce/chunk fix does not "
+ "calculate a per-atom vector");
+ if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
+ error->all(FLERR,"Compute reduce/chunk fix does not "
+ "calculate a per-atom array");
+ if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
+ error->all(FLERR,"Compute reduce/chunk fix array is "
+ "accessed out-of-range");
+
+ } else if (which[i] == VARIABLE) {
+ int ivariable = input->variable->find(ids[i]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for compute reduce/chunk does not exist");
+ if (input->variable->atomstyle(ivariable) == 0)
+ error->all(FLERR,"Compute reduce/chunk variable is "
+ "not atom-style variable");
+ }
+ }
+
+ // this compute produces either a vector or array
+
+ if (nvalues == 1) {
+ vector_flag = 1;
+ size_vector_variable = 1;
+ extvector = 0;
+ } else {
+ array_flag = 1;
+ size_array_rows_variable = 1;
+ size_array_cols = nvalues;
+ extarray = 0;
+ }
+
+ // setup
+
+ if (mode == SUM) initvalue = 0.0;
+ else if (mode == MINN) initvalue = BIG;
+ else if (mode == MAXX) initvalue = -BIG;
+
+ maxchunk = 0;
+ vlocal = vglobal = NULL;
+ alocal = aglobal = NULL;
+
+ maxatom = 0;
+ varatom = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeReduceChunk::~ComputeReduceChunk()
+{
+ delete [] idchunk;
+
+ delete [] which;
+ delete [] argindex;
+ for (int m = 0; m < nvalues; m++) delete [] ids[m];
+ delete [] ids;
+ delete [] value2index;
+
+ memory->destroy(vlocal);
+ memory->destroy(vglobal);
+ memory->destroy(alocal);
+ memory->destroy(aglobal);
+
+ memory->destroy(varatom);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeReduceChunk::init()
+{
+ init_chunk();
+
+ // set indices of all computes,fixes,variables
+
+ for (int m = 0; m < nvalues; m++) {
+ if (which[m] == COMPUTE) {
+ int icompute = modify->find_compute(ids[m]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for compute reduce/chunk does not exist");
+ value2index[m] = icompute;
+
+ } else if (which[m] == FIX) {
+ int ifix = modify->find_fix(ids[m]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for compute reduce/chunk does not exist");
+ value2index[m] = ifix;
+
+ } else if (which[m] == VARIABLE) {
+ int ivariable = input->variable->find(ids[m]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for compute reduce/chunk does not exist");
+ value2index[m] = ivariable;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeReduceChunk::init_chunk()
+{
+ int icompute = modify->find_compute(idchunk);
+ if (icompute < 0)
+ error->all(FLERR,"Chunk/atom compute does not exist for "
+ "compute reduce/chunk");
+ cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+ if (strcmp(cchunk->style,"chunk/atom") != 0)
+ error->all(FLERR,"Compute reduce/chunk does not use chunk/atom compute");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeReduceChunk::compute_vector()
+{
+ invoked_vector = update->ntimestep;
+
+ // compute chunk/atom assigns atoms to chunk IDs
+ // extract ichunk index vector from compute
+ // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+ nchunk = cchunk->setup_chunks();
+ cchunk->compute_ichunk();
+ ichunk = cchunk->ichunk;
+ if (!nchunk) return;
+
+ size_vector = nchunk;
+
+ if (nchunk > maxchunk) {
+ memory->destroy(vlocal);
+ memory->destroy(vglobal);
+ maxchunk = nchunk;
+ memory->create(vlocal,maxchunk,"reduce/chunk:vlocal");
+ memory->create(vglobal,maxchunk,"reduce/chunk:vglobal");
+ vector = vglobal;
+ }
+
+ // perform local reduction of single peratom value
+
+ compute_one(0,vlocal,1);
+
+ // reduce the per-chunk values across all procs
+
+ if (mode == SUM)
+ MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+ else if (mode == MINN)
+ MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MIN,world);
+ else if (mode == MAXX)
+ MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeReduceChunk::compute_array()
+{
+ invoked_array = update->ntimestep;
+
+ // compute chunk/atom assigns atoms to chunk IDs
+ // extract ichunk index vector from compute
+ // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+ nchunk = cchunk->setup_chunks();
+ cchunk->compute_ichunk();
+ ichunk = cchunk->ichunk;
+ if (!nchunk) return;
+
+ size_array_rows = nchunk;
+
+ if (nchunk > maxchunk) {
+ memory->destroy(alocal);
+ memory->destroy(aglobal);
+ maxchunk = nchunk;
+ memory->create(alocal,maxchunk,nvalues,"reduce/chunk:alocal");
+ memory->create(aglobal,maxchunk,nvalues,"reduce/chunk:aglobal");
+ array = aglobal;
+ }
+
+ // perform local reduction of all peratom values
+
+ for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues);
+
+ // reduce the per-chunk values across all procs
+
+ if (mode == SUM)
+ MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
+ MPI_DOUBLE,MPI_SUM,world);
+ else if (mode == MINN)
+ MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
+ MPI_DOUBLE,MPI_MIN,world);
+ else if (mode == MAXX)
+ MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues,
+ MPI_DOUBLE,MPI_MAX,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
+{
+ // initialize per-chunk values in accumulation vector
+
+ for (int i = 0; i < nchunk; i += nstride) vchunk[i] = initvalue;
+
+ // loop over my atoms
+ // use peratom input and chunk ID of each atom to update vector
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ int index;
+
+ if (which[m] == COMPUTE) {
+ Compute *compute = modify->compute[value2index[m]];
+
+ if (!(compute->invoked_flag & INVOKED_PERATOM)) {
+ compute->compute_peratom();
+ compute->invoked_flag |= INVOKED_PERATOM;
+ }
+
+ if (argindex[m] == 0) {
+ double *vcompute = compute->vector_atom;
+ for (int i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ combine(vchunk[index*nstride],vcompute[i]);
+ }
+ } else {
+ double **acompute = compute->array_atom;
+ int argindexm1 = argindex[m] - 1;
+ for (int i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ combine(vchunk[index*nstride],acompute[i][argindexm1]);
+ }
+ }
+
+ // access fix fields, check if fix frequency is a match
+
+ } else if (which[m] == FIX) {
+ Fix *fix = modify->fix[value2index[m]];
+ if (update->ntimestep % fix->peratom_freq)
+ error->all(FLERR,"Fix used in compute reduce/chunk not "
+ "computed at compatible time");
+
+ if (argindex[m] == 0) {
+ double *vfix = fix->vector_atom;
+ for (int i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ combine(vchunk[index*nstride],vfix[i]);
+ }
+ } else {
+ double **afix = fix->array_atom;
+ int argindexm1 = argindex[m] - 1;
+ for (int i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ combine(vchunk[index*nstride],afix[i][argindexm1]);
+ }
+ }
+
+ // evaluate atom-style variable
+
+ } else if (which[m] == VARIABLE) {
+ if (atom->nmax > maxatom) {
+ memory->destroy(varatom);
+ maxatom = atom->nmax;
+ memory->create(varatom,maxatom,"reduce/chunk:varatom");
+ }
+
+ input->variable->compute_atom(value2index[m],igroup,varatom,1,0);
+ for (int i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ combine(vchunk[index*nstride],varatom[i]);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ combine two values according to reduction mode
+------------------------------------------------------------------------- */
+
+void ComputeReduceChunk::combine(double &one, double two)
+{
+ if (mode == SUM) one += two;
+ else if (mode == MINN) {
+ if (two < one) one = two;
+ } else if (mode == MAXX) {
+ if (two > one) one = two;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ lock methods: called by fix ave/time
+ these methods insure vector/array size is locked for Nfreq epoch
+ by passing lock info along to compute chunk/atom
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ increment lock counter
+------------------------------------------------------------------------- */
+
+void ComputeReduceChunk::lock_enable()
+{
+ cchunk->lockcount++;
+}
+
+/* ----------------------------------------------------------------------
+ decrement lock counter in compute chunk/atom, if it still exists
+------------------------------------------------------------------------- */
+
+void ComputeReduceChunk::lock_disable()
+{
+ int icompute = modify->find_compute(idchunk);
+ if (icompute >= 0) {
+ cchunk = (ComputeChunkAtom *) modify->compute[icompute];
+ cchunk->lockcount--;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ calculate and return # of chunks = length of vector/array
+------------------------------------------------------------------------- */
+
+int ComputeReduceChunk::lock_length()
+{
+ nchunk = cchunk->setup_chunks();
+ return nchunk;
+}
+
+/* ----------------------------------------------------------------------
+ set the lock from startstep to stopstep
+------------------------------------------------------------------------- */
+
+void ComputeReduceChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
+{
+ cchunk->lock(fixptr,startstep,stopstep);
+}
+
+/* ----------------------------------------------------------------------
+ unset the lock
+------------------------------------------------------------------------- */
+
+void ComputeReduceChunk::unlock(Fix *fixptr)
+{
+ cchunk->unlock(fixptr);
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeReduceChunk::memory_usage()
+{
+ double bytes = (bigint) maxatom * sizeof(double);
+ if (nvalues == 1) bytes += (bigint) maxchunk * 2 * sizeof(double);
+ else bytes += (bigint) maxchunk * nvalues * 2 * sizeof(double);
+ return bytes;
+}
diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h
new file mode 100644
index 0000000000..ac556907b7
--- /dev/null
+++ b/src/compute_reduce_chunk.h
@@ -0,0 +1,77 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(reduce/chunk,ComputeReduceChunk)
+
+#else
+
+#ifndef LMP_COMPUTE_REDUCE_CHUNK_H
+#define LMP_COMPUTE_REDUCE_CHUNK_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeReduceChunk : public Compute {
+ public:
+ ComputeReduceChunk(class LAMMPS *, int, char **);
+ ~ComputeReduceChunk();
+ void init();
+ void compute_vector();
+ void compute_array();
+
+ void lock_enable();
+ void lock_disable();
+ int lock_length();
+ void lock(class Fix *, bigint, bigint);
+ void unlock(class Fix *);
+
+ double memory_usage();
+
+ private:
+ int mode,nvalues;
+ int *which,*argindex,*value2index;
+ char *idchunk;
+ char **ids;
+
+ int nchunk;
+ int maxchunk,maxatom;
+ double initvalue;
+ double *vlocal,*vglobal;
+ double **alocal,**aglobal;
+ double *varatom;
+
+ class ComputeChunkAtom *cchunk;
+ int *ichunk;
+
+ void init_chunk();
+ void compute_one(int, double *, int);
+ void combine(double &, double);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
--
GitLab
From e3ce702eec1c6d8b2d875827de642c68e6b4e77d Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 31 Aug 2018 13:53:02 -0600
Subject: [PATCH 204/332] doc adjust
---
doc/src/compute_chunk_spread_atom.txt | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt
index 59662035e5..f84ef67974 100644
--- a/doc/src/compute_chunk_spread_atom.txt
+++ b/doc/src/compute_chunk_spread_atom.txt
@@ -98,7 +98,8 @@ compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre
:line
Here is an example of writing a dump file the with the center-of-mass
-(COM) for the chunk each atom is in:
+(COM) for the chunk each atom is in. The commands below can be added
+to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
@@ -124,10 +125,10 @@ calculation, so that the effect of periodic boundaries is accounted
for properly.
Over time this applied force could shrink each polymer chain's radius
-of gyration in a polymer mixture simulation. Here is output after
-adding the above lines to the bench/in.chain script. The thermo
-output is shown for 1000 steps, where the last column is the average
-radius of gyration over all 320 chains in the 32000 atom system:
+of gyration in a polymer mixture simulation. Here is output from the
+bench/in.chain script. Thermo output is shown for 1000 steps, where
+the last column is the average radius of gyration over all 320 chains
+in the 32000 atom system:
compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
--
GitLab
From a989d04d09025e41770b2f71e9e8571c7ded95c0 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 31 Aug 2018 14:17:36 -0600
Subject: [PATCH 205/332] think this flag should not be set by this fix
---
src/fix_ave_chunk.cpp | 1 -
1 file changed, 1 deletion(-)
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 1aead70644..fc3ef6ed6e 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -63,7 +63,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
strcpy(idchunk,arg[6]);
global_freq = nfreq;
- peratom_freq = nfreq;
no_change_box = 1;
// expand args if any have wildcard character "*"
--
GitLab
From bc62002b1ca3f5fea860e95bab48346dc9f12ee4 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 31 Aug 2018 16:05:24 -0600
Subject: [PATCH 206/332] units and doc changes
---
doc/src/fix_client_md.txt | 7 ++---
doc/src/server_mc.txt | 1 +
doc/src/server_md.txt | 43 +++++++++++++++++++++++-------
examples/COUPLE/README | 6 +++--
examples/COUPLE/lammps_mc/Makefile | 5 ++--
examples/COUPLE/lammps_mc/README | 34 +++++++++++++++++------
examples/COUPLE/lammps_vasp/README | 38 +++++++++++++++++++++++---
src/MESSAGE/fix_client_md.cpp | 19 ++++++++-----
src/MESSAGE/server_md.cpp | 23 +++++++++-------
9 files changed, 132 insertions(+), 44 deletions(-)
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
index 1712e1615e..5b62d5617d 100644
--- a/doc/src/fix_client_md.txt
+++ b/doc/src/fix_client_md.txt
@@ -44,10 +44,11 @@ running {ab initio} MD with quantum forces.
The group associated with this fix is ignored.
-The protocol for message format and content that LAMMPS exchanges with
-the server code is defined on the "server md"_server_md.html doc page.
+The protocol and "units"_units.html for message format and content
+that LAMMPS exchanges with the server code is defined on the "server
+md"_server_md.html doc page.
-Note that when using LAMMPS in this mode, your LAMMPS input script
+Note that when using LAMMPS as an MD client, your LAMMPS input script
should not normally contain force field commands, like a
"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
"kspace_style"_kspace_style.html commmand. However it is possible for
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index 3f7b3b8893..53ccfc8ecd 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -37,6 +37,7 @@ signals when it is done sending messages to LAMMPS, at which point the
loop will exit, and the remainder of the LAMMPS script will be
processed.
+The "server"_server.html doc page gives other options for using LAMMPS
See an example of how this command is used in
examples/COUPLE/lammps_mc/in.server.
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 58dfa7f762..0db7bbe16b 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -37,7 +37,8 @@ signals when it is done sending messages to LAMMPS, at which point the
loop will exit, and the remainder of the LAMMPS script will be
processed.
-See an example of how this command is used in
+The "server"_server.html doc page gives other options for using LAMMPS
+in server mode. See an example of how this command is used in
examples/message/in.message.server.
:line
@@ -45,13 +46,13 @@ examples/message/in.message.server.
When using this command, LAMMPS (as the server code) receives the
current coordinates of all particles from the client code each
timestep, computes their interaction, and returns the energy, forces,
-and virial for the interacting particles to the client code, so it can
-complete the timestep. This command could also be used with a client
-code that performs energy minimization, using the server to compute
-forces and energy each iteration of its minimizer.
+and pressure for the interacting particles to the client code, so it
+can complete the timestep. This command could also be used with a
+client code that performs energy minimization, using the server to
+compute forces and energy each iteration of its minimizer.
When using the "fix client/md" command, LAMMPS (as the client code)
-does the timestepping and receives needed energy, forces, and virial
+does the timestepping and receives needed energy, forces, and pressure
values from the server code.
The format and content of the exchanged messages are explained here in
@@ -70,7 +71,7 @@ The following pseudo-code uses these values, defined as enums.
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL,ERROR}; :pre
+enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre
[Client sends 2 kinds of messages]:
@@ -101,11 +102,35 @@ cs->pack(BOX,9,box) # 3 edge vectors of simulation box
[Server replies to either kind of message]:
+# required fields: FORCES, ENERGY, PRESSURE
+# optional fields: ERROR :pre
+
cs->send(msgID,nfields) # msgID with nfields
cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
cs->pack(ENERGY,1,poteng) # total potential energy of system
-cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector)
-cs->pack(ERROR,6,virial) # server had an error (e.g. DFT non-convergence) :pre
+cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
+cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre
+
+:line
+
+The units for various quantities that are sent and received iva
+messages are defined for atomic-scale simulations in the table below.
+The client and server codes (including LAMMPS) can use internal units
+different than these (e.g. "real units"_units.html in LAMMPS), so long
+as they convert to these units for meesaging.
+
+COORDS, ORIGIN, BOX = Angstroms
+CHARGE = multiple of electron charge (1.0 is a proton)
+ENERGY = eV
+FORCES = eV/Angstrom
+PRESSURE = bars :ul
+
+Note that these are "metal units"_units.html in LAMMPS.
+
+If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
+units"_units.html, then the client and server should exchange a UNITS
+message as indicated above, and both the client and server should
+agree on the units for the data they exchange.
:line
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index 2d09ed7d4b..0e611befbd 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -34,11 +34,13 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
-lammps_mc client/server coupling Monte Carlo with LAMMPS MD
+lammps_mc client/server coupling of Monte Carlo client
+ with LAMMPS server for energy evaluation
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
-lammps_vasp client/server coupling LAMMPS MD with VASP quantum DFT
+lammps_vasp client/server coupling of LAMMPS client with
+ VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile
index 821eb58134..c75bd08c73 100644
--- a/examples/COUPLE/lammps_mc/Makefile
+++ b/examples/COUPLE/lammps_mc/Makefile
@@ -19,10 +19,9 @@ LINKFLAGS = -g -O -L$(CSLIB)
# targets
mc: $(OBJ)
-# this line if built the CSlib within lib/message with ZMQ support
-# note this is using the serial (no-mpi) version of the CSlib
+# first line if built the CSlib within lib/message with ZMQ support
+# second line if built the CSlib without ZMQ support
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
-# this line if built the CSlib without ZMQ support
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
clean:
diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README
index af4d86f92f..c201a6351c 100644
--- a/examples/COUPLE/lammps_mc/README
+++ b/examples/COUPLE/lammps_mc/README
@@ -22,25 +22,43 @@ change, and to run dynamics between MC moves.
----------------
-Build LAMMPS and the MC client code
+Build LAMMPS with its MESSAGE package installed:
-First, build LAMMPS with its MESSAGE package installed:
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
% cd lammps/lib/message
% python Install.py -m -z # build CSlib with MPI and ZMQ support
-% python Install.py -s -z # also build serial lib and ZMQ support
% cd lammps/src
% make yes-message
% make mpi
You can leave off the -z if you do not have ZMQ on your system.
-Next build the MC client code, which will link with the serial CSlib.
+----------------
+
+Build the MC client code
+
+The source files for the MC code are in this dir. It links with the
+CSlib library in lib/message/cslib.
+
+You must first build the CSlib in serial mode, e.g.
+
+% cd lammps/lib/message/cslib/src
+% make lib # build serial and parallel lib with ZMQ support
+% make lib zmq=no # build serial and parallel lib without ZMQ support
-First edit the Makefile in this dir. The CSLIB variable should be the
-path to where the LAMMPS lib/message dir is on your system. If you
-built the CSlib without ZMQ support you will also need to
-comment/uncomment two lines. Then you can just type
+Then edit the Makefile in this dir. The CSLIB variable should be the
+path to where the LAMMPS lib/message/cslib/src dir is on your system.
+If you built the CSlib without ZMQ support you will also need to
+comment/uncomment one line. Then you can just type
% make
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
index b301bd779f..e942d52535 100644
--- a/examples/COUPLE/lammps_vasp/README
+++ b/examples/COUPLE/lammps_vasp/README
@@ -24,6 +24,16 @@ MPI.
Build LAMMPS with its MESSAGE package installed:
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
+
cd lammps/lib/message
python Install.py -m -z # build CSlib with MPI and ZMQ support
cd lammps/src
@@ -34,6 +44,27 @@ You can leave off the -z if you do not have ZMQ on your system.
----------------
+Build the CSlib in a form usable by the vasp_wrapper.py script:
+
+% cd lammps/lib/message/cslib/src
+% make shlib # build serial and parallel shared lib with ZMQ support
+% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
+
+This will make a shared library versions of the CSlib, which Python
+requires. Python must be able to find both the cslib.py script and
+the libcsnompi.so library in your lammps/lib/message/cslib/src
+directory. If it is not able to do this, you will get an error when
+you run vasp_wrapper.py.
+
+You can do this by augmenting two environment variables, either
+from the command line, or in your shell start-up script.
+Here is the sample syntax for the csh or tcsh shells:
+
+setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
+
+----------------
+
Prepare to use VASP and the vasp_wrapper.py script
You can run the vasp_wrap.py script as-is to test that the coupling
@@ -68,13 +99,14 @@ POSCAR_W matches in.client.W.
Once you run VASP yourself, the vasprun.xml file will be overwritten.
-NOTE: explain how vasp_wrapper.py finds the cslib.py wrapper on the
-CSlib to import.
-
----------------
To run in client/server mode:
+NOTE: The vasp_wrap.py script must be run with Python version 2, not
+3. This is because it used the CSlib python wrapper, which only
+supports version 2. We plan to upgrade CSlib to support Python 3.
+
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
messaging mode, namely file or zmq. This is an argument to the
vasp_wrap.py code; it can be selected by setting the "mode" variable
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index bfcca4841b..dbaada9b50 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -32,7 +32,7 @@ using namespace FixConst;
enum{OTHER,REAL,METAL};
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL,ERROR};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
/* ---------------------------------------------------------------------- */
@@ -67,10 +67,10 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
// otherwise not needed
// message received in METAL units, convert to local REAL units
- fconvert = econvert = vconvert = 1.0;
+ fconvert = econvert = pconvert = 1.0;
if (units == REAL) {
- fconvert = econvert = 23.06035;
- vconvert = 0.986923;
+ fconvert = econvert = 23.06035; // eV -> Kcal/mole
+ pconvert = 0.986923; // bars -> atmospheres
}
}
@@ -274,7 +274,7 @@ void FixClientMD::pack_box()
/* ----------------------------------------------------------------------
receive message from server
- required fields: FORCES, ENERGY, VIRIAL
+ required fields: FORCES, ENERGY, PRESSURE
optional field: ERROR
------------------------------------------------------------------------- */
@@ -307,9 +307,14 @@ void FixClientMD::receive_fev(int vflag)
eng = econvert * cs->unpack_double(ENERGY);
if (vflag) {
- double *v = (double *) cs->unpack(VIRIAL);
+ double *v = (double *) cs->unpack(PRESSURE);
+
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = inv_nprocs * pconvert * volume / nktv2p;
+
for (int i = 0; i < 6; i++)
- virial[i] = inv_nprocs * vconvert * v[i];
+ virial[i] = factor * v[i];
}
// error return
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
index e51571e972..aa771b7d46 100644
--- a/src/MESSAGE/server_md.cpp
+++ b/src/MESSAGE/server_md.cpp
@@ -37,7 +37,7 @@ using namespace CSLIB_NS;
enum{OTHER,REAL,METAL};
enum{SETUP=1,STEP};
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,VIRIAL,ERROR};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
/* ---------------------------------------------------------------------- */
@@ -58,10 +58,10 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
// otherwise not needed
// local computation in REAL units, send message in METAL units
- fconvert = econvert = vconvert = 1.0;
+ fconvert = econvert = pconvert = 1.0;
if (units == REAL) {
- fconvert = econvert = 1.0 / 23.06035;
- vconvert = 1.0 / 0.986923;
+ fconvert = econvert = 1.0 / 23.06035; // Kcal/mole -> eV
+ pconvert = 1.0 / 0.986923; // atmospheres -> bars
}
fcopy = NULL;
@@ -339,7 +339,7 @@ void ServerMD::box_change(double *origin, double *box)
/* ----------------------------------------------------------------------
return message with forces, energy, pressure tensor
pressure tensor should be just pair and KSpace contributions
- required fields: FORCES, ENERGY, VIRIAL
+ required fields: FORCES, ENERGY, PRESSURE
optional field: ERROR (not ever sending)
------------------------------------------------------------------------- */
@@ -374,11 +374,16 @@ void ServerMD::send_fev(int msgID)
double v[6],vall[6];
for (int i = 0; i < 6; i++)
v[i] = force->pair->virial[i];
+ MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
+
if (force->kspace)
for (int i = 0; i < 6; i++)
- v[i] += force->kspace->virial[i];
+ vall[i] += force->kspace->virial[i];
- for (int i = 0; i < 6; i++) v[i] *= vconvert;
- MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
- cs->pack(VIRIAL,4,6,vall);
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = pconvert / volume * nktv2p;
+ for (int i = 0; i < 6; i++) vall[i] *= factor;
+
+ cs->pack(PRESSURE,4,6,vall);
}
--
GitLab
From f66ce801ad23c42d28f56b776a859bf1993909c9 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 31 Aug 2018 16:21:45 -0600
Subject: [PATCH 207/332] final testing
---
examples/COUPLE/lammps_vasp/log.client.output | 69 +++++++++++--------
src/MESSAGE/fix_client_md.cpp | 1 +
src/MESSAGE/fix_client_md.h | 2 +-
src/MESSAGE/server_md.h | 2 +-
4 files changed, 44 insertions(+), 30 deletions(-)
diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output
index de37c7cbaf..fa8f4f920a 100644
--- a/examples/COUPLE/lammps_vasp/log.client.output
+++ b/examples/COUPLE/lammps_vasp/log.client.output
@@ -1,63 +1,76 @@
-LAMMPS (20 Apr 2018)
+LAMMPS (22 Aug 2018)
# small W unit cell for use with VASP
-#message client aimd file tmp.couple
-message client aimd zmq localhost:5555
-#message client aimd mpi/two tmp.couple
-#message client aimd mpi/one tmp.couple
+variable mode index file
-units real
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
+message client md zmq localhost:5555
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
atom_style atomic
atom_modify sort 0 0.0 map yes
read_data data.W
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
- 1 by 1 by 1 MPI processor grid
+ 1 by 1 by 2 MPI processor grid
reading atoms ...
2 atoms
-mass 1 1.0
+mass 1 183.85
-#velocity all create 300.0 87287 loop geom
+replicate $x $y $z
+replicate 1 $y $z
+replicate 1 1 $z
+replicate 1 1 1
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 2 MPI processor grid
+ 2 atoms
+ Time spent = 0.000148058 secs
+
+velocity all create 300.0 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 10 check no
fix 1 all nve
-fix 2 all message/aimd
+fix 2 all client/md
fix_modify 2 energy yes
thermo 1
-run 2
+run 3
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 0 0 -48.069571 -172694.2
- 1 0.063865861 0 0 -48.069381 -172693.93
- 2 0.25546344 0 0 -48.06881 -172693.1
-Loop time of 0.281842 on 1 procs for 2 steps with 2 atoms
+ 0 300 0 0 -48.030793 -78159.503
+ 1 298.24318 0 0 -48.03102 -78167.19
+ 2 296.85584 0 0 -48.031199 -78173.26
+ 3 295.83795 0 0 -48.031331 -78177.714
+Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
-Performance: 0.613 ns/day, 39.145 hours/ns, 7.096 timesteps/s
-0.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 3.0994e-06 | 3.0994e-06 | 3.0994e-06 | 0.0 | 0.00
-Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.03
-Modify | 0.28174 | 0.28174 | 0.28174 | 0.0 | 99.97
-Other | | 5.96e-06 | | | 0.00
-
-Nlocal: 2 ave 2 max 2 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 7 ave 7 max 7 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
+Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
+Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
+Other | | 1.204e-05 | | | 0.00
+
+Nlocal: 1 ave 1 max 1 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 4 ave 4 max 4 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds not checked
-Total wall time: 0:00:06
+Total wall time: 0:01:21
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index dbaada9b50..aca5cd41f9 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -18,6 +18,7 @@
#include "atom.h"
#include "comm.h"
#include "domain.h"
+#include "force.h"
#include "memory.h"
#include "error.h"
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
index 262a4736ed..1c874c7278 100644
--- a/src/MESSAGE/fix_client_md.h
+++ b/src/MESSAGE/fix_client_md.h
@@ -40,7 +40,7 @@ class FixClientMD : public Fix {
int maxatom,units,server_error;
double eng;
double inv_nprocs;
- double fconvert,econvert,vconvert;
+ double fconvert,econvert,pconvert;
double box[3][3];
double *xpbc;
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
index 35daad8df0..289d70bdd8 100644
--- a/src/MESSAGE/server_md.h
+++ b/src/MESSAGE/server_md.h
@@ -26,7 +26,7 @@ class ServerMD : protected Pointers {
private:
int units;
- double fconvert,econvert,vconvert;
+ double fconvert,econvert,pconvert;
double **fcopy;
void box_change(double *, double *);
--
GitLab
From 5f0423b97d64ff06b9317ddb5c140c805cf8f1b6 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 31 Aug 2018 17:04:27 -0600
Subject: [PATCH 208/332] change -mpi to -mpicolor
---
doc/src/Howto_client_server.txt | 11 ++++++-----
doc/src/Run_options.txt | 4 ++--
doc/src/message.txt | 10 +++++-----
examples/message/README | 8 ++++----
examples/message/Script.sh | 8 ++++----
src/lammps.cpp | 1 +
6 files changed, 22 insertions(+), 20 deletions(-)
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index ce9bbc0763..714c23f066 100644
--- a/doc/src/Howto_client_server.txt
+++ b/doc/src/Howto_client_server.txt
@@ -119,12 +119,13 @@ For message exchange in {mpi/one} mode:
Launch both codes in a single mpirun command:
-mpirun -np 2 lmp_mpi -mpi 2 -in in.message.client -log log.client : -np 4 lmp_mpi -mpi 2 -in in.message.server -log log.server
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
The two -np values determine how many procs the client and the server
run on.
-A LAMMPS executable run in this manner must use the -mpi P
-command-line option as their first option, where P is the number of
-processors the first code in the mpirun command (client or server) is
-running on.
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as their its option, where color is an integer
+label that will be used to distinguish one executable from another in
+the multiple executables that the mpirun command launches. In this
+example the client was colored with a 0, and the server with a 1.
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index b58aaa16e1..27f436ed55 100644
--- a/doc/src/Run_options.txt
+++ b/doc/src/Run_options.txt
@@ -18,7 +18,7 @@ letter abbreviation can be used:
"-i or -in"_#file
"-k or -kokkos"_#run-kokkos
"-l or -log"_#log
-"-m or -mpi"_#mpi
+"-m or -mpicolor"_#mpicolor
"-nc or -nocite"_#nocite
"-pk or -package"_#package
"-p or -partition"_#partition
@@ -176,7 +176,7 @@ Option -plog will override the name of the partition log files file.N.
:line
-[-mpi] color :link(mpi)
+[-mpicolor] color :link(mpi)
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
diff --git a/doc/src/message.txt b/doc/src/message.txt
index 6c84f3135c..cca1a5b369 100644
--- a/doc/src/message.txt
+++ b/doc/src/message.txt
@@ -105,12 +105,12 @@ mode on a parallel machine, e.g. a cluster with many nodes.
For mode {mpi/one}, the 2 codes communicate via MPI and are launched
by the same mpirun command, e.g. with this syntax for OpenMPI:
-mpirun -np 2 lmp_mpi -mpi 2 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
-mpirun -np 2 othercode args : -np 4 lmp_mpi -mpi 2 -in in.server # LAMMPS is server :pre
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
+mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre
-Note the use of the "-mpi P" command-line argument with LAMMPS. See
-the "command-line args"_Run_options.html doc page for further
-explanation.
+Note the use of the "-mpicolor color" command-line argument with
+LAMMPS. See the "command-line args"_Run_options.html doc page for
+further explanation.
For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
be 2 separate mpirun commands. The specified {filename} argument is a
diff --git a/examples/message/README b/examples/message/README
index 34a5794e7a..6cd99d5c09 100644
--- a/examples/message/README
+++ b/examples/message/README
@@ -105,13 +105,13 @@ Mpi/one mode of messaging:
Launch LAMMPS twice in a single mpirun command:
-% mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.server
+% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server
Or run with in.message.tilt.client/server.
The two -np values determine how many procs the client and the server
run on.
-A LAMMPS executable run in this manner must use the -mpi color
-command-line option as their first option, where color is set to
-one integer value for the 1st app, and another value for the 2nd app.
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as its first option, where color is set to one
+integer value for the 1st app, and another value for the 2nd app.
diff --git a/examples/message/Script.sh b/examples/message/Script.sh
index 0125bdd500..fdcd6f1188 100644
--- a/examples/message/Script.sh
+++ b/examples/message/Script.sh
@@ -13,7 +13,7 @@ mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
-mpirun -np 1 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
+mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
# message on 2/4 procs each
@@ -28,7 +28,7 @@ mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
-mpirun -np 2 lmp_mpi -mpi 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -mpi 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
+mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
# message.tilt on 1 proc each
@@ -40,7 +40,7 @@ mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.mes
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
-mpirun -np 1 lmp_mpi -mpi 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -mpi 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
+mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
# message.tilt on 2/4 procs each
@@ -52,4 +52,4 @@ mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.mes
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
-mpirun -np 2 lmp_mpi -mpi 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -mpi 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
+mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
diff --git a/src/lammps.cpp b/src/lammps.cpp
index dec4a57186..fcdfecf30a 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -879,6 +879,7 @@ void LAMMPS::help()
"-in filename : read input from file, not stdin (-i)\n"
"-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n"
"-log none/filename : where to send log output (-l)\n"
+ "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n"
"-nocite : disable writing log.cite file (-nc)\n"
"-package style ... : invoke package command (-pk)\n"
"-partition size1 size2 ... : assign partition sizes (-p)\n"
--
GitLab
From 9e03bf7db993ded945ac9e3a853e93814d349905 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 1 Sep 2018 19:12:46 -0400
Subject: [PATCH 209/332] make USER-DIFFRACTION input example fully consistent
with output and remove additional input file
---
examples/USER/diffraction/BulkNi.in | 5 ++--
examples/USER/diffraction/Output/BulkNi.in | 35 ----------------------
2 files changed, 3 insertions(+), 37 deletions(-)
delete mode 100644 examples/USER/diffraction/Output/BulkNi.in
diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in
index 0fa9c1b74c..8315e57750 100644
--- a/examples/USER/diffraction/BulkNi.in
+++ b/examples/USER/diffraction/BulkNi.in
@@ -17,8 +17,9 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.05 echo manual
+compute SAED all saed 0.0251 Ni Kmax 0.85 &
+ Zone 0 0 0 c 0.025 0.025 0.025 &
+ dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
diff --git a/examples/USER/diffraction/Output/BulkNi.in b/examples/USER/diffraction/Output/BulkNi.in
deleted file mode 100644
index 8315e57750..0000000000
--- a/examples/USER/diffraction/Output/BulkNi.in
+++ /dev/null
@@ -1,35 +0,0 @@
-variable A string bulkNi
-log $A.log
-
-boundary p p p
-
-units metal
-timestep 0.001
-
-lattice fcc 3.52
-region box block 0 20 0 20 0 20
-create_box 1 box
-create_atoms 1 box
-
-pair_style none
-mass * 58.71
-atom_modify sort 0 0
-
-compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-
-compute SAED all saed 0.0251 Ni Kmax 0.85 &
- Zone 0 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.01 echo manual
-
-fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
- mode vector file $A.hist.xrd
-
-fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
-
-dump 1 all custom 1 $A.dump id x y z
-run 0
-
-unfix 1
-unfix 2
-uncompute XRD
-uncompute SAED
--
GitLab
From ba4ff7744b5209a5164228673b58785b1acda63c Mon Sep 17 00:00:00 2001
From: RomainVermorel <romain.vermorel@univ-pau.fr>
Date: Mon, 3 Sep 2018 16:26:36 +0200
Subject: [PATCH 210/332] new USER-MOP package submitted
---
src/USER-MOP/README | 35 ++
src/USER-MOP/compute_mop.cpp | 424 +++++++++++++++++++++++
src/USER-MOP/compute_mop.example | 62 ++++
src/USER-MOP/compute_mop.h | 74 ++++
src/USER-MOP/compute_mop.txt | 71 ++++
src/USER-MOP/compute_mop_profile.cpp | 490 +++++++++++++++++++++++++++
src/USER-MOP/compute_mop_profile.h | 81 +++++
src/USER-MOP/compute_mop_profile.txt | 72 ++++
8 files changed, 1309 insertions(+)
create mode 100644 src/USER-MOP/README
create mode 100755 src/USER-MOP/compute_mop.cpp
create mode 100755 src/USER-MOP/compute_mop.example
create mode 100755 src/USER-MOP/compute_mop.h
create mode 100755 src/USER-MOP/compute_mop.txt
create mode 100755 src/USER-MOP/compute_mop_profile.cpp
create mode 100755 src/USER-MOP/compute_mop_profile.h
create mode 100755 src/USER-MOP/compute_mop_profile.txt
diff --git a/src/USER-MOP/README b/src/USER-MOP/README
new file mode 100644
index 0000000000..d8e7d2f732
--- /dev/null
+++ b/src/USER-MOP/README
@@ -0,0 +1,35 @@
+USER-MOP
+============
+
+This package provides the mop and mop/profile compute styles.
+See the doc page for compute mop or compute mop/profile command for how to use
+them.
+
+PACKAGE DESCRIPTION
+-------------------
+
+This is a LAMMPS (http://lammps.sandia.gov/) compute style that calculates
+components of the local stress tensor using the method of planes as described in
+the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure
+tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)).
+
+This package contains the source files of two compute styles:
+* compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
+* compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
+
+The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour.
+Contact them directly if you have questions.
+
+Laurent Joly
+Institut Lumière Matière
+Université Lyon 1 et CNRS
+43 boulevard du 11 novembre 1918
+69622 Villeurbanne Cedex
+e-mail: laurent.joly@univ-lyon1.fr
+
+Romain Vermorel
+Laboratory of Complex Fluids and their Reservoirs (LFCR)
+Université de Pau et des Pays de l'Adour
+Avenue de l'Université
+64012 Pau
+e-mail: romain.vermorel@univ-pau.fr
diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp
new file mode 100755
index 0000000000..42639d73ab
--- /dev/null
+++ b/src/USER-MOP/compute_mop.cpp
@@ -0,0 +1,424 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#include "math.h"
+#include "mpi.h"
+#include "string.h"
+#include "stdlib.h"
+#include "compute_mop.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "group.h"
+#include "modify.h"
+#include "fix.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "error.h"
+#include "memory.h"
+
+#include <iostream>
+
+using namespace LAMMPS_NS;
+
+enum{X,Y,Z};
+enum{TOTAL,CONF,KIN};
+
+#define BIG 1000000000
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg < 6) error->all(FLERR,"Illegal compute mop command");
+
+ MPI_Comm_rank(world,&me);
+
+ //set compute mode and direction of plane(s) for pressure calculation
+
+ if (strcmp(arg[3],"x")==0){
+ dir = X;
+ }
+ else if (strcmp(arg[3],"y")==0){
+ dir = Y;
+ }
+ else if (strcmp(arg[3],"z")==0){
+ dir = Z;
+ }
+ else error->all(FLERR,"Illegal compute mop command");
+
+ //Position of the plane
+ if (strcmp(arg[4],"lower")==0){
+ pos = domain->boxlo[dir];
+ }
+ else if (strcmp(arg[4],"upper")==0){
+ pos = domain->boxhi[dir];
+ }
+ else if (strcmp(arg[4],"center")==0){
+ pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
+ }
+ else pos = force->numeric(FLERR,arg[4]);
+
+ if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
+ pos1 = pos + domain->prd[dir];
+ } else {
+ pos1 = pos - domain->prd[dir];
+ }
+
+ // parse values until one isn't recognized
+
+ which = new int[3*(narg-5)];
+ nvalues = 0;
+ int i;
+
+ int iarg=5;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"conf") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = CONF;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"kin") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = KIN;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"total") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = TOTAL;
+ nvalues++;
+ }
+ } else error->all(FLERR, "Illegal compute mop command"); //break;
+
+ iarg++;
+ }
+
+ //Error check
+ // 3D only
+ if (domain->dimension<3)
+ error->all(FLERR, "Compute mop incompatible with simulation dimension");
+ // orthogonal simulation box
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
+ // plane inside the box
+ if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+ error->all(FLERR, "Plane for compute mop is out of bounds");
+
+
+ // Initialize some variables
+ values_local = values_global = vector = NULL;
+
+ // this fix produces a global vector
+
+ memory->create(vector,nvalues,"mop:vector");
+ memory->create(values_local,nvalues,"mop/spatial:values_local");
+ memory->create(values_global,nvalues,"mop/spatial:values_global");
+ size_vector = nvalues;
+
+ vector_flag = 1;
+ extvector = 0;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMop::~ComputeMop()
+{
+
+ delete [] which;
+
+ memory->destroy(values_local);
+ memory->destroy(values_global);
+ memory->destroy(vector);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMop::init()
+{
+
+ //Conversion constants
+ nktv2p = force->nktv2p;
+ ftm2v = force->ftm2v;
+
+ //Plane area
+ area = 1;
+ int i;
+ for (i=0; i<3; i++){
+ if (i!=dir) area = area*domain->prd[i];
+ }
+
+ //Timestep Value
+ dt = update->dt;
+
+// Error check
+
+// Compute mop requires fixed simulation box
+if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute mop requires a fixed simulation box");
+
+//This compute requires a pair style with pair_single method implemented
+if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute mop");
+if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute mop");
+
+// Warnings
+if (me==0){
+ //Compute mop only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute mop does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute mop does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute mop does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute mop does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop does not account for kspace contributions");
+ }
+
+ // need an occasional half neighbor list
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMop::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+
+/* ----------------------------------------------------------------------
+ compute output vector
+ ------------------------------------------------------------------------- */
+
+void ComputeMop::compute_vector()
+{
+
+ invoked_array = update->ntimestep;
+
+ //Compute pressures on separate procs
+ compute_pairs();
+
+ // sum pressure contributions over all procs
+ MPI_Allreduce(values_local,values_global,nvalues,
+ MPI_DOUBLE,MPI_SUM,world);
+
+ int m;
+ for (m=0; m<nvalues; m++) {
+ vector[m] = values_global[m];
+ }
+
+}
+
+
+/*------------------------------------------------------------------------
+ compute pressure contribution of local proc
+ -------------------------------------------------------------------------*/
+
+void ComputeMop::compute_pairs()
+
+{
+ int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
+ double delx,dely,delz;
+ double rsq,eng,fpair,factor_coul,factor_lj;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+
+ // zero out arrays for one sample
+ for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
+
+ // invoke half neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ //Parse values
+ double xi[3];
+ double vi[3];
+ double fi[3];
+ double xj[3];
+
+ m = 0;
+ while (m<nvalues) {
+ if (which[m] == CONF || which[m] == TOTAL) {
+
+ //Compute configurational contribution to pressure
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ // skip if neither I nor J are in group
+ if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
+
+ xj[0] = atom->x[j][0];
+ xj[1] = atom->x[j][1];
+ xj[2] = atom->x[j][2];
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+ if (rsq >= cutsq[itype][jtype]) continue;
+
+ if (newton_pair || j < nlocal) {
+
+ //check if ij pair is accross plane, add contribution to pressure
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+ else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ } else {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ }
+
+ }
+
+ }
+
+ }
+
+
+ if (which[m] == KIN || which[m] == TOTAL){
+ //Compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+
+ double vcm[3];
+ double masstotal,sgn;
+
+ //Velocity of the center of mass
+ //int ivcm,vcmbit;
+ //ivcm = igroup;
+ //vcmbit = groupbit;
+ //masstotal = group->mass(ivcm);
+ //group->vcm(ivcm,masstotal,vcm);
+
+ for (int i = 0; i < nlocal; i++){
+
+ // skip if I is not in group
+ if (mask[i] & groupbit){
+
+ itype = type[i];
+
+ //coordinates at t
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+
+ //velocities at t
+ vi[0] = atom->v[i][0];
+ vi[1] = atom->v[i][1];
+ vi[2] = atom->v[i][2];
+
+ //forces at t
+ fi[0] = atom->f[i][0];
+ fi[1] = atom->f[i][1];
+ fi[2] = atom->f[i][2];
+
+ //coordinates at t-dt (based on Velocity-Verlet alg.)
+ xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
+ xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
+ xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+
+ //because LAMMPS does not put atoms back in the box at each timestep, must check
+ //atoms going through the image of the plane that is closest to the box
+ double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir];
+ if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
+
+ if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)){
+
+ //sgn = copysign(1,vi[dir]-vcm[dir]);
+ sgn = copysign(1,vi[dir]);
+
+ //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+ double vcross[3];
+ vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
+ vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
+ vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+
+ values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+ }
+ }
+ }
+ }
+ m+=3;
+ }
+}
+
diff --git a/src/USER-MOP/compute_mop.example b/src/USER-MOP/compute_mop.example
new file mode 100755
index 0000000000..8dea9aecbd
--- /dev/null
+++ b/src/USER-MOP/compute_mop.example
@@ -0,0 +1,62 @@
+variable T equal 0.8
+variable p_solid equal 0.05
+
+lattice fcc 1.0
+region box block 0.0 6.0 0.0 6.0 -2.0 12.0
+create_box 2 box
+
+mass * 1.0
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+region solid_bottom block INF INF INF INF -1.1 0.1
+region liquid block INF INF INF INF 1.1 8.9
+region solid_up block INF INF INF INF 9.9 11.1
+
+create_atoms 1 region liquid
+delete_atoms porosity liquid 0.26 88765
+group liquid region liquid
+
+create_atoms 2 region solid_bottom
+group solid_bottom region solid_bottom
+create_atoms 2 region solid_up
+group solid_up region solid_up
+group solid union solid_bottom solid_up
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix_modify nvtliq temp Tliq
+
+thermo 10000
+thermo_modify flush yes temp Tliq
+
+dump 1 all atom 10000 dump.lammpstrj
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+velocity liquid create $T 47298 dist gaussian rot yes
+run 50000
+undump 1
+reset_timestep 0
+
+compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
+
+compute liquidStress_ke liquid stress/atom NULL ke
+compute liquidStress_vir liquid stress/atom NULL virial
+fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
+
+compute mopz0 all mop z center kin conf
+fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+
+compute moppz liquid mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 40000
+
diff --git a/src/USER-MOP/compute_mop.h b/src/USER-MOP/compute_mop.h
new file mode 100755
index 0000000000..53fa1e9d5c
--- /dev/null
+++ b/src/USER-MOP/compute_mop.h
@@ -0,0 +1,74 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(mop,ComputeMop)
+
+#else
+
+#ifndef LMP_COMPUTE_MOP_H
+#define LMP_COMPUTE_MOP_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+ class ComputeMop : public Compute {
+ public:
+ ComputeMop(class LAMMPS *, int, char **);
+ virtual ~ComputeMop();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_vector();
+
+ private:
+
+ void compute_pairs();
+
+ int me,nvalues,dir;
+ int *which;
+
+ double *values_local,*values_global;
+ double pos,pos1,dt,nktv2p,ftm2v;
+ double area;
+ class NeighList *list;
+
+ };
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+ E: Illegal ... command
+
+ Self-explanatory. Check the input script syntax and compare to the
+ documentation for the command. You can use -echo screen as a
+ command-line option when running LAMMPS to see the offending line.
+
+ E: Pair style does not support compute mop
+
+ The pair style does not have a single() function, so it can
+ not be invoked by compute mop/spatial.
+
+
+
+*/
+
diff --git a/src/USER-MOP/compute_mop.txt b/src/USER-MOP/compute_mop.txt
new file mode 100755
index 0000000000..ff6e85dff7
--- /dev/null
+++ b/src/USER-MOP/compute_mop.txt
@@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute mop command :h3
+
+[Syntax:]
+
+compute ID group-ID mop dir pos keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+mop = style name of this compute command
+dir = {x} or {y} or {z} is the direction normal to the plane
+pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
+between one and three keywords can be appended
+keyword = {kin} or {conf} or {total} :ul
+
+[Examples:]
+:link(mop-examples)
+
+compute 1 all mop x lower total
+compute 1 liquid mop z 0.0 kin conf
+fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
+fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
+
+[Description:]
+
+Define a computation that calculates components of the local stress tensor using the method of planes "(Todd)"_#mop-todd.
+Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the plane.
+
+Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
+
+The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the global system pressure.
+
+[Output info:]
+
+This compute calculates a global vector (indices starting at 1), with 3 values for each declared keyword (in the order the keywords have been declared). For each keyword, the stress tensor components are ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+
+The values are in pressure "units"_units.html.
+
+The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
+
+[Restrictions:]
+
+The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
+
+[Related commands:]
+
+"compute mop/profile"_compute_mop_profile.html, "compute stress/atom"_compute_stress_atom.html
+
+[Default:] none
+
+:line
+
+:link(mop-todd)
+[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp
new file mode 100755
index 0000000000..8c9e9041c4
--- /dev/null
+++ b/src/USER-MOP/compute_mop_profile.cpp
@@ -0,0 +1,490 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#include "math.h"
+#include "mpi.h"
+#include "string.h"
+#include "stdlib.h"
+#include "compute_mop_profile.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "group.h"
+#include "modify.h"
+#include "fix.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "error.h"
+#include "memory.h"
+
+#include <iostream>
+
+using namespace LAMMPS_NS;
+
+enum{X,Y,Z};
+enum{LOWER,CENTER,UPPER,COORD};
+enum{TOTAL,CONF,KIN};
+
+#define BIG 1000000000
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg < 7) error->all(FLERR,"Illegal compute mop/profile command");
+
+ MPI_Comm_rank(world,&me);
+
+ //set compute mode and direction of plane(s) for pressure calculation
+
+ if (strcmp(arg[3],"x")==0){
+ dir = X;
+ }
+ else if (strcmp(arg[3],"y")==0){
+ dir = Y;
+ }
+ else if (strcmp(arg[3],"z")==0){
+ dir = Z;
+ }
+ else error->all(FLERR,"Illegal compute mop/profile command");
+
+ //Bin parameters
+ if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
+ else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
+ else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
+ else originflag = COORD;
+ if (originflag == COORD)
+ origin = force->numeric(FLERR,arg[4]);
+ delta = force->numeric(FLERR,arg[5]);
+ invdelta = 1.0/delta;
+
+ // parse values until one isn't recognized
+
+ which = new int[3*(narg-6)];
+ nvalues = 0;
+ int i;
+
+ int iarg=6;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"conf") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = CONF;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"kin") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = KIN;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"total") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = TOTAL;
+ nvalues++;
+ }
+ } else error->all(FLERR, "Illegal compute mop/profile command"); //break;
+
+ iarg++;
+ }
+
+ //Check domain relared errors
+ // 3D only
+ if (domain->dimension<3)
+ error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
+ // orthogonal simulation box
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
+
+ // Initialize some variables
+ nbins = 0;
+ coord = coordp = NULL;
+ values_local = values_global = array = NULL;
+
+ //Bin setup
+ setup_bins();
+
+ // this fix produces a global array
+
+ memory->create(array,nbins,1+nvalues,"mop/profile:array");
+ size_array_rows = nbins;
+ size_array_cols = 1 + nvalues;
+
+ array_flag = 1;
+ extarray = 0;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMopProfile::~ComputeMopProfile()
+{
+
+ delete [] which;
+
+ memory->destroy(coord);
+ memory->destroy(coordp);
+ memory->destroy(values_local);
+ memory->destroy(values_global);
+ memory->destroy(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMopProfile::init()
+{
+
+ //Conversion constants
+ nktv2p = force->nktv2p;
+ ftm2v = force->ftm2v;
+
+ //Plane area
+ area = 1;
+ int i;
+ for (i=0; i<3; i++){
+ if (i!=dir) area = area*domain->prd[i];
+ }
+
+ //Timestep Value
+ dt = update->dt;
+
+ // Error check
+ // Compute mop/profile requires fixed simulation box
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
+
+ //This compute requires a pair style with pair_single method implemented
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute mop/profile");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute mop/profile");
+
+ // Warnings
+ if (me==0){
+ //Compute mop/profile only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
+ }
+
+ // need an occasional half neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMopProfile::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+
+/* ----------------------------------------------------------------------
+ compute output array
+ ------------------------------------------------------------------------- */
+
+void ComputeMopProfile::compute_array()
+{
+
+ invoked_array = update->ntimestep;
+
+ //Compute pressures on separate procs
+ compute_pairs();
+
+ // sum pressure contributions over all procs
+ MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
+ MPI_DOUBLE,MPI_SUM,world);
+
+ int ibin,m,mo;
+ for (ibin=0; ibin<nbins; ibin++) {
+ array[ibin][0] = coord[ibin][0];
+ mo=1;
+
+ m = 0;
+ while (m<nvalues) {
+ array[ibin][m+mo] = values_global[ibin][m];
+ m++;
+ }
+ }
+
+}
+
+
+/*------------------------------------------------------------------------
+ compute pressure contribution of local proc
+ -------------------------------------------------------------------------*/
+
+void ComputeMopProfile::compute_pairs()
+
+{
+ int i,j,m,n,ii,jj,inum,jnum,itype,jtype,ibin;
+ double delx,dely,delz;
+ double rsq,eng,fpair,factor_coul,factor_lj;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double pos,pos1,pos_temp;
+
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+
+ // zero out arrays for one sample
+ for (m = 0; m < nbins; m++) {
+ for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0;
+ }
+
+ // invoke half neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ //Parse values
+ double xi[3];
+ double vi[3];
+ double fi[3];
+ double xj[3];
+
+ m = 0;
+ while (m<nvalues) {
+ if (which[m] == CONF || which[m] == TOTAL) {
+
+ //Compute configurational contribution to pressure
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ // skip if neither I nor J are in group
+ if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
+
+ xj[0] = atom->x[j][0];
+ xj[1] = atom->x[j][1];
+ xj[2] = atom->x[j][2];
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+ if (rsq >= cutsq[itype][jtype]) continue;
+
+ if (newton_pair || j < nlocal) {
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ //check if ij pair is accross plane, add contribution to pressure
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+ else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ }
+
+ } else {
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ //check if ij pair is accross plane, add contribution to pressure
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ }
+
+ }
+
+ }
+
+ }
+
+ }
+
+
+ if (which[m] == KIN || which[m] == TOTAL){
+ //Compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+
+ double vcm[3];
+ double masstotal,sgn;
+
+ for (int i = 0; i < nlocal; i++){
+
+ // skip if I is not in group
+ if (mask[i] & groupbit){
+
+ itype = type[i];
+
+ //coordinates at t
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+
+ //velocities at t
+ vi[0] = atom->v[i][0];
+ vi[1] = atom->v[i][1];
+ vi[2] = atom->v[i][2];
+
+ //forces at t
+ fi[0] = atom->f[i][0];
+ fi[1] = atom->f[i][1];
+ fi[2] = atom->f[i][2];
+
+ //coordinates at t-dt (based on Velocity-Verlet alg.)
+ xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
+ xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
+ xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ if (((xi[dir]-pos)*(xj[dir]-pos)*(xi[dir]-pos1)*(xj[dir]-pos1)<0)){
+
+ sgn = copysign(1,vi[dir]);
+
+ //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+ double vcross[3];
+ vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
+ vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
+ vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+
+ values_local[ibin][m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+ }
+
+ }
+
+ }
+ }
+ }
+ m+=3;
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ setup 1d bins and their extent and coordinates
+ called at init()
+ ------------------------------------------------------------------------- */
+
+void ComputeMopProfile::setup_bins()
+{
+ int i,j,k,m,n;
+ double lo,hi,coord1,coord2;
+
+ double *boxlo,*boxhi,*prd;
+ boxlo = domain->boxlo;
+ boxhi = domain->boxhi;
+ prd = domain->prd;
+
+ if (originflag == LOWER) origin = boxlo[dir];
+ else if (originflag == UPPER) origin = boxhi[dir];
+ else if (originflag == CENTER)
+ origin = 0.5 * (boxlo[dir] + boxhi[dir]);
+
+ if (origin < boxlo[dir]) {
+ error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" );
+ } else {
+ n = static_cast<int> ((origin - boxlo[dir]) * invdelta);
+ lo = origin - n*delta;
+ }
+ if (origin < boxhi[dir]) {
+ n = static_cast<int> ((boxhi[dir] - origin) * invdelta);
+ hi = origin + n*delta;
+ } else {
+ error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" );
+ }
+
+ offset = lo;
+ nbins = static_cast<int> ((hi-lo) * invdelta + 1.5);
+
+ //allocate bin arrays
+ memory->create(coord,nbins,1,"mop/profile:coord");
+ memory->create(coordp,nbins,1,"mop/profile:coordp");
+ memory->create(values_local,nbins,nvalues,"mop/profile:values_local");
+ memory->create(values_global,nbins,nvalues,"mop/profile:values_global");
+
+ // set bin coordinates
+ for (i = 0; i < nbins; i++) {
+ coord[i][0] = offset + i*delta;
+ if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
+ coordp[i][0] = coord[i][0] + domain->prd[dir];
+ } else {
+ coordp[i][0] = coord[i][0] - domain->prd[dir];
+ }
+ }
+
+}
diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h
new file mode 100755
index 0000000000..3cb46087ae
--- /dev/null
+++ b/src/USER-MOP/compute_mop_profile.h
@@ -0,0 +1,81 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(mop/profile,ComputeMopProfile)
+
+#else
+
+#ifndef LMP_COMPUTE_MOP_PROFILE_H
+#define LMP_COMPUTE_MOP_PROFILE_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+ class ComputeMopProfile : public Compute {
+ public:
+ ComputeMopProfile(class LAMMPS *, int, char **);
+ virtual ~ComputeMopProfile();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_array();
+
+ private:
+
+ void compute_pairs();
+ void setup_bins();
+
+ int me,nvalues,dir;
+ int *which;
+
+ int originflag;
+ double origin,delta,offset,invdelta;
+ int nbins;
+ double **coord,**coordp;
+ double **values_local,**values_global;
+
+ int ndim;
+ double dt,nktv2p,ftm2v;
+ double area;
+ class NeighList *list;
+
+ };
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+ E: Illegal ... command
+
+ Self-explanatory. Check the input script syntax and compare to the
+ documentation for the command. You can use -echo screen as a
+ command-line option when running LAMMPS to see the offending line.
+
+ E: Pair style does not support compute mop/profile
+
+ The pair style does not have a single() function, so it can
+ not be invoked by compute mop/profile.
+
+
+
+*/
+
diff --git a/src/USER-MOP/compute_mop_profile.txt b/src/USER-MOP/compute_mop_profile.txt
new file mode 100755
index 0000000000..24b624a144
--- /dev/null
+++ b/src/USER-MOP/compute_mop_profile.txt
@@ -0,0 +1,72 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute mop/profile command :h3
+
+[Syntax:]
+
+compute ID group-ID mop/profile dir origin delta keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+mop/profile = style name of this compute command
+dir = {x} or {y} or {z} is the direction normal to the planes
+origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
+delta = value (distance units) is the distance between planes
+between one and three keywords can be appended
+keyword = {kin} or {conf} or {total} :ul
+
+[Examples:]
+:link(mop-examples)
+
+compute 1 all mop/profile x lower 0.1 total
+compute 1 liquid mop/profile z 0.0 0.25 kin conf
+fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
+
+
+[Description:]
+
+Define a computation that calculates profiles of components of the local stress tensor using the method of planes "(Todd)"_#mop-todd, applied on an array of regularly spaced planes.
+Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the planes.
+
+Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
+
+The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the global system pressure.
+
+[Output info:]
+
+This compute calculates a global array, with 1 column giving the position of the planes where the stress tensor was computed, and with 3 columns of values for each declared keyword (in the order the keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z.
+
+The values are in pressure "units"_units.html.
+
+The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
+
+[Restrictions:]
+
+The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
+
+[Related commands:]
+
+"compute mop"_compute_mop.html, "compute stress/atom"_compute_stress_atom.html
+
+[Default:] none
+
+:line
+
+:link(mop-todd)
+[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
--
GitLab
From 7b423c6d4b2ad482c7c1466f34e31a244dd402dd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 3 Sep 2018 23:37:25 -0400
Subject: [PATCH 211/332] integrate USER-MOP package into build and documentat
system. apply latest LAMMPS programming style conventions
---
cmake/CMakeLists.txt | 4 +-
doc/src/Packages_details.txt | 24 ++
doc/src/Packages_user.txt | 1 +
doc/src/compute_mop.txt | 111 +++++++++
doc/src/computes.txt | 1 +
doc/src/lammps.book | 1 +
.../USER/mop/in.compute_mop | 4 +-
.../USER/mop/log.31Aug18.compute_mop.g++.1 | 186 ++++++++++++++
examples/USER/mop/moppz.time.reference | 226 +++++++++++++++++
examples/USER/mop/mopz0.time.reference | 6 +
examples/USER/mop/profile.z.reference | 227 ++++++++++++++++++
src/.gitignore | 4 +
src/Makefile | 2 +-
src/USER-MOP/compute_mop.cpp | 134 +++++------
src/USER-MOP/compute_mop.h | 0
src/USER-MOP/compute_mop.txt | 71 ------
src/USER-MOP/compute_mop_profile.cpp | 154 ++++++------
src/USER-MOP/compute_mop_profile.h | 0
src/USER-MOP/compute_mop_profile.txt | 72 ------
19 files changed, 939 insertions(+), 289 deletions(-)
create mode 100644 doc/src/compute_mop.txt
rename src/USER-MOP/compute_mop.example => examples/USER/mop/in.compute_mop (94%)
mode change 100755 => 100644
create mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.1
create mode 100644 examples/USER/mop/moppz.time.reference
create mode 100644 examples/USER/mop/mopz0.time.reference
create mode 100644 examples/USER/mop/profile.z.reference
mode change 100755 => 100644 src/USER-MOP/compute_mop.cpp
mode change 100755 => 100644 src/USER-MOP/compute_mop.h
delete mode 100755 src/USER-MOP/compute_mop.txt
mode change 100755 => 100644 src/USER-MOP/compute_mop_profile.cpp
mode change 100755 => 100644 src/USER-MOP/compute_mop_profile.h
delete mode 100755 src/USER-MOP/compute_mop_profile.txt
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 53ac20f5d9..190ef3b2e0 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -215,8 +215,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
- USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
- USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+ USER-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
+ USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 381dc2e995..16f867b7c0 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -84,6 +84,7 @@ as contained in the file name.
"USER-MGPT"_#PKG-USER-MGPT,
"USER-MISC"_#PKG-USER-MISC,
"USER-MOFFF"_#PKG-USER-MOFFF,
+"USER-MOP"_#PKG-USER-MOP,
"USER-MOLFILE"_#PKG-USER-MOLFILE,
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
@@ -1572,6 +1573,29 @@ examples/USER/mofff :ul
:line
+USER-MOP package :link(PKG-USER-MOP),h4
+
+[Contents:]
+
+This package contains two compute styles: compute mop and compute mop/profile.
+
+compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
+
+compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
+
+[Author:] Laurent Joly (University of Lyon 1)
+Romain Vermorel at (University of Pau and Pays de l'Adour)
+
+[Supporting info:]
+
+src/USER-MOP: filenames -> commands
+src/USER-MOP/README
+"compute mop"_compute_mop.html
+"compute mop/profile"_compute_mop.html
+examples/USER/mop :ul
+
+:line
+
USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 7db2fa895c..731cf7ff10 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -57,6 +57,7 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
+"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
diff --git a/doc/src/compute_mop.txt b/doc/src/compute_mop.txt
new file mode 100644
index 0000000000..732f55657a
--- /dev/null
+++ b/doc/src/compute_mop.txt
@@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute mop command :h3
+compute mop/profile command :h3
+
+
+[Syntax:]
+
+compute ID group-ID style dir args keywords ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+style = {mop} or {mop/profile}
+dir = {x} or {y} or {z} is the direction normal to the plane
+args = argument specific to the compute style
+keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
+ {mop} args = pos
+ pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
+ {mop/profile} args = origin delta
+ origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
+ delta = value (distance units) is the distance between planes :pre
+
+compute 1 all mop x lower total
+compute 1 liquid mop z 0.0 kin conf
+fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
+fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
+
+compute 1 all mop/profile x lower 0.1 total
+compute 1 liquid mop/profile z 0.0 0.25 kin conf
+fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
+
+
+[Description:]
+
+Compute {mop} and compute {mop/profile} define computations that
+calculate components of the local stress tensor using the method of
+planes "(Todd)"_#mop-todd. Specifically in compute {mop} calculates 3
+components are computed in directions {dir},{x}; {dir},{y}; and
+{dir},{z}; where {dir} is the direction normal to the plane, while
+in compute {mop/profile} the profile of the stress is computed.
+
+Contrary to methods based on histograms of atomic stress (i.e. using
+"compute stress/atom"_compute_stress_atom.html), the method of planes is
+compatible with mechanical balance in heterogeneous systems and at
+interfaces "(Todd)"_#mop-todd.
+
+The stress tensor is the sum of a kinetic term and a configurational
+term, which are given respectively by Eq. (21) and Eq. (16) in
+"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
+atoms have crossed the plane if their positions at times t-dt and t are
+one on either side of the plane, and uses the velocity at time t-dt/2
+given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which
+contributions to the stress must be computed: kinetic stress (kin),
+configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the global system pressure.
+
+[Output info:]
+
+Compute {mop} calculates a global vector (indices starting at 1), with 3
+values for each declared keyword (in the order the keywords have been
+declared). For each keyword, the stress tensor components are ordered as
+follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+
+Compute {mop/profile} instead calculates a global array, with 1 column
+giving the position of the planes where the stress tensor was computed,
+and with 3 columns of values for each declared keyword (in the order the
+keywords have been declared). For each keyword, the profiles of stress
+tensor components are ordered as follows: stress_dir,x; stress_dir,y;
+and stress_dir,z.
+
+The values are in pressure "units"_units.html.
+
+The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
+
+[Restrictions:]
+
+This style is part of the USER-MOP package. It is only enabled if LAMMPS
+is built with that package. See the "Build package"_Build_package.html
+doc page on for more info.
+
+The method is only implemented for 3d orthogonal simulation boxes whose
+size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it
+requires the class method pair->single() to be implemented. In
+particular, it does not work with more than two-body pair interactions,
+intra-molecular interactions, and long range (kspace) interactions.
+
+[Related commands:]
+
+"compute stress/atom"_compute_stress_atom.html
+
+[Default:] none
+
+:line
+
+:link(mop-todd)
+[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 46dd30f757..c431f1c184 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -55,6 +55,7 @@ Computes :h1
compute_meso_e_atom
compute_meso_rho_atom
compute_meso_t_atom
+ compute_mop
compute_msd
compute_msd_chunk
compute_msd_nongauss
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c296ff4039..0aa382ae39 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -446,6 +446,7 @@ compute_ke_rigid.html
compute_meso_e_atom.html
compute_meso_rho_atom.html
compute_meso_t_atom.html
+compute_mop.html
compute_msd.html
compute_msd_chunk.html
compute_msd_nongauss.html
diff --git a/src/USER-MOP/compute_mop.example b/examples/USER/mop/in.compute_mop
old mode 100755
new mode 100644
similarity index 94%
rename from src/USER-MOP/compute_mop.example
rename to examples/USER/mop/in.compute_mop
index 8dea9aecbd..ab9552796f
--- a/src/USER-MOP/compute_mop.example
+++ b/examples/USER/mop/in.compute_mop
@@ -38,12 +38,12 @@ fix_modify nvtliq temp Tliq
thermo 10000
thermo_modify flush yes temp Tliq
-dump 1 all atom 10000 dump.lammpstrj
+# dump 1 all atom 10000 dump.lammpstrj
fix fxbal all balance 1000 1.05 shift z 10 1.05
velocity liquid create $T 47298 dist gaussian rot yes
run 50000
-undump 1
+# undump 1
reset_timestep 0
compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 b/examples/USER/mop/log.31Aug18.compute_mop.g++.1
new file mode 100644
index 0000000000..98b403b444
--- /dev/null
+++ b/examples/USER/mop/log.31Aug18.compute_mop.g++.1
@@ -0,0 +1,186 @@
+LAMMPS (31 Aug 2018)
+variable T equal 0.8
+variable p_solid equal 0.05
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0.0 6.0 0.0 6.0 -2.0 12.0
+create_box 2 box
+Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
+ 1 by 1 by 1 MPI processor grid
+
+mass * 1.0
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+region solid_bottom block INF INF INF INF -1.1 0.1
+region liquid block INF INF INF INF 1.1 8.9
+region solid_up block INF INF INF INF 9.9 11.1
+
+create_atoms 1 region liquid
+Created 1080 atoms
+ Time spent = 0.000631094 secs
+delete_atoms porosity liquid 0.26 88765
+Deleted 257 atoms, new total = 823
+group liquid region liquid
+823 atoms in group liquid
+
+create_atoms 2 region solid_bottom
+Created 216 atoms
+ Time spent = 0.000221014 secs
+group solid_bottom region solid_bottom
+216 atoms in group solid_bottom
+create_atoms 2 region solid_up
+Created 216 atoms
+ Time spent = 0.000169039 secs
+group solid_up region solid_up
+216 atoms in group solid_up
+group solid union solid_bottom solid_up
+432 atoms in group solid
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+variable faSolid equal 0.05*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix nvtliq liquid nvt temp 0.8 $T 0.5
+fix nvtliq liquid nvt temp 0.8 0.8 0.5
+fix_modify nvtliq temp Tliq
+WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404)
+
+thermo 10000
+thermo_modify flush yes temp Tliq
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
+
+# dump 1 all atom 10000 dump.lammpstrj
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+velocity liquid create $T 47298 dist gaussian rot yes
+velocity liquid create 0.8 47298 dist gaussian rot yes
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016
+ 10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016
+ 20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016
+ 30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016
+ 40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016
+ 50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
+Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms
+
+Performance: 531401.825 tau/day, 1230.097 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 28.102 | 28.102 | 28.102 | 0.0 | 69.14
+Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20
+Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25
+Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00
+Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45
+Other | | 0.3879 | | | 0.95
+
+Nlocal: 1255 ave 1255 max 1255 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2268 ave 2268 max 2268 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40149 ave 40149 max 40149 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40149
+Ave neighs/atom = 31.9912
+Neighbor list builds = 5714
+Dangerous builds = 0
+# undump 1
+reset_timestep 0
+
+compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
+
+compute liquidStress_ke liquid stress/atom NULL ke
+compute liquidStress_vir liquid stress/atom NULL virial
+fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
+
+compute mopz0 all mop z center kin conf
+fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+
+compute moppz liquid mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 40000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 3 neighbor lists, perpetual/occasional/extra = 1 2 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute mop, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (3) compute mop/profile, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
+ 10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016
+ 20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016
+ 30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016
+ 40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016
+Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms
+
+Performance: 380198.462 tau/day, 880.089 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 25.456 | 25.456 | 25.456 | 0.0 | 56.01
+Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47
+Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62
+Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00
+Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21
+Other | | 0.3131 | | | 0.69
+
+Nlocal: 1255 ave 1255 max 1255 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2269 ave 2269 max 2269 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40325 ave 40325 max 40325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40325
+Ave neighs/atom = 32.1315
+Neighbor list builds = 4587
+Dangerous builds = 0
+
+Total wall time: 0:01:26
diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/mop/moppz.time.reference
new file mode 100644
index 0000000000..f8d4b532ea
--- /dev/null
+++ b/examples/USER/mop/moppz.time.reference
@@ -0,0 +1,226 @@
+# Time-averaged data for fix moppzt
+# TimeStep Number-of-rows
+# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
+40000 222
+1 -3.1 0 0 0 0 0 0
+2 -3 0 0 0 0 0 0
+3 -2.9 0 0 0 0 0 0
+4 -2.8 0 0 0 0 0 0
+5 -2.7 0 0 0 0 0 0
+6 -2.6 0 0 0 0 0 0
+7 -2.5 0 0 0 0 0 0
+8 -2.4 0 0 0 0 0 0
+9 -2.3 0 0 0 0 0 0
+10 -2.2 0 0 0 0 0 0
+11 -2.1 0 0 0 0 0 0
+12 -2 0 0 0 0 0 0
+13 -1.9 0 0 0 0 0 0
+14 -1.8 0 0 0 0 0 0
+15 -1.7 0 0 0 0 0 0
+16 -1.6 0 0 0 0 0 0
+17 -1.5 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+18 -1.4 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+19 -1.3 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+20 -1.2 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+21 -1.1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+22 -1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+23 -0.9 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+24 -0.8 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+25 -0.7 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+26 -0.6 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+27 -0.5 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+28 -0.4 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+29 -0.3 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+30 -0.2 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+31 -0.1 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+32 0 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+33 0.1 0 0 0 -0.00643877 -0.00486842 0.0289193
+34 0.2 0 0 0 -0.00643877 -0.00486842 0.0289193
+35 0.3 0 0 0 -0.00643877 -0.00486842 0.0289193
+36 0.4 0 0 0 -0.00643877 -0.00486842 0.0289193
+37 0.5 0 0 0 -0.00643877 -0.00486842 0.0289193
+38 0.6 -0.00279194 0.0093508 0.013353 -0.00639358 -0.00380391 0.021025
+39 0.7 -0.00373537 0.0122501 0.0840939 -0.00503616 -0.0112127 -0.132562
+40 0.8 0.061158 -0.0280862 0.636594 0.00453591 -0.00214426 -0.557591
+41 0.9 -0.000266217 -0.0385723 0.969803 -0.0100643 0.00387732 -0.972644
+42 1 -0.0667633 -0.0208723 0.846848 0.0121337 -0.000646173 -0.936078
+43 1.1 -0.0479918 0.0444386 0.783228 0.0206387 -0.00229641 -0.640358
+44 1.2 0.0907347 -0.00458127 0.508479 0.0271462 -0.0136805 -0.427689
+45 1.3 0.0346947 -0.015182 0.397443 0.0162624 -0.0165167 -0.323227
+46 1.4 0.0576422 -0.00277706 0.359744 0.0291978 -0.0156949 -0.265795
+47 1.5 0.0596081 -0.00318334 0.238852 0.0157713 -0.0150214 -0.273303
+48 1.6 0.016955 0.0183139 0.459661 0.00421857 -0.0129777 -0.340127
+49 1.7 0.0697698 -0.0115622 0.431809 -0.0258679 0.00300245 -0.510533
+50 1.8 0.100399 -0.0797432 0.71209 -0.0501721 0.00810306 -0.680932
+51 1.9 0.0500614 -0.0191708 0.789407 -0.0486138 0.0173172 -0.750564
+52 2 -0.00914799 -0.0341791 0.626456 -0.0471521 0.000678372 -0.701829
+53 2.1 0.0369963 0.0256396 0.706456 -0.0509059 0.0173155 -0.620292
+54 2.2 -0.0579061 -0.0608427 0.484532 -0.0294166 0.000458726 -0.521648
+55 2.3 0.00709018 -0.0497913 0.439925 -0.0279961 -0.0102977 -0.43579
+56 2.4 -0.00695344 -0.000619047 0.441961 -0.0248115 -0.0244491 -0.417814
+57 2.5 -0.0375477 0.0725146 0.521221 -0.0140031 -0.0302539 -0.426543
+58 2.6 -0.00333415 0.0411399 0.550053 -0.0244236 -0.0246652 -0.444765
+59 2.7 0.0325652 -0.0422058 0.421026 -0.00606598 -0.038332 -0.507456
+60 2.8 -0.0246015 -0.0468897 0.635467 -0.035645 -0.0428363 -0.541653
+61 2.9 -0.00247499 0.00564888 0.643559 -0.0442198 -0.0211607 -0.539113
+62 3 -0.0320027 -0.0392749 0.603448 -0.0273872 -0.0458147 -0.544274
+63 3.1 -0.00250831 0.0294524 0.630966 -0.0228213 -0.00709569 -0.534171
+64 3.2 -0.0115271 0.0256808 0.597281 -0.00722677 0.00276478 -0.493192
+65 3.3 -0.00826942 -0.0763258 0.569383 -0.0294055 0.00152838 -0.470596
+66 3.4 -4.4607e-05 0.00409392 0.454468 0.00536302 0.00576224 -0.443972
+67 3.5 -0.00145279 -0.0180142 0.532694 0.0162497 0.0129368 -0.488614
+68 3.6 -0.0435087 -0.0436055 0.544955 0.0257295 0.0204122 -0.51687
+69 3.7 -0.0154394 0.0136176 0.609813 0.0132893 -0.00555839 -0.551156
+70 3.8 -0.011446 -0.00706375 0.661117 0.0380525 0.0191365 -0.531052
+71 3.9 -0.0804251 -0.0761665 0.563738 0.0489132 0.0190947 -0.509251
+72 4 0.0127481 0.0455454 0.566261 0.038016 0.0126592 -0.515555
+73 4.1 -0.00153026 -0.025983 0.584368 0.0243742 0.00388593 -0.487748
+74 4.2 0.0488435 0.00522856 0.535885 0.0161854 -0.000859699 -0.487082
+75 4.3 -0.118588 0.134127 0.503423 -0.00404382 -0.00428885 -0.494589
+76 4.4 0.0134608 -0.0373908 0.598776 -0.0285097 -0.00468738 -0.48047
+77 4.5 0.0765487 0.055302 0.608029 -0.0450575 -0.0157753 -0.509701
+78 4.6 -0.05585 -0.0462818 0.618931 -0.0170038 -0.0358189 -0.55692
+79 4.7 0.0164839 -0.0352014 0.611466 -0.0237058 -0.0240414 -0.617077
+80 4.8 0.0436038 -0.00458656 0.612365 0.00997088 -0.0562156 -0.613109
+81 4.9 0.0352871 -0.0611231 0.776314 0.0338943 -0.0604021 -0.613378
+82 5 -0.0568251 -0.0247083 0.510044 0.00279028 -0.028082 -0.595866
+83 5.1 -1.10188e-05 -0.0120973 0.53437 0.00398708 -0.02584 -0.573631
+84 5.2 0.00992898 0.0313027 0.59329 0.00561749 0.00711019 -0.522198
+85 5.3 0.00120683 -0.0356538 0.548184 -0.0200955 0.0381984 -0.52012
+86 5.4 0.0762501 -0.00822531 0.541107 -0.0241871 0.0330327 -0.540077
+87 5.5 0.0461718 0.0519605 0.629188 -0.0222764 0.0226954 -0.551385
+88 5.6 -0.0590515 0.0287662 0.549344 -0.0420534 0.031427 -0.540878
+89 5.7 -0.021125 -0.0231434 0.508528 -0.0342499 0.0495904 -0.52078
+90 5.8 0.00366259 0.0218644 0.572742 -0.0417272 0.0150681 -0.502333
+91 5.9 -0.0198693 -0.0259311 0.564659 -0.0309091 0.0326989 -0.512076
+92 6 0.00390271 -0.00109073 0.543964 -0.00911548 -0.00232516 -0.51614
+93 6.1 0.0628801 -0.0660743 0.587361 0.00381158 0.0024442 -0.515185
+94 6.2 0.00152013 0.0147332 0.572594 0.0229772 0.0059129 -0.507687
+95 6.3 0.026454 0.0873166 0.571276 0.0178474 0.00279111 -0.513827
+96 6.4 0.0951526 -0.0589118 0.598299 0.00448651 0.0259024 -0.53599
+97 6.5 0.0619766 0.0863723 0.669836 -0.00873277 -0.00553461 -0.523788
+98 6.6 -0.0634325 0.0307315 0.69454 -0.0196477 0.0147324 -0.502773
+99 6.7 0.012962 0.00747902 0.51076 -0.0151695 0.0156039 -0.52839
+100 6.8 -0.039811 -0.00360989 0.6489 0.0120414 0.00259849 -0.491579
+101 6.9 -0.0327932 0.0484302 0.616791 -0.0091501 0.0040499 -0.499037
+102 7 0.0490981 0.105001 0.502159 0.0042417 0.00326159 -0.506754
+103 7.1 -0.0581682 0.0395551 0.590876 -0.00115276 0.025084 -0.510536
+104 7.2 -0.0278943 -0.0337449 0.607452 -0.0238974 0.0310696 -0.495835
+105 7.3 -0.0493484 -0.0370496 0.660977 0.0111283 0.0129981 -0.491408
+106 7.4 -0.0206342 -0.0567824 0.5974 0.0172099 -0.00710845 -0.51165
+107 7.5 -0.00940992 0.0303369 0.49934 0.0124837 -0.03568 -0.524051
+108 7.6 -0.0366305 0.0394555 0.459697 -0.00731655 -0.0233235 -0.52555
+109 7.7 -0.0110182 0.0639483 0.563437 -0.00857366 -0.00211197 -0.542335
+110 7.8 0.010323 0.0810661 0.550813 0.00585594 0.0131706 -0.540418
+111 7.9 -0.048191 0.0123444 0.551013 -0.0166757 0.00475367 -0.538792
+112 8 -0.0214946 0.0509729 0.576751 0.0195793 0.0328914 -0.532263
+113 8.1 0.0456292 0.0094789 0.558949 0.00867662 0.0158926 -0.524578
+114 8.2 -0.0512688 -0.091908 0.641645 0.00301901 0.00974779 -0.534635
+115 8.3 -0.00783193 -0.0632416 0.552394 0.00796143 0.0380808 -0.524053
+116 8.4 0.01777 -0.0376654 0.511021 0.0161297 0.0278027 -0.542342
+117 8.5 -0.0327248 -0.0899092 0.578655 0.0137482 0.0472277 -0.524035
+118 8.6 -0.0636407 -0.0252334 0.590898 -0.00601759 0.049413 -0.533022
+119 8.7 -0.0572488 0.0633104 0.744174 0.00670858 0.0337276 -0.548476
+120 8.8 -0.100349 0.0190862 0.738246 0.0194621 0.0386781 -0.547124
+121 8.9 0.0284238 -0.0710504 0.616557 -0.00223469 0.0256231 -0.545488
+122 9 0.0455527 0.0379271 0.549399 0.0219986 7.02084e-05 -0.554089
+123 9.1 -0.00572797 -0.0537564 0.619963 0.0151132 0.00535174 -0.541016
+124 9.2 0.0209666 0.0411495 0.526906 0.00505244 -0.0117546 -0.543559
+125 9.3 0.0350478 0.0441003 0.520438 -0.0102555 -0.0105673 -0.536683
+126 9.4 0.0546092 -0.0171837 0.598682 0.00942578 -0.0283571 -0.520765
+127 9.5 0.0180568 0.00850647 0.720246 0.0282267 -0.0412171 -0.533637
+128 9.6 0.0106648 0.0437645 0.575689 0.0151481 -0.0346536 -0.558032
+129 9.7 -0.155141 -0.00267266 0.637799 0.00208151 -0.0132553 -0.567237
+130 9.8 -0.00666603 -0.103109 0.55371 -0.00920682 0.0140328 -0.515539
+131 9.9 0.0146007 0.0526576 0.484032 -0.0113123 -0.0112639 -0.503197
+132 10 0.0146807 0.0352591 0.573481 0.015403 -0.0258601 -0.471611
+133 10.1 0.00213124 -0.036368 0.623151 0.00161826 -0.0216583 -0.471559
+134 10.2 -1.19073e-05 -0.0619808 0.588624 -0.0259091 0.00687593 -0.462229
+135 10.3 0.0570578 0.0539259 0.656283 -0.0441705 0.000600941 -0.490565
+136 10.4 -0.00888513 0.0460147 0.630823 -0.0474928 0.00205316 -0.502978
+137 10.5 0.0573266 0.0238284 0.547514 -0.0310441 0.00283003 -0.511855
+138 10.6 0.121504 0.0275327 0.615782 -0.030126 -0.0249915 -0.502326
+139 10.7 -0.0156129 -0.0437632 0.630716 0.00504067 -0.0180025 -0.545656
+140 10.8 -0.0218563 -0.0432434 0.605473 0.0104081 -0.041452 -0.579481
+141 10.9 -0.020486 0.0829505 0.610883 0.0122548 -0.0306657 -0.542298
+142 11 0.0195236 0.0729355 0.664827 0.0428504 -0.0338841 -0.517077
+143 11.1 0.0139034 0.0474138 0.664459 0.0249658 -0.0397278 -0.50611
+144 11.2 0.0179999 0.0121222 0.559603 0.0412521 -0.0516893 -0.454643
+145 11.3 0.0268913 -0.0259516 0.494548 0.0514919 -0.0324735 -0.432382
+146 11.4 0.0700355 0.00851857 0.474027 0.0146607 -0.0194147 -0.460328
+147 11.5 0.0274298 -0.0148551 0.667014 0.0264921 -0.0415723 -0.515389
+148 11.6 0.0463183 0.0187287 0.515272 -0.00909174 -0.0310966 -0.558989
+149 11.7 -0.0235634 -0.0412073 0.7427 -0.0125128 -0.0333824 -0.61481
+150 11.8 0.0321678 -0.0192894 0.644069 -0.0285241 -0.0157538 -0.581231
+151 11.9 -0.00435038 -0.0267837 0.544583 -0.0261629 -0.00830545 -0.547874
+152 12 -0.0336443 0.0295318 0.549275 -0.0400734 -0.00236707 -0.486501
+153 12.1 0.00727018 0.00541209 0.492761 -0.0257499 -0.00129429 -0.419029
+154 12.2 0.0283158 -0.0109625 0.530612 -0.00905248 0.000440108 -0.356769
+155 12.3 -0.0733773 0.0287381 0.36636 0.000887014 -0.0072063 -0.350062
+156 12.4 -0.0117385 -0.00497835 0.472524 0.010125 -0.00605897 -0.402028
+157 12.5 0.0748365 -0.0280141 0.641205 -0.00788459 -0.00190551 -0.514353
+158 12.6 -0.031287 -0.0304264 0.781403 -0.0189155 -0.02107 -0.651886
+159 12.7 -0.0453856 0.100627 0.761746 -0.0140253 -0.0328365 -0.713566
+160 12.8 -0.024117 -0.0238699 0.732155 -0.0397416 -0.0143651 -0.632622
+161 12.9 0.0464686 -0.00881426 0.518078 -0.01575 0.0039229 -0.477048
+162 13 0.0662285 -0.053418 0.494651 -0.0215236 -0.00156911 -0.31744
+163 13.1 -0.00957157 -0.0114031 0.198665 -0.0144126 -0.00116237 -0.165427
+164 13.2 0.0148721 -0.0146141 0.144808 -0.013809 0.00154277 -0.0432649
+165 13.3 0.0130082 -0.0195798 0.0662957 -0.0178279 0.00125713 0.0215737
+166 13.4 0.000829942 -0.00381453 0.00218714 -0.0108116 0.0018927 0.0425618
+167 13.5 -0.00384864 -0.005638 0.00637594 -0.00704578 0.00378489 0.0161925
+168 13.6 0 0 0 -0.00602844 0.00291108 -0.0553474
+169 13.7 0 0 0 -0.00530979 -0.00289004 -0.14481
+170 13.8 0 0 0 -0.00906266 -0.00176311 -0.200465
+171 13.9 0 0 0 0.00289955 0.000223381 -0.252608
+172 14 0 0 0 0.00277034 -0.00194448 -0.279276
+173 14.1 0 0 0 0.000240431 -0.000785394 -0.292009
+174 14.2 0 0 0 4.27688e-05 8.277e-05 -0.289271
+175 14.3 0 0 0 -3.58165e-05 5.05721e-05 -0.265846
+176 14.4 0 0 0 -2.28735e-05 3.83404e-05 -0.211496
+177 14.5 0 0 0 -1.50266e-05 1.53466e-05 -0.143001
+178 14.6 0 0 0 -1.89125e-05 2.17035e-05 -0.0975257
+179 14.7 0 0 0 -3.9367e-06 1.12808e-05 -0.0528117
+180 14.8 0 0 0 -8.97431e-06 -2.01724e-06 -0.0235133
+181 14.9 0 0 0 -8.31871e-06 -7.90657e-07 -0.00959154
+182 15 0 0 0 -4.39578e-06 1.15242e-06 -0.00663168
+183 15.1 0 0 0 -4.81121e-06 1.14868e-06 -0.00374977
+184 15.2 0 0 0 -4.6114e-06 -1.95408e-06 -0.0028924
+185 15.3 0 0 0 -4.24836e-06 -5.84343e-06 -0.00186821
+186 15.4 0 0 0 1.63908e-07 -5.33026e-06 -0.00123763
+187 15.5 0 0 0 -4.38526e-06 -4.50778e-06 -0.000652976
+188 15.6 0 0 0 -4.21332e-07 -2.92016e-07 -0.000215754
+189 15.7 0 0 0 3.72451e-08 -1.02432e-08 -5.34533e-05
+190 15.8 0 0 0 5.31804e-08 -3.83997e-07 -3.16961e-05
+191 15.9 0 0 0 0 0 0
+192 16 0 0 0 0 0 0
+193 16.1 0 0 0 0 0 0
+194 16.2 0 0 0 0 0 0
+195 16.3 0 0 0 0 0 0
+196 16.4 0 0 0 0 0 0
+197 16.5 0 0 0 0 0 0
+198 16.6 0 0 0 0 0 0
+199 16.7 0 0 0 0 0 0
+200 16.8 0 0 0 0 0 0
+201 16.9 0 0 0 0 0 0
+202 17 0 0 0 0 0 0
+203 17.1 0 0 0 0 0 0
+204 17.2 0 0 0 0 0 0
+205 17.3 0 0 0 0 0 0
+206 17.4 0 0 0 0 0 0
+207 17.5 0 0 0 0 0 0
+208 17.6 0 0 0 0 0 0
+209 17.7 0 0 0 0 0 0
+210 17.8 0 0 0 0 0 0
+211 17.9 0 0 0 0 0 0
+212 18 0 0 0 0 0 0
+213 18.1 0 0 0 0 0 0
+214 18.2 0 0 0 0 0 0
+215 18.3 0 0 0 0 0 0
+216 18.4 0 0 0 0 0 0
+217 18.5 0 0 0 0 0 0
+218 18.6 0 0 0 0 0 0
+219 18.7 0 0 0 0 0 0
+220 18.8 0 0 0 0 0 0
+221 18.9 0 0 0 0 0 0
+222 19 0 0 0 0 0 0
diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/mop/mopz0.time.reference
new file mode 100644
index 0000000000..6341d22906
--- /dev/null
+++ b/examples/USER/mop/mopz0.time.reference
@@ -0,0 +1,6 @@
+# Time-averaged data for fix mopz0t
+# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
+10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264
+20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147
+30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132
+40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305
diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/mop/profile.z.reference
new file mode 100644
index 0000000000..1e0d1bf26b
--- /dev/null
+++ b/examples/USER/mop/profile.z.reference
@@ -0,0 +1,227 @@
+# Chunk-averaged data for fix profile_z and group temp
+# Timestep Number-of-chunks Total-count
+# Chunk Coord1 Ncount density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6]
+40000 223 3292
+ 1 -3.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 2 -3.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 3 -2.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 4 -2.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 5 -2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 6 -2.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 7 -2.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 8 -2.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 9 -2.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 10 -2.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 11 -2.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 12 -2.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 13 -1.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 14 -1.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 15 -1.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 16 -1.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 17 -1.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 18 -1.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 19 -1.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 20 -1.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 21 -1.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 22 -1.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 23 -0.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 24 -0.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 25 -0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 26 -0.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 27 -0.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 28 -0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 29 -0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 30 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 31 -0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 32 -0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 33 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 34 0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 35 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 36 0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 37 0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 38 0.55 0.0155 0.00170866 0.77827 -0.823106 -0.662616 -0.84909 0.0895728 -0.0915996 -0.0170938 -9.39041 -10.0498 -10.5424 -0.265868 -0.0729269 -0.626454
+ 39 0.65 0.65625 0.0723425 0.805015 -0.786824 -0.81346 -0.814762 0.0155975 0.0168616 -0.0213122 -2.89739 -2.89092 -5.81642 -0.0313195 0.230066 -0.0388364
+ 40 0.75 4.18625 0.461476 0.79884 -0.814511 -0.792997 -0.789012 -0.00942159 0.00597072 -0.00127992 -0.0143748 -0.0512459 -2.64067 0.0488393 0.0797603 0.0243815
+ 41 0.85 9.79625 1.0799 0.79714 -0.80439 -0.79918 -0.78785 -0.00331374 0.00487411 -0.00151215 1.12418 1.08693 -0.84425 -0.00560715 -0.00540606 0.0136964
+ 42 0.95 11.8853 1.31018 0.796174 -0.794167 -0.80514 -0.789215 0.00723814 -0.00234092 0.00056184 1.42901 1.47052 0.953436 0.0152978 -0.00835816 -0.0143227
+ 43 1.05 9.50925 1.04826 0.790145 -0.778307 -0.798065 -0.794064 -0.00458567 0.00288496 0.00383306 1.34248 1.35909 2.2058 -0.00480159 -0.00651465 0.0107925
+ 44 1.15 6.62475 0.730287 0.792109 -0.78276 -0.792956 -0.80061 -0.000304313 0.00429876 -0.000168134 1.26277 1.22489 2.4073 -0.00702209 0.0123268 0.0158178
+ 45 1.25 4.843 0.533874 0.782372 -0.788056 -0.769346 -0.789713 -0.00686069 0.00712471 0.00418369 1.11904 1.10737 2.14058 -0.0215052 -0.0228293 0.0027643
+ 46 1.35 3.83075 0.422287 0.79523 -0.795215 -0.781756 -0.808717 0.00249536 0.00991401 0.00380274 0.82578 0.918645 1.46731 0.0226069 0.0224161 0.0177933
+ 47 1.45 3.677 0.405338 0.795643 -0.800148 -0.796298 -0.790481 -0.00645737 0.00817994 0.00550917 0.759125 0.737731 0.94736 0.0047934 -0.0525048 0.0098318
+ 48 1.55 4.02825 0.444059 0.7931 -0.809145 -0.767991 -0.802164 0.00796467 -0.00254477 -0.00515821 0.711573 0.700294 0.278708 -0.00223064 0.0425578 -0.0182506
+ 49 1.65 5.21025 0.574358 0.786639 -0.782146 -0.790073 -0.787698 -0.00628926 0.0029031 -0.00469372 0.731644 0.711902 -0.4288 0.0255459 0.0230297 -0.0116029
+ 50 1.75 7.042 0.776283 0.790913 -0.78969 -0.794201 -0.788849 0.00258833 -0.00622832 -0.00564932 0.890595 0.855746 -0.411099 -0.0301627 0.0064535 0.0103202
+ 51 1.85 8.46525 0.933177 0.792581 -0.802268 -0.785881 -0.789593 -0.0101489 -0.00231339 -0.00725399 0.995328 0.96239 0.0331328 -0.0719804 -0.00124182 0.00072388
+ 52 1.95 8.65475 0.954067 0.787864 -0.781802 -0.789244 -0.792545 0.00513504 0.00406419 -0.00879172 1.00435 0.961078 0.632404 -0.0517082 -0.0159131 0.00526744
+ 53 2.05 7.8595 0.866401 0.786055 -0.770225 -0.794059 -0.79388 -0.00752288 0.00623117 -0.00420196 1.00125 0.93989 1.08666 -0.0435495 0.0161905 0.0286065
+ 54 2.15 6.82475 0.752334 0.77991 -0.776702 -0.775219 -0.78781 0.00471997 0.00826834 0.00277604 0.85253 0.86241 1.24674 0.0246189 0.00530171 0.0353102
+ 55 2.25 5.89225 0.649539 0.781394 -0.766258 -0.795723 -0.782202 -0.00469749 7.49004e-05 -0.00738222 0.761321 0.690047 1.13698 0.0102827 0.00209006 -0.0164468
+ 56 2.35 5.42025 0.597508 0.785789 -0.774668 -0.790234 -0.792466 -0.00930276 0.00394548 -0.0106206 0.655063 0.695732 0.918347 -0.0225504 -0.0119507 0.0511995
+ 57 2.45 5.34525 0.58924 0.797039 -0.787684 -0.791749 -0.811683 0.00599798 0.00191556 -0.00434674 0.694615 0.671933 0.640961 -0.00323138 0.0273467 -0.0105561
+ 58 2.55 5.87275 0.64739 0.794482 -0.795196 -0.793495 -0.794755 -0.0158646 -0.00938029 -0.00871214 0.665991 0.601126 0.314868 -0.0128127 0.0289784 -0.0535967
+ 59 2.65 6.54775 0.721799 0.793027 -0.795599 -0.807693 -0.775789 -0.00379113 -0.00798908 0.00414433 0.687052 0.625958 0.250015 0.0223168 -0.0142519 0.0240892
+ 60 2.75 7.17375 0.790807 0.789337 -0.803269 -0.779503 -0.78524 0.00170161 -0.00681561 0.00356121 0.775713 0.774137 0.355147 -0.0206119 0.0273384 0.0344849
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+ 158 12.55 7.18325 0.791854 0.810347 -0.810077 -0.814291 -0.806672 0.00606941 0.00378615 -0.00723346 1.19284 1.19182 1.73528 -0.0195636 0.00861507 0.00981433
+ 159 12.65 8.364 0.922015 0.802831 -0.793745 -0.815213 -0.799533 0.00888945 -0.00221246 -0.0013096 1.28316 1.24633 1.27452 -0.00603367 0.0133191 0.001417
+ 160 12.75 8.39525 0.92546 0.800371 -0.787459 -0.809856 -0.803797 0.00118127 0.00299289 -0.000135661 1.19417 1.20767 0.720865 -0.0135762 0.00482602 0.00623344
+ 161 12.85 6.92675 0.763578 0.798754 -0.79668 -0.801189 -0.798394 -0.00251568 0.00367251 -0.000655615 1.05994 1.04185 0.204339 0.044213 -0.0055401 0.030704
+ 162 12.95 5.13075 0.565594 0.81208 -0.834401 -0.804813 -0.797027 0.00305957 0.00144876 -0.00793753 0.856388 0.890923 -0.41972 0.0506972 0.019741 0.00876421
+ 163 13.05 3.40875 0.375768 0.799165 -0.816098 -0.797641 -0.783757 0.00113601 -0.00364604 -0.00220459 0.675005 0.636073 -1.09022 0.0229893 0.0509697 -0.0359039
+ 164 13.15 1.8995 0.209394 0.807532 -0.785503 -0.814629 -0.822464 0.025825 -0.0395374 -0.000260578 -0.0119014 0.121821 -1.87804 -0.0788917 -0.134749 -0.067008
+ 165 13.25 0.8055 0.0887952 0.843214 -0.810206 -0.880537 -0.838901 0.039551 -0.0997588 0.0234894 -2.39237 -2.01058 -4.14878 0.223851 0.231795 -0.352153
+ 166 13.35 0.272 0.0299842 0.666721 -0.779612 -0.626689 -0.593862 -0.0393791 0.00154035 -0.00625556 -1.37505 -1.38233 -3.36414 0.00300675 -0.0372793 -0.243736
+ 167 13.45 0.07925 0.00873622 0.782435 -1.07607 -0.598123 -0.673115 0.117468 0.1185 -0.0878719 -3.7526 -3.60044 -5.09311 0.910831 0.205838 -0.276478
+ 168 13.55 0.0095 0.00104724 0.19248 -0.161758 -0.293769 -0.121913 0.0596029 -0.0388238 0.000461593 -0.419057 -0.823036 -1.04983 0.0273182 -0.129878 0.392706
+ 169 13.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 170 13.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 171 13.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 172 13.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 173 14.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 174 14.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 175 14.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 176 14.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 177 14.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 178 14.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 179 14.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 180 14.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 181 14.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 182 14.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 183 15.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 184 15.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 185 15.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 186 15.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 187 15.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 188 15.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 189 15.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 190 15.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 191 15.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 192 15.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 193 16.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 194 16.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 195 16.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 196 16.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 197 16.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 198 16.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 199 16.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 200 16.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 201 16.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 202 16.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 203 17.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 204 17.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 205 17.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 206 17.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 207 17.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 208 17.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 209 17.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 210 17.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 211 17.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 212 17.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 213 18.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 214 18.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 215 18.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 216 18.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 217 18.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 218 18.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 219 18.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 220 18.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 221 18.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 222 18.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 223 19.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff --git a/src/.gitignore b/src/.gitignore
index df3a22a5cd..c7aaa8ab64 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -288,6 +288,10 @@
/compute_meso_rho_atom.h
/compute_meso_t_atom.cpp
/compute_meso_t_atom.h
+/compute_mop.cpp
+/compute_mop.h
+/compute_mop_profile.cpp
+/compute_mop_profile.h
/compute_msd_nongauss.cpp
/compute_msd_nongauss.h
/compute_pe_tally.cpp
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe..6b1a2bdb98 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
- user-mgpt user-misc user-mofff user-molfile \
+ user-mgpt user-misc user-mop user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp
old mode 100755
new mode 100644
index 42639d73ab..ba6b458172
--- a/src/USER-MOP/compute_mop.cpp
+++ b/src/USER-MOP/compute_mop.cpp
@@ -15,10 +15,11 @@
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
--------------------------------------------------------------------------*/
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
#include "compute_mop.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +35,6 @@
#include "error.h"
#include "memory.h"
-#include <iostream>
-
using namespace LAMMPS_NS;
enum{X,Y,Z};
@@ -52,30 +51,25 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_rank(world,&me);
- //set compute mode and direction of plane(s) for pressure calculation
+ // set compute mode and direction of plane(s) for pressure calculation
- if (strcmp(arg[3],"x")==0){
+ if (strcmp(arg[3],"x")==0) {
dir = X;
- }
- else if (strcmp(arg[3],"y")==0){
+ } else if (strcmp(arg[3],"y")==0) {
dir = Y;
- }
- else if (strcmp(arg[3],"z")==0){
+ } else if (strcmp(arg[3],"z")==0) {
dir = Z;
- }
- else error->all(FLERR,"Illegal compute mop command");
+ } else error->all(FLERR,"Illegal compute mop command");
+
+ // Position of the plane
- //Position of the plane
- if (strcmp(arg[4],"lower")==0){
+ if (strcmp(arg[4],"lower")==0) {
pos = domain->boxlo[dir];
- }
- else if (strcmp(arg[4],"upper")==0){
+ } else if (strcmp(arg[4],"upper")==0) {
pos = domain->boxhi[dir];
- }
- else if (strcmp(arg[4],"center")==0){
+ } else if (strcmp(arg[4],"center")==0) {
pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
- }
- else pos = force->numeric(FLERR,arg[4]);
+ } else pos = force->numeric(FLERR,arg[4]);
if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
pos1 = pos + domain->prd[dir];
@@ -111,19 +105,22 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
- //Error check
- // 3D only
- if (domain->dimension<3)
- error->all(FLERR, "Compute mop incompatible with simulation dimension");
- // orthogonal simulation box
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
- // plane inside the box
- if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
- error->all(FLERR, "Plane for compute mop is out of bounds");
+ // Error check
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute mop incompatible with simulation dimension");
+
+ // orthogonal simulation box
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
+ // plane inside the box
+ if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+ error->all(FLERR, "Plane for compute mop is out of bounds");
// Initialize some variables
+
values_local = values_global = vector = NULL;
// this fix produces a global vector
@@ -155,54 +152,60 @@ ComputeMop::~ComputeMop()
void ComputeMop::init()
{
- //Conversion constants
+ // Conversion constants
+
nktv2p = force->nktv2p;
ftm2v = force->ftm2v;
- //Plane area
+ // Plane area
+
area = 1;
int i;
for (i=0; i<3; i++){
if (i!=dir) area = area*domain->prd[i];
}
- //Timestep Value
+ // Timestep Value
+
dt = update->dt;
-// Error check
+ // Error check
-// Compute mop requires fixed simulation box
-if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ // Compute mop requires fixed simulation box
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
error->all(FLERR, "Compute mop requires a fixed simulation box");
-//This compute requires a pair style with pair_single method implemented
-if (force->pair == NULL)
+ // This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute mop");
-if (force->pair->single_enable == 0)
+ if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute mop");
-// Warnings
-if (me==0){
- //Compute mop only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
- if (force->bond!=NULL)
+ // Warnings
+
+ if (me==0){
+
+ //Compute mop only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
error->warning(FLERR,"compute mop does not account for bond potentials");
- if (force->angle!=NULL)
+ if (force->angle!=NULL)
error->warning(FLERR,"compute mop does not account for angle potentials");
- if (force->dihedral!=NULL)
+ if (force->dihedral!=NULL)
error->warning(FLERR,"compute mop does not account for dihedral potentials");
- if (force->improper!=NULL)
+ if (force->improper!=NULL)
error->warning(FLERR,"compute mop does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop does not account for kspace contributions");
- }
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop does not account for kspace contributions");
+ }
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
-
}
/* ---------------------------------------------------------------------- */
@@ -219,7 +222,6 @@ void ComputeMop::init_list(int id, NeighList *ptr)
void ComputeMop::compute_vector()
{
-
invoked_array = update->ntimestep;
//Compute pressures on separate procs
@@ -259,9 +261,11 @@ void ComputeMop::compute_pairs()
// zero out arrays for one sample
+
for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
// invoke half neighbor list (will copy or build if necessary)
+
neighbor->build_one(list);
inum = list->inum;
@@ -274,7 +278,8 @@ void ComputeMop::compute_pairs()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
- //Parse values
+ // Parse values
+
double xi[3];
double vi[3];
double fi[3];
@@ -354,20 +359,13 @@ void ComputeMop::compute_pairs()
}
- if (which[m] == KIN || which[m] == TOTAL){
- //Compute kinetic contribution to pressure
- // counts local particles transfers across the plane
+ // Compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+ if (which[m] == KIN || which[m] == TOTAL){
double vcm[3];
double masstotal,sgn;
- //Velocity of the center of mass
- //int ivcm,vcmbit;
- //ivcm = igroup;
- //vcmbit = groupbit;
- //masstotal = group->mass(ivcm);
- //group->vcm(ivcm,masstotal,vcm);
-
for (int i = 0; i < nlocal; i++){
// skip if I is not in group
@@ -395,8 +393,10 @@ void ComputeMop::compute_pairs()
xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
- //because LAMMPS does not put atoms back in the box at each timestep, must check
- //atoms going through the image of the plane that is closest to the box
+ // because LAMMPS does not put atoms back in the box
+ // at each timestep, must check atoms going through the
+ // image of the plane that is closest to the box
+
double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir];
if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
diff --git a/src/USER-MOP/compute_mop.h b/src/USER-MOP/compute_mop.h
old mode 100755
new mode 100644
diff --git a/src/USER-MOP/compute_mop.txt b/src/USER-MOP/compute_mop.txt
deleted file mode 100755
index ff6e85dff7..0000000000
--- a/src/USER-MOP/compute_mop.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute mop command :h3
-
-[Syntax:]
-
-compute ID group-ID mop dir pos keyword ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-mop = style name of this compute command
-dir = {x} or {y} or {z} is the direction normal to the plane
-pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
-between one and three keywords can be appended
-keyword = {kin} or {conf} or {total} :ul
-
-[Examples:]
-:link(mop-examples)
-
-compute 1 all mop x lower total
-compute 1 liquid mop z 0.0 kin conf
-fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
-fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
-
-[Description:]
-
-Define a computation that calculates components of the local stress tensor using the method of planes "(Todd)"_#mop-todd.
-Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the plane.
-
-Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
-
-The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
-
-Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
-
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
-
-NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the global system pressure.
-
-[Output info:]
-
-This compute calculates a global vector (indices starting at 1), with 3 values for each declared keyword (in the order the keywords have been declared). For each keyword, the stress tensor components are ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
-
-The values are in pressure "units"_units.html.
-
-The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
-
-[Restrictions:]
-
-The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
-
-The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
-
-[Related commands:]
-
-"compute mop/profile"_compute_mop_profile.html, "compute stress/atom"_compute_stress_atom.html
-
-[Default:] none
-
-:line
-
-:link(mop-todd)
-[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
-Phys. Rev. E 52, 1627 (1995).
diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp
old mode 100755
new mode 100644
index 8c9e9041c4..df62518c53
--- a/src/USER-MOP/compute_mop_profile.cpp
+++ b/src/USER-MOP/compute_mop_profile.cpp
@@ -15,10 +15,11 @@
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
--------------------------------------------------------------------------*/
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
#include "compute_mop_profile.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +35,6 @@
#include "error.h"
#include "memory.h"
-#include <iostream>
-
using namespace LAMMPS_NS;
enum{X,Y,Z};
@@ -53,20 +52,18 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_rank(world,&me);
- //set compute mode and direction of plane(s) for pressure calculation
+ // set compute mode and direction of plane(s) for pressure calculation
- if (strcmp(arg[3],"x")==0){
+ if (strcmp(arg[3],"x")==0) {
dir = X;
- }
- else if (strcmp(arg[3],"y")==0){
+ } else if (strcmp(arg[3],"y")==0) {
dir = Y;
- }
- else if (strcmp(arg[3],"z")==0){
+ } else if (strcmp(arg[3],"z")==0) {
dir = Z;
- }
- else error->all(FLERR,"Illegal compute mop/profile command");
+ } else error->all(FLERR,"Illegal compute mop/profile command");
+
+ // bin parameters
- //Bin parameters
if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
@@ -104,20 +101,26 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
- //Check domain relared errors
- // 3D only
- if (domain->dimension<3)
- error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
- // orthogonal simulation box
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
+ // check domain related errors
+
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
+
+ // orthogonal simulation box
+
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
+
+ // initialize some variables
- // Initialize some variables
nbins = 0;
coord = coordp = NULL;
values_local = values_global = array = NULL;
- //Bin setup
+ // bin setup
+
setup_bins();
// this fix produces a global array
@@ -128,7 +131,6 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
-
}
/* ---------------------------------------------------------------------- */
@@ -150,46 +152,54 @@ ComputeMopProfile::~ComputeMopProfile()
void ComputeMopProfile::init()
{
- //Conversion constants
+ // conversion constants
+
nktv2p = force->nktv2p;
ftm2v = force->ftm2v;
- //Plane area
+ // plane area
+
area = 1;
int i;
- for (i=0; i<3; i++){
+ for (i=0; i<3; i++) {
if (i!=dir) area = area*domain->prd[i];
}
- //Timestep Value
+ // timestep Value
+
dt = update->dt;
// Error check
- // Compute mop/profile requires fixed simulation box
- if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
- error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
+ // Compute mop/profile requires fixed simulation box
+
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
- //This compute requires a pair style with pair_single method implemented
- if (force->pair == NULL)
- error->all(FLERR,"No pair style is defined for compute mop/profile");
- if (force->pair->single_enable == 0)
- error->all(FLERR,"Pair style does not support compute mop/profile");
+ //This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute mop/profile");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute mop/profile");
- // Warnings
- if (me==0){
- //Compute mop/profile only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
- if (force->bond!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for bond potentials");
- if (force->angle!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for angle potentials");
- if (force->dihedral!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
- if (force->improper!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
- }
+ // Warnings
+
+ if (me==0){
+
+ //Compute mop/profile only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
+ }
// need an occasional half neighbor list
@@ -197,7 +207,6 @@ void ComputeMopProfile::init()
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
-
}
/* ---------------------------------------------------------------------- */
@@ -214,7 +223,6 @@ void ComputeMopProfile::init_list(int id, NeighList *ptr)
void ComputeMopProfile::compute_array()
{
-
invoked_array = update->ntimestep;
//Compute pressures on separate procs
@@ -235,7 +243,6 @@ void ComputeMopProfile::compute_array()
m++;
}
}
-
}
@@ -267,6 +274,7 @@ void ComputeMopProfile::compute_pairs()
}
// invoke half neighbor list (will copy or build if necessary)
+
neighbor->build_one(list);
inum = list->inum;
@@ -279,7 +287,8 @@ void ComputeMopProfile::compute_pairs()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
- //Parse values
+ // parse values
+
double xi[3];
double vi[3];
double fi[3];
@@ -289,7 +298,8 @@ void ComputeMopProfile::compute_pairs()
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL) {
- //Compute configurational contribution to pressure
+ // Compute configurational contribution to pressure
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -307,6 +317,7 @@ void ComputeMopProfile::compute_pairs()
j &= NEIGHMASK;
// skip if neither I nor J are in group
+
if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
xj[0] = atom->x[j][0];
@@ -326,15 +337,18 @@ void ComputeMopProfile::compute_pairs()
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
- }
- else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
+
+ } else if ( ((xi[dir]<pos) && (xj[dir]>pos))
+ || ((xi[dir]<pos1) && (xj[dir]>pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
@@ -342,9 +356,7 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
}
-
}
-
} else {
for (ibin=0;ibin<nbins;ibin++) {
@@ -352,7 +364,9 @@ void ComputeMopProfile::compute_pairs()
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
@@ -360,21 +374,16 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
}
-
}
-
}
-
}
-
}
-
}
+ // compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
if (which[m] == KIN || which[m] == TOTAL){
- //Compute kinetic contribution to pressure
- // counts local particles transfers across the plane
double vcm[3];
double masstotal,sgn;
@@ -382,6 +391,7 @@ void ComputeMopProfile::compute_pairs()
for (int i = 0; i < nlocal; i++){
// skip if I is not in group
+
if (mask[i] & groupbit){
itype = type[i];
@@ -424,9 +434,7 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
}
-
}
-
}
}
}
@@ -434,7 +442,6 @@ void ComputeMopProfile::compute_pairs()
}
}
-
/* ----------------------------------------------------------------------
setup 1d bins and their extent and coordinates
called at init()
@@ -486,5 +493,4 @@ void ComputeMopProfile::setup_bins()
coordp[i][0] = coord[i][0] - domain->prd[dir];
}
}
-
}
diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h
old mode 100755
new mode 100644
diff --git a/src/USER-MOP/compute_mop_profile.txt b/src/USER-MOP/compute_mop_profile.txt
deleted file mode 100755
index 24b624a144..0000000000
--- a/src/USER-MOP/compute_mop_profile.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute mop/profile command :h3
-
-[Syntax:]
-
-compute ID group-ID mop/profile dir origin delta keyword ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-mop/profile = style name of this compute command
-dir = {x} or {y} or {z} is the direction normal to the planes
-origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
-delta = value (distance units) is the distance between planes
-between one and three keywords can be appended
-keyword = {kin} or {conf} or {total} :ul
-
-[Examples:]
-:link(mop-examples)
-
-compute 1 all mop/profile x lower 0.1 total
-compute 1 liquid mop/profile z 0.0 0.25 kin conf
-fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
-
-
-[Description:]
-
-Define a computation that calculates profiles of components of the local stress tensor using the method of planes "(Todd)"_#mop-todd, applied on an array of regularly spaced planes.
-Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the planes.
-
-Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
-
-The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
-
-Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
-
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
-
-NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the global system pressure.
-
-[Output info:]
-
-This compute calculates a global array, with 1 column giving the position of the planes where the stress tensor was computed, and with 3 columns of values for each declared keyword (in the order the keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z.
-
-The values are in pressure "units"_units.html.
-
-The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
-
-[Restrictions:]
-
-The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
-
-The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
-
-[Related commands:]
-
-"compute mop"_compute_mop.html, "compute stress/atom"_compute_stress_atom.html
-
-[Default:] none
-
-:line
-
-:link(mop-todd)
-[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
-Phys. Rev. E 52, 1627 (1995).
--
GitLab
From f6f4b58167cb4ef78cae3b0fa2cb6a3ae266f1ee Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 3 Sep 2018 23:42:52 -0400
Subject: [PATCH 212/332] add parallel reference output
---
.../USER/mop/log.31Aug18.compute_mop.g++.4 | 188 ++++++++++++++++++
1 file changed, 188 insertions(+)
create mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.4
diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.4 b/examples/USER/mop/log.31Aug18.compute_mop.g++.4
new file mode 100644
index 0000000000..16ef8a2ce1
--- /dev/null
+++ b/examples/USER/mop/log.31Aug18.compute_mop.g++.4
@@ -0,0 +1,188 @@
+LAMMPS (31 Aug 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+variable T equal 0.8
+variable p_solid equal 0.05
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0.0 6.0 0.0 6.0 -2.0 12.0
+create_box 2 box
+Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
+ 1 by 1 by 4 MPI processor grid
+
+mass * 1.0
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+region solid_bottom block INF INF INF INF -1.1 0.1
+region liquid block INF INF INF INF 1.1 8.9
+region solid_up block INF INF INF INF 9.9 11.1
+
+create_atoms 1 region liquid
+Created 1080 atoms
+ Time spent = 0.000378132 secs
+delete_atoms porosity liquid 0.26 88765
+Deleted 288 atoms, new total = 792
+group liquid region liquid
+792 atoms in group liquid
+
+create_atoms 2 region solid_bottom
+Created 216 atoms
+ Time spent = 0.000345945 secs
+group solid_bottom region solid_bottom
+216 atoms in group solid_bottom
+create_atoms 2 region solid_up
+Created 216 atoms
+ Time spent = 0.000124454 secs
+group solid_up region solid_up
+216 atoms in group solid_up
+group solid union solid_bottom solid_up
+432 atoms in group solid
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+variable faSolid equal 0.05*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix nvtliq liquid nvt temp 0.8 $T 0.5
+fix nvtliq liquid nvt temp 0.8 0.8 0.5
+fix_modify nvtliq temp Tliq
+WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
+
+thermo 10000
+thermo_modify flush yes temp Tliq
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
+
+# dump 1 all atom 10000 dump.lammpstrj
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+velocity liquid create $T 47298 dist gaussian rot yes
+velocity liquid create 0.8 47298 dist gaussian rot yes
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.122 | 3.135 | 3.147 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.8 -3.4905808 0 -2.7150906 -0.59565852 2016
+ 10000 0.82075861 -3.1822235 0 -2.3866107 0.013840263 2016
+ 20000 0.76467575 -3.0955084 0 -2.3542602 -0.076868925 2016
+ 30000 0.75803557 -3.1011543 0 -2.3663428 -0.052887049 2016
+ 40000 0.81732724 -3.064259 0 -2.2719724 0.070708808 2016
+ 50000 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
+Loop time of 22.1566 on 4 procs for 50000 steps with 1224 atoms
+
+Performance: 974879.887 tau/day, 2256.666 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 10.732 | 13.012 | 14.39 | 38.0 | 58.73
+Neigh | 2.47 | 3.7351 | 4.3661 | 38.4 | 16.86
+Comm | 1.881 | 3.4383 | 5.8722 | 79.7 | 15.52
+Output | 0.00014567 | 0.0003581 | 0.0009892 | 0.0 | 0.00
+Modify | 1.1006 | 1.5188 | 2.6121 | 51.3 | 6.85
+Other | | 0.4521 | | | 2.04
+
+Nlocal: 306 ave 312 max 295 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost: 1242.75 ave 1373 max 944 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs: 9770.25 ave 10807 max 8736 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 39081
+Ave neighs/atom = 31.9289
+Neighbor list builds = 5704
+Dangerous builds = 0
+# undump 1
+reset_timestep 0
+
+compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
+
+compute liquidStress_ke liquid stress/atom NULL ke
+compute liquidStress_vir liquid stress/atom NULL virial
+fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
+
+compute mopz0 all mop z center kin conf
+fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+
+compute moppz liquid mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 40000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 3 neighbor lists, perpetual/occasional/extra = 1 2 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute mop, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (3) compute mop/profile, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.147 | 4.15 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
+ 10000 0.82372476 -3.1299329 0 -2.3314448 -0.14706101 2016
+ 20000 0.80692892 -3.1278896 0 -2.3456828 -0.085123604 2016
+ 30000 0.78458951 -3.0966006 0 -2.3360488 0.13637007 2016
+ 40000 0.80106495 -3.1135836 0 -2.3370611 -0.14404185 2016
+Loop time of 31.4145 on 4 procs for 40000 steps with 1224 atoms
+
+Performance: 550065.249 tau/day, 1273.299 timesteps/s
+92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 10.199 | 12.307 | 13.428 | 35.4 | 39.18
+Neigh | 2.1261 | 3.1416 | 3.6373 | 33.5 | 10.00
+Comm | 3.5381 | 4.476 | 6.229 | 48.9 | 14.25
+Output | 0.00062943 | 0.0031546 | 0.0040004 | 2.6 | 0.01
+Modify | 10.186 | 10.862 | 12.26 | 24.8 | 34.58
+Other | | 0.6247 | | | 1.99
+
+Nlocal: 306 ave 315 max 299 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost: 1221.5 ave 1347 max 912 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs: 9710.25 ave 10301 max 8980 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 38841
+Ave neighs/atom = 31.7328
+Neighbor list builds = 4573
+Dangerous builds = 0
+
+Total wall time: 0:00:53
--
GitLab
From a797a0d193cacfad1ca0329927ddb52f19799f58 Mon Sep 17 00:00:00 2001
From: RomainVermorel <romain.vermorel@univ-pau.fr>
Date: Tue, 4 Sep 2018 14:02:19 +0200
Subject: [PATCH 213/332] changed computes names to stress/mop and
stress/mop/profile
---
doc/src/compute_stress_mop.txt | 111 +++++
examples/USER/mop/in.compute_stress_mop | 62 +++
src/USER-MOP/README | 10 +-
src/USER-MOP/compute_stress_mop.cpp | 424 +++++++++++++++++
src/USER-MOP/compute_stress_mop.h | 102 ++++
src/USER-MOP/compute_stress_mop_profile.cpp | 496 ++++++++++++++++++++
src/USER-MOP/compute_stress_mop_profile.h | 113 +++++
7 files changed, 1313 insertions(+), 5 deletions(-)
create mode 100644 doc/src/compute_stress_mop.txt
create mode 100755 examples/USER/mop/in.compute_stress_mop
create mode 100644 src/USER-MOP/compute_stress_mop.cpp
create mode 100644 src/USER-MOP/compute_stress_mop.h
create mode 100644 src/USER-MOP/compute_stress_mop_profile.cpp
create mode 100644 src/USER-MOP/compute_stress_mop_profile.h
diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt
new file mode 100644
index 0000000000..8d95ef42e2
--- /dev/null
+++ b/doc/src/compute_stress_mop.txt
@@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute stress/mop command :h3
+compute stress/mop/profile command :h3
+
+
+[Syntax:]
+
+compute ID group-ID style dir args keywords ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+style = {stress/mop} or {stress/mop/profile}
+dir = {x} or {y} or {z} is the direction normal to the plane
+args = argument specific to the compute style
+keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
+ {stress/mop} args = pos
+ pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
+ {stress/mop/profile} args = origin delta
+ origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
+ delta = value (distance units) is the distance between planes :pre
+
+compute 1 all stress/mop x lower total
+compute 1 liquid stress/mop z 0.0 kin conf
+fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
+fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
+
+compute 1 all stress/mop/profile x lower 0.1 total
+compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf
+fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
+
+
+[Description:]
+
+Compute {stress/mop} and compute {stress/mop/profile} define computations that
+calculate components of the local stress tensor using the method of
+planes "(Todd)"_#mop-todd. Specifically in compute {stress/mop} calculates 3
+components are computed in directions {dir},{x}; {dir},{y}; and
+{dir},{z}; where {dir} is the direction normal to the plane, while
+in compute {stress/mop/profile} the profile of the stress is computed.
+
+Contrary to methods based on histograms of atomic stress (i.e. using
+"compute stress/atom"_compute_stress_atom.html), the method of planes is
+compatible with mechanical balance in heterogeneous systems and at
+interfaces "(Todd)"_#mop-todd.
+
+The stress tensor is the sum of a kinetic term and a configurational
+term, which are given respectively by Eq. (21) and Eq. (16) in
+"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
+atoms have crossed the plane if their positions at times t-dt and t are
+one on either side of the plane, and uses the velocity at time t-dt/2
+given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which
+contributions to the stress must be computed: kinetic stress (kin),
+configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the global system pressure.
+
+[Output info:]
+
+Compute {stress/mop} calculates a global vector (indices starting at 1), with 3
+values for each declared keyword (in the order the keywords have been
+declared). For each keyword, the stress tensor components are ordered as
+follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+
+Compute {stress/mop/profile} instead calculates a global array, with 1 column
+giving the position of the planes where the stress tensor was computed,
+and with 3 columns of values for each declared keyword (in the order the
+keywords have been declared). For each keyword, the profiles of stress
+tensor components are ordered as follows: stress_dir,x; stress_dir,y;
+and stress_dir,z.
+
+The values are in pressure "units"_units.html.
+
+The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
+
+[Restrictions:]
+
+This style is part of the USER-MOP package. It is only enabled if LAMMPS
+is built with that package. See the "Build package"_Build_package.html
+doc page on for more info.
+
+The method is only implemented for 3d orthogonal simulation boxes whose
+size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it
+requires the class method pair->single() to be implemented. In
+particular, it does not work with more than two-body pair interactions,
+intra-molecular interactions, and long range (kspace) interactions.
+
+[Related commands:]
+
+"compute stress/atom"_compute_stress_atom.html
+
+[Default:] none
+
+:line
+
+:link(mop-todd)
+[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/mop/in.compute_stress_mop
new file mode 100755
index 0000000000..cfa97f5dfe
--- /dev/null
+++ b/examples/USER/mop/in.compute_stress_mop
@@ -0,0 +1,62 @@
+variable T equal 0.8
+variable p_solid equal 0.05
+
+lattice fcc 1.0
+region box block 0.0 6.0 0.0 6.0 -2.0 12.0
+create_box 2 box
+
+mass * 1.0
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+region solid_bottom block INF INF INF INF -1.1 0.1
+region liquid block INF INF INF INF 1.1 8.9
+region solid_up block INF INF INF INF 9.9 11.1
+
+create_atoms 1 region liquid
+delete_atoms porosity liquid 0.26 88765
+group liquid region liquid
+
+create_atoms 2 region solid_bottom
+group solid_bottom region solid_bottom
+create_atoms 2 region solid_up
+group solid_up region solid_up
+group solid union solid_bottom solid_up
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix_modify nvtliq temp Tliq
+
+thermo 10000
+thermo_modify flush yes temp Tliq
+
+dump 1 all atom 10000 dump.lammpstrj
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+velocity liquid create $T 47298 dist gaussian rot yes
+run 50000
+undump 1
+reset_timestep 0
+
+compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
+
+compute liquidStress_ke liquid stress/atom NULL ke
+compute liquidStress_vir liquid stress/atom NULL virial
+fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
+
+compute mopz0 all stress/mop z center kin conf
+fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+
+compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 40000
+
diff --git a/src/USER-MOP/README b/src/USER-MOP/README
index d8e7d2f732..15fcb3701a 100644
--- a/src/USER-MOP/README
+++ b/src/USER-MOP/README
@@ -1,21 +1,21 @@
USER-MOP
============
-This package provides the mop and mop/profile compute styles.
-See the doc page for compute mop or compute mop/profile command for how to use
+This package provides the stress/mop and stress/mop/profile compute styles.
+See the doc page for compute stress/mop or compute stress/mop/profile command for how to use
them.
PACKAGE DESCRIPTION
-------------------
-This is a LAMMPS (http://lammps.sandia.gov/) compute style that calculates
+These are LAMMPS (http://lammps.sandia.gov/) compute styles that calculate
components of the local stress tensor using the method of planes as described in
the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure
tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)).
This package contains the source files of two compute styles:
-* compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
-* compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
+* compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
+* compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour.
Contact them directly if you have questions.
diff --git a/src/USER-MOP/compute_stress_mop.cpp b/src/USER-MOP/compute_stress_mop.cpp
new file mode 100644
index 0000000000..f764e0ee7e
--- /dev/null
+++ b/src/USER-MOP/compute_stress_mop.cpp
@@ -0,0 +1,424 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
+#include "compute_stress_mop.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "group.h"
+#include "modify.h"
+#include "fix.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "error.h"
+#include "memory.h"
+
+using namespace LAMMPS_NS;
+
+enum{X,Y,Z};
+enum{TOTAL,CONF,KIN};
+
+#define BIG 1000000000
+
+/* ---------------------------------------------------------------------- */
+
+ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg < 6) error->all(FLERR,"Illegal compute stress/mop command");
+
+ MPI_Comm_rank(world,&me);
+
+ // set compute mode and direction of plane(s) for pressure calculation
+
+ if (strcmp(arg[3],"x")==0) {
+ dir = X;
+ } else if (strcmp(arg[3],"y")==0) {
+ dir = Y;
+ } else if (strcmp(arg[3],"z")==0) {
+ dir = Z;
+ } else error->all(FLERR,"Illegal compute stress/mop command");
+
+ // Position of the plane
+
+ if (strcmp(arg[4],"lower")==0) {
+ pos = domain->boxlo[dir];
+ } else if (strcmp(arg[4],"upper")==0) {
+ pos = domain->boxhi[dir];
+ } else if (strcmp(arg[4],"center")==0) {
+ pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
+ } else pos = force->numeric(FLERR,arg[4]);
+
+ if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
+ pos1 = pos + domain->prd[dir];
+ } else {
+ pos1 = pos - domain->prd[dir];
+ }
+
+ // parse values until one isn't recognized
+
+ which = new int[3*(narg-5)];
+ nvalues = 0;
+ int i;
+
+ int iarg=5;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"conf") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = CONF;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"kin") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = KIN;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"total") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = TOTAL;
+ nvalues++;
+ }
+ } else error->all(FLERR, "Illegal compute stress/mop command"); //break;
+
+ iarg++;
+ }
+
+ // Error check
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute stress/mop incompatible with simulation dimension");
+
+ // orthogonal simulation box
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box");
+ // plane inside the box
+ if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+ error->all(FLERR, "Plane for compute stress/mop is out of bounds");
+
+
+ // Initialize some variables
+
+ values_local = values_global = vector = NULL;
+
+ // this fix produces a global vector
+
+ memory->create(vector,nvalues,"stress/mop:vector");
+ memory->create(values_local,nvalues,"stress/mop/spatial:values_local");
+ memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
+ size_vector = nvalues;
+
+ vector_flag = 1;
+ extvector = 0;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeStressMop::~ComputeStressMop()
+{
+
+ delete [] which;
+
+ memory->destroy(values_local);
+ memory->destroy(values_global);
+ memory->destroy(vector);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeStressMop::init()
+{
+
+ // Conversion constants
+
+ nktv2p = force->nktv2p;
+ ftm2v = force->ftm2v;
+
+ // Plane area
+
+ area = 1;
+ int i;
+ for (i=0; i<3; i++){
+ if (i!=dir) area = area*domain->prd[i];
+ }
+
+ // Timestep Value
+
+ dt = update->dt;
+
+ // Error check
+
+ // Compute stress/mop requires fixed simulation box
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute stress/mop requires a fixed simulation box");
+
+ // This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute stress/mop");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute stress/mop");
+
+ // Warnings
+
+ if (me==0){
+
+ //Compute stress/mop only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute stress/mop does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute stress/mop does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute stress/mop does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
+ }
+
+ // need an occasional half neighbor list
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeStressMop::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+
+/* ----------------------------------------------------------------------
+ compute output vector
+ ------------------------------------------------------------------------- */
+
+void ComputeStressMop::compute_vector()
+{
+ invoked_array = update->ntimestep;
+
+ //Compute pressures on separate procs
+ compute_pairs();
+
+ // sum pressure contributions over all procs
+ MPI_Allreduce(values_local,values_global,nvalues,
+ MPI_DOUBLE,MPI_SUM,world);
+
+ int m;
+ for (m=0; m<nvalues; m++) {
+ vector[m] = values_global[m];
+ }
+
+}
+
+
+/*------------------------------------------------------------------------
+ compute pressure contribution of local proc
+ -------------------------------------------------------------------------*/
+
+void ComputeStressMop::compute_pairs()
+
+{
+ int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
+ double delx,dely,delz;
+ double rsq,eng,fpair,factor_coul,factor_lj;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+
+ // zero out arrays for one sample
+
+ for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
+
+ // invoke half neighbor list (will copy or build if necessary)
+
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ // Parse values
+
+ double xi[3];
+ double vi[3];
+ double fi[3];
+ double xj[3];
+
+ m = 0;
+ while (m<nvalues) {
+ if (which[m] == CONF || which[m] == TOTAL) {
+
+ //Compute configurational contribution to pressure
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ // skip if neither I nor J are in group
+ if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
+
+ xj[0] = atom->x[j][0];
+ xj[1] = atom->x[j][1];
+ xj[2] = atom->x[j][2];
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+ if (rsq >= cutsq[itype][jtype]) continue;
+
+ if (newton_pair || j < nlocal) {
+
+ //check if ij pair is accross plane, add contribution to pressure
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+ else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ } else {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+
+ }
+
+ }
+
+ }
+
+ }
+
+
+ // Compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+
+ if (which[m] == KIN || which[m] == TOTAL){
+ double vcm[3];
+ double masstotal,sgn;
+
+ for (int i = 0; i < nlocal; i++){
+
+ // skip if I is not in group
+ if (mask[i] & groupbit){
+
+ itype = type[i];
+
+ //coordinates at t
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+
+ //velocities at t
+ vi[0] = atom->v[i][0];
+ vi[1] = atom->v[i][1];
+ vi[2] = atom->v[i][2];
+
+ //forces at t
+ fi[0] = atom->f[i][0];
+ fi[1] = atom->f[i][1];
+ fi[2] = atom->f[i][2];
+
+ //coordinates at t-dt (based on Velocity-Verlet alg.)
+ xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
+ xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
+ xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+
+ // because LAMMPS does not put atoms back in the box
+ // at each timestep, must check atoms going through the
+ // image of the plane that is closest to the box
+
+ double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir];
+ if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
+
+ if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)){
+
+ //sgn = copysign(1,vi[dir]-vcm[dir]);
+ sgn = copysign(1,vi[dir]);
+
+ //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+ double vcross[3];
+ vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
+ vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
+ vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+
+ values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+ }
+ }
+ }
+ }
+ m+=3;
+ }
+}
+
diff --git a/src/USER-MOP/compute_stress_mop.h b/src/USER-MOP/compute_stress_mop.h
new file mode 100644
index 0000000000..2047d1d54f
--- /dev/null
+++ b/src/USER-MOP/compute_stress_mop.h
@@ -0,0 +1,102 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(stress/mop,ComputeStressMop)
+
+#else
+
+#ifndef LMP_COMPUTE_STRESS_MOP_H
+#define LMP_COMPUTE_STRESS_MOP_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+ class ComputeStressMop : public Compute {
+ public:
+ ComputeStressMop(class LAMMPS *, int, char **);
+ virtual ~ComputeStressMop();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_vector();
+
+ private:
+
+ void compute_pairs();
+
+ int me,nvalues,dir;
+ int *which;
+
+ double *values_local,*values_global;
+ double pos,pos1,dt,nktv2p,ftm2v;
+ double area;
+ class NeighList *list;
+
+ };
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+ E: Illegal ... command
+
+ Self-explanatory. Check the input script syntax and compare to the
+ documentation for the command. You can use -echo screen as a
+ command-line option when running LAMMPS to see the offending line.
+
+ E: Compute stress/mop incompatible with simulation dimension
+
+ Compute stress/mop only works with 3D simulations.
+
+ E: Compute stress/mop incompatible with triclinic simulation box
+
+ Self-explanatory.
+
+ E: Compute stress/mop requires a fixed simulation box
+
+ Compute stress/mop is not compatible with any change of volume or shape
+ or boundary conditions of the simulation box.
+
+ E: No pair style is defined for compute stress/mop
+
+ Self-explanatory. Compute stress/mop requires the definition of a pair style.
+
+ E: Pair style does not support compute stress/mop
+
+ The pair style does not have a single() function, so it can
+ not be invoked by compute stress/mop.
+
+ W: compute stress/mop does not account for bond potentials
+
+ W: compute stress/mop does not account for angle potentials
+
+ W: compute stress/mop does not account for dihedral potentials
+
+ W: compute stress/mop does not account for improper potentials
+
+ W: compute stress/mop does not account for kspace contributions
+
+ Compute stress/mop only accounts for pairwise additive interactions for
+ the computation of local stress tensor components.
+
+ */
+
diff --git a/src/USER-MOP/compute_stress_mop_profile.cpp b/src/USER-MOP/compute_stress_mop_profile.cpp
new file mode 100644
index 0000000000..7ba0622aa4
--- /dev/null
+++ b/src/USER-MOP/compute_stress_mop_profile.cpp
@@ -0,0 +1,496 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
+#include "compute_stress_mop_profile.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "group.h"
+#include "modify.h"
+#include "fix.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "error.h"
+#include "memory.h"
+
+using namespace LAMMPS_NS;
+
+enum{X,Y,Z};
+enum{LOWER,CENTER,UPPER,COORD};
+enum{TOTAL,CONF,KIN};
+
+#define BIG 1000000000
+
+/* ---------------------------------------------------------------------- */
+
+ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command");
+
+ MPI_Comm_rank(world,&me);
+
+ // set compute mode and direction of plane(s) for pressure calculation
+
+ if (strcmp(arg[3],"x")==0) {
+ dir = X;
+ } else if (strcmp(arg[3],"y")==0) {
+ dir = Y;
+ } else if (strcmp(arg[3],"z")==0) {
+ dir = Z;
+ } else error->all(FLERR,"Illegal compute stress/mop/profile command");
+
+ // bin parameters
+
+ if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
+ else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
+ else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
+ else originflag = COORD;
+ if (originflag == COORD)
+ origin = force->numeric(FLERR,arg[4]);
+ delta = force->numeric(FLERR,arg[5]);
+ invdelta = 1.0/delta;
+
+ // parse values until one isn't recognized
+
+ which = new int[3*(narg-6)];
+ nvalues = 0;
+ int i;
+
+ int iarg=6;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"conf") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = CONF;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"kin") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = KIN;
+ nvalues++;
+ }
+ } else if (strcmp(arg[iarg],"total") == 0) {
+ for (i=0; i<3; i++) {
+ which[nvalues] = TOTAL;
+ nvalues++;
+ }
+ } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
+
+ iarg++;
+ }
+
+ // check domain related errors
+
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute stress/mop/profile incompatible with simulation dimension");
+
+ // orthogonal simulation box
+
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute stress/mop/profile incompatible with triclinic simulation box");
+
+ // initialize some variables
+
+ nbins = 0;
+ coord = coordp = NULL;
+ values_local = values_global = array = NULL;
+
+ // bin setup
+
+ setup_bins();
+
+ // this fix produces a global array
+
+ memory->create(array,nbins,1+nvalues,"stress/mop/profile:array");
+ size_array_rows = nbins;
+ size_array_cols = 1 + nvalues;
+
+ array_flag = 1;
+ extarray = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeStressMopProfile::~ComputeStressMopProfile()
+{
+
+ delete [] which;
+
+ memory->destroy(coord);
+ memory->destroy(coordp);
+ memory->destroy(values_local);
+ memory->destroy(values_global);
+ memory->destroy(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeStressMopProfile::init()
+{
+
+ // conversion constants
+
+ nktv2p = force->nktv2p;
+ ftm2v = force->ftm2v;
+
+ // plane area
+
+ area = 1;
+ int i;
+ for (i=0; i<3; i++) {
+ if (i!=dir) area = area*domain->prd[i];
+ }
+
+ // timestep Value
+
+ dt = update->dt;
+
+ // Error check
+ // Compute stress/mop/profile requires fixed simulation box
+
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute stress/mop/profile requires a fixed simulation box");
+
+ //This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute stress/mop/profile");
+
+ // Warnings
+
+ if (me==0){
+
+ //Compute stress/mop/profile only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
+ }
+
+ // need an occasional half neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeStressMopProfile::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+
+/* ----------------------------------------------------------------------
+ compute output array
+ ------------------------------------------------------------------------- */
+
+void ComputeStressMopProfile::compute_array()
+{
+ invoked_array = update->ntimestep;
+
+ //Compute pressures on separate procs
+ compute_pairs();
+
+ // sum pressure contributions over all procs
+ MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
+ MPI_DOUBLE,MPI_SUM,world);
+
+ int ibin,m,mo;
+ for (ibin=0; ibin<nbins; ibin++) {
+ array[ibin][0] = coord[ibin][0];
+ mo=1;
+
+ m = 0;
+ while (m<nvalues) {
+ array[ibin][m+mo] = values_global[ibin][m];
+ m++;
+ }
+ }
+}
+
+
+/*------------------------------------------------------------------------
+ compute pressure contribution of local proc
+ -------------------------------------------------------------------------*/
+
+void ComputeStressMopProfile::compute_pairs()
+
+{
+ int i,j,m,n,ii,jj,inum,jnum,itype,jtype,ibin;
+ double delx,dely,delz;
+ double rsq,eng,fpair,factor_coul,factor_lj;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double pos,pos1,pos_temp;
+
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+
+ // zero out arrays for one sample
+ for (m = 0; m < nbins; m++) {
+ for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0;
+ }
+
+ // invoke half neighbor list (will copy or build if necessary)
+
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ // parse values
+
+ double xi[3];
+ double vi[3];
+ double fi[3];
+ double xj[3];
+
+ m = 0;
+ while (m<nvalues) {
+ if (which[m] == CONF || which[m] == TOTAL) {
+
+ // Compute configurational contribution to pressure
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ // skip if neither I nor J are in group
+
+ if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
+
+ xj[0] = atom->x[j][0];
+ xj[1] = atom->x[j][1];
+ xj[2] = atom->x[j][2];
+ delx = xi[0] - xj[0];
+ dely = xi[1] - xj[1];
+ delz = xi[2] - xj[2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+ if (rsq >= cutsq[itype][jtype]) continue;
+
+ if (newton_pair || j < nlocal) {
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ //check if ij pair is accross plane, add contribution to pressure
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+
+ } else if ( ((xi[dir]<pos) && (xj[dir]>pos))
+ || ((xi[dir]<pos1) && (xj[dir]>pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+ }
+ } else {
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ //check if ij pair is accross plane, add contribution to pressure
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
+ values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
+ values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+
+ if (which[m] == KIN || which[m] == TOTAL){
+
+ double vcm[3];
+ double masstotal,sgn;
+
+ for (int i = 0; i < nlocal; i++){
+
+ // skip if I is not in group
+
+ if (mask[i] & groupbit){
+
+ itype = type[i];
+
+ //coordinates at t
+ xi[0] = atom->x[i][0];
+ xi[1] = atom->x[i][1];
+ xi[2] = atom->x[i][2];
+
+ //velocities at t
+ vi[0] = atom->v[i][0];
+ vi[1] = atom->v[i][1];
+ vi[2] = atom->v[i][2];
+
+ //forces at t
+ fi[0] = atom->f[i][0];
+ fi[1] = atom->f[i][1];
+ fi[2] = atom->f[i][2];
+
+ //coordinates at t-dt (based on Velocity-Verlet alg.)
+ xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
+ xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
+ xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+
+ for (ibin=0;ibin<nbins;ibin++) {
+ pos = coord[ibin][0];
+ pos1 = coordp[ibin][0];
+
+ if (((xi[dir]-pos)*(xj[dir]-pos)*(xi[dir]-pos1)*(xj[dir]-pos1)<0)){
+
+ sgn = copysign(1,vi[dir]);
+
+ //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+ double vcross[3];
+ vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
+ vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
+ vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+
+ values_local[ibin][m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
+ values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
+ }
+ }
+ }
+ }
+ }
+ m+=3;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ setup 1d bins and their extent and coordinates
+ called at init()
+ ------------------------------------------------------------------------- */
+
+void ComputeStressMopProfile::setup_bins()
+{
+ int i,j,k,m,n;
+ double lo,hi,coord1,coord2;
+
+ double *boxlo,*boxhi,*prd;
+ boxlo = domain->boxlo;
+ boxhi = domain->boxhi;
+ prd = domain->prd;
+
+ if (originflag == LOWER) origin = boxlo[dir];
+ else if (originflag == UPPER) origin = boxhi[dir];
+ else if (originflag == CENTER)
+ origin = 0.5 * (boxlo[dir] + boxhi[dir]);
+
+ if (origin < boxlo[dir]) {
+ error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
+ } else {
+ n = static_cast<int> ((origin - boxlo[dir]) * invdelta);
+ lo = origin - n*delta;
+ }
+ if (origin < boxhi[dir]) {
+ n = static_cast<int> ((boxhi[dir] - origin) * invdelta);
+ hi = origin + n*delta;
+ } else {
+ error->all(FLERR,"Origin of bins for compute stress/mop/profile is out of bounds" );
+ }
+
+ offset = lo;
+ nbins = static_cast<int> ((hi-lo) * invdelta + 1.5);
+
+ //allocate bin arrays
+ memory->create(coord,nbins,1,"stress/mop/profile:coord");
+ memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
+ memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
+ memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
+
+ // set bin coordinates
+ for (i = 0; i < nbins; i++) {
+ coord[i][0] = offset + i*delta;
+ if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
+ coordp[i][0] = coord[i][0] + domain->prd[dir];
+ } else {
+ coordp[i][0] = coord[i][0] - domain->prd[dir];
+ }
+ }
+}
diff --git a/src/USER-MOP/compute_stress_mop_profile.h b/src/USER-MOP/compute_stress_mop_profile.h
new file mode 100644
index 0000000000..648d86cc7f
--- /dev/null
+++ b/src/USER-MOP/compute_stress_mop_profile.h
@@ -0,0 +1,113 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+/*------------------------------------------------------------------------
+ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+ --------------------------------------------------------------------------*/
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(stress/mop/profile,ComputeStressMopProfile)
+
+#else
+
+#ifndef LMP_COMPUTE_STRESS_MOP_PROFILE_H
+#define LMP_COMPUTE_STRESS_MOP_PROFILE_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+ class ComputeStressMopProfile : public Compute {
+ public:
+ ComputeStressMopProfile(class LAMMPS *, int, char **);
+ virtual ~ComputeStressMopProfile();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_array();
+
+ private:
+
+ void compute_pairs();
+ void setup_bins();
+
+ int me,nvalues,dir;
+ int *which;
+
+ int originflag;
+ double origin,delta,offset,invdelta;
+ int nbins;
+ double **coord,**coordp;
+ double **values_local,**values_global;
+
+ int ndim;
+ double dt,nktv2p,ftm2v;
+ double area;
+ class NeighList *list;
+
+ };
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+ E: Illegal ... command
+
+ Self-explanatory. Check the input script syntax and compare to the
+ documentation for the command. You can use -echo screen as a
+ command-line option when running LAMMPS to see the offending line.
+
+ E: Compute stress/mop/profile incompatible with simulation dimension
+
+ Compute stress/mop/profile only works with 3D simulations.
+
+ E: Compute stress/mop/profile incompatible with triclinic simulation box
+
+ Self-explanatory.
+
+ E: Compute stress/mop/profile requires a fixed simulation box
+
+ Compute stress/mop/profile is not compatible with any change of volume or shape
+ or boundary conditions of the simulation box.
+
+ E: No pair style is defined for compute stress/mop/profile
+
+ Self-explanatory. Compute stress/mop/profile requires the definition of a pair style.
+
+ E: Pair style does not support compute stress/mop/profile
+
+ The pair style does not have a single() function, so it can
+ not be invoked by compute stress/mop/profile.
+
+ E: Origin of bins for compute stress/mop/profile is out of bounds
+
+ Self-explanatory.
+
+ W: compute stress/mop/profile does not account for bond potentials
+
+ W: compute stress/mop/profile does not account for angle potentials
+
+ W: compute stress/mop/profile does not account for dihedral potentials
+
+ W: compute stress/mop/profile does not account for improper potentials
+
+ W: compute stress/mop/profile does not account for kspace contributions
+
+ Compute stress/mop/profile only accounts for pairwise additive interactions for
+ the computation of local stress tensor components.
+
+*/
+
--
GitLab
From cb4ffaf95c7de455a2a15e8c3f0bbe4c50b2b5e7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 4 Sep 2018 08:42:32 -0400
Subject: [PATCH 214/332] update docs and references for name changes in
USER-MOP package, remove obsoleted files
---
doc/src/Packages_details.txt | 10 +-
doc/src/Packages_user.txt | 2 +-
doc/src/compute_mop.txt | 111 ----
doc/src/computes.txt | 2 +-
doc/src/lammps.book | 2 +-
examples/USER/mop/in.compute_mop | 62 ---
examples/USER/mop/in.compute_stress_mop | 0
.../USER/mop/log.31Aug18.compute_mop.g++.1 | 186 -------
.../USER/mop/log.31Aug18.compute_mop.g++.4 | 188 -------
src/.gitignore | 8 +-
src/USER-MOP/compute_mop.cpp | 424 ---------------
src/USER-MOP/compute_mop.h | 74 ---
src/USER-MOP/compute_mop_profile.cpp | 496 ------------------
src/USER-MOP/compute_mop_profile.h | 81 ---
14 files changed, 12 insertions(+), 1634 deletions(-)
delete mode 100644 doc/src/compute_mop.txt
delete mode 100644 examples/USER/mop/in.compute_mop
mode change 100755 => 100644 examples/USER/mop/in.compute_stress_mop
delete mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.1
delete mode 100644 examples/USER/mop/log.31Aug18.compute_mop.g++.4
delete mode 100644 src/USER-MOP/compute_mop.cpp
delete mode 100644 src/USER-MOP/compute_mop.h
delete mode 100644 src/USER-MOP/compute_mop_profile.cpp
delete mode 100644 src/USER-MOP/compute_mop_profile.h
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 16f867b7c0..36071064c0 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1577,11 +1577,11 @@ USER-MOP package :link(PKG-USER-MOP),h4
[Contents:]
-This package contains two compute styles: compute mop and compute mop/profile.
+This package contains two compute styles: compute stress/mop and compute stress/mop/profile.
-compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
+compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
-compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
+compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
[Author:] Laurent Joly (University of Lyon 1)
Romain Vermorel at (University of Pau and Pays de l'Adour)
@@ -1590,8 +1590,8 @@ Romain Vermorel at (University of Pau and Pays de l'Adour)
src/USER-MOP: filenames -> commands
src/USER-MOP/README
-"compute mop"_compute_mop.html
-"compute mop/profile"_compute_mop.html
+"compute stress/mop"_compute_stress_mop.html
+"compute stress/mop/profile"_compute_stress_mop.html
examples/USER/mop :ul
:line
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 731cf7ff10..5b9b8734b3 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -57,7 +57,7 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
-"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no
+"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
diff --git a/doc/src/compute_mop.txt b/doc/src/compute_mop.txt
deleted file mode 100644
index 732f55657a..0000000000
--- a/doc/src/compute_mop.txt
+++ /dev/null
@@ -1,111 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute mop command :h3
-compute mop/profile command :h3
-
-
-[Syntax:]
-
-compute ID group-ID style dir args keywords ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-style = {mop} or {mop/profile}
-dir = {x} or {y} or {z} is the direction normal to the plane
-args = argument specific to the compute style
-keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
- {mop} args = pos
- pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
- {mop/profile} args = origin delta
- origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
- delta = value (distance units) is the distance between planes :pre
-
-compute 1 all mop x lower total
-compute 1 liquid mop z 0.0 kin conf
-fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
-fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
-
-compute 1 all mop/profile x lower 0.1 total
-compute 1 liquid mop/profile z 0.0 0.25 kin conf
-fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
-
-
-[Description:]
-
-Compute {mop} and compute {mop/profile} define computations that
-calculate components of the local stress tensor using the method of
-planes "(Todd)"_#mop-todd. Specifically in compute {mop} calculates 3
-components are computed in directions {dir},{x}; {dir},{y}; and
-{dir},{z}; where {dir} is the direction normal to the plane, while
-in compute {mop/profile} the profile of the stress is computed.
-
-Contrary to methods based on histograms of atomic stress (i.e. using
-"compute stress/atom"_compute_stress_atom.html), the method of planes is
-compatible with mechanical balance in heterogeneous systems and at
-interfaces "(Todd)"_#mop-todd.
-
-The stress tensor is the sum of a kinetic term and a configurational
-term, which are given respectively by Eq. (21) and Eq. (16) in
-"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
-atoms have crossed the plane if their positions at times t-dt and t are
-one on either side of the plane, and uses the velocity at time t-dt/2
-given by the velocity-Verlet algorithm.
-
-Between one and three keywords can be used to indicate which
-contributions to the stress must be computed: kinetic stress (kin),
-configurational stress (conf), and/or total stress (total).
-
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
-
-NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the global system pressure.
-
-[Output info:]
-
-Compute {mop} calculates a global vector (indices starting at 1), with 3
-values for each declared keyword (in the order the keywords have been
-declared). For each keyword, the stress tensor components are ordered as
-follows: stress_dir,x, stress_dir,y, and stress_dir,z.
-
-Compute {mop/profile} instead calculates a global array, with 1 column
-giving the position of the planes where the stress tensor was computed,
-and with 3 columns of values for each declared keyword (in the order the
-keywords have been declared). For each keyword, the profiles of stress
-tensor components are ordered as follows: stress_dir,x; stress_dir,y;
-and stress_dir,z.
-
-The values are in pressure "units"_units.html.
-
-The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
-
-[Restrictions:]
-
-This style is part of the USER-MOP package. It is only enabled if LAMMPS
-is built with that package. See the "Build package"_Build_package.html
-doc page on for more info.
-
-The method is only implemented for 3d orthogonal simulation boxes whose
-size does not change in time, and axis-aligned planes.
-
-The method only works with two-body pair interactions, because it
-requires the class method pair->single() to be implemented. In
-particular, it does not work with more than two-body pair interactions,
-intra-molecular interactions, and long range (kspace) interactions.
-
-[Related commands:]
-
-"compute stress/atom"_compute_stress_atom.html
-
-[Default:] none
-
-:line
-
-:link(mop-todd)
-[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
-Phys. Rev. E 52, 1627 (1995).
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index c431f1c184..158389bda9 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -55,7 +55,6 @@ Computes :h1
compute_meso_e_atom
compute_meso_rho_atom
compute_meso_t_atom
- compute_mop
compute_msd
compute_msd_chunk
compute_msd_nongauss
@@ -99,6 +98,7 @@ Computes :h1
compute_sna_atom
compute_spin
compute_stress_atom
+ compute_stress_mop
compute_tally
compute_tdpd_cc_atom
compute_temp
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0aa382ae39..c177757695 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -446,7 +446,6 @@ compute_ke_rigid.html
compute_meso_e_atom.html
compute_meso_rho_atom.html
compute_meso_t_atom.html
-compute_mop.html
compute_msd.html
compute_msd_chunk.html
compute_msd_nongauss.html
@@ -490,6 +489,7 @@ compute_smd_vol.html
compute_sna_atom.html
compute_spin.html
compute_stress_atom.html
+compute_stress_mop.html
compute_tally.html
compute_tdpd_cc_atom.html
compute_temp.html
diff --git a/examples/USER/mop/in.compute_mop b/examples/USER/mop/in.compute_mop
deleted file mode 100644
index ab9552796f..0000000000
--- a/examples/USER/mop/in.compute_mop
+++ /dev/null
@@ -1,62 +0,0 @@
-variable T equal 0.8
-variable p_solid equal 0.05
-
-lattice fcc 1.0
-region box block 0.0 6.0 0.0 6.0 -2.0 12.0
-create_box 2 box
-
-mass * 1.0
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 2 0.5 1.0
-pair_coeff 2 2 0.0 0.0
-neigh_modify delay 0
-
-region solid_bottom block INF INF INF INF -1.1 0.1
-region liquid block INF INF INF INF 1.1 8.9
-region solid_up block INF INF INF INF 9.9 11.1
-
-create_atoms 1 region liquid
-delete_atoms porosity liquid 0.26 88765
-group liquid region liquid
-
-create_atoms 2 region solid_bottom
-group solid_bottom region solid_bottom
-create_atoms 2 region solid_up
-group solid_up region solid_up
-group solid union solid_bottom solid_up
-
-variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
-fix piston_up solid_up aveforce NULL NULL -${faSolid}
-fix freeze_up solid_up setforce 0.0 0.0 NULL
-fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
-fix nvesol solid nve
-compute Tliq liquid temp
-fix nvtliq liquid nvt temp $T $T 0.5
-fix_modify nvtliq temp Tliq
-
-thermo 10000
-thermo_modify flush yes temp Tliq
-
-# dump 1 all atom 10000 dump.lammpstrj
-
-fix fxbal all balance 1000 1.05 shift z 10 1.05
-velocity liquid create $T 47298 dist gaussian rot yes
-run 50000
-# undump 1
-reset_timestep 0
-
-compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
-
-compute liquidStress_ke liquid stress/atom NULL ke
-compute liquidStress_vir liquid stress/atom NULL virial
-fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
-
-compute mopz0 all mop z center kin conf
-fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
-
-compute moppz liquid mop/profile z 0.0 0.1 kin conf
-fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
-
-run 40000
-
diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/mop/in.compute_stress_mop
old mode 100755
new mode 100644
diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 b/examples/USER/mop/log.31Aug18.compute_mop.g++.1
deleted file mode 100644
index 98b403b444..0000000000
--- a/examples/USER/mop/log.31Aug18.compute_mop.g++.1
+++ /dev/null
@@ -1,186 +0,0 @@
-LAMMPS (31 Aug 2018)
-variable T equal 0.8
-variable p_solid equal 0.05
-
-lattice fcc 1.0
-Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
-region box block 0.0 6.0 0.0 6.0 -2.0 12.0
-create_box 2 box
-Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
- 1 by 1 by 1 MPI processor grid
-
-mass * 1.0
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 2 0.5 1.0
-pair_coeff 2 2 0.0 0.0
-neigh_modify delay 0
-
-region solid_bottom block INF INF INF INF -1.1 0.1
-region liquid block INF INF INF INF 1.1 8.9
-region solid_up block INF INF INF INF 9.9 11.1
-
-create_atoms 1 region liquid
-Created 1080 atoms
- Time spent = 0.000631094 secs
-delete_atoms porosity liquid 0.26 88765
-Deleted 257 atoms, new total = 823
-group liquid region liquid
-823 atoms in group liquid
-
-create_atoms 2 region solid_bottom
-Created 216 atoms
- Time spent = 0.000221014 secs
-group solid_bottom region solid_bottom
-216 atoms in group solid_bottom
-create_atoms 2 region solid_up
-Created 216 atoms
- Time spent = 0.000169039 secs
-group solid_up region solid_up
-216 atoms in group solid_up
-group solid union solid_bottom solid_up
-432 atoms in group solid
-
-variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
-variable faSolid equal 0.05*lx*ly/count(solid_up)
-fix piston_up solid_up aveforce NULL NULL -${faSolid}
-fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
-fix freeze_up solid_up setforce 0.0 0.0 NULL
-fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
-fix nvesol solid nve
-compute Tliq liquid temp
-fix nvtliq liquid nvt temp $T $T 0.5
-fix nvtliq liquid nvt temp 0.8 $T 0.5
-fix nvtliq liquid nvt temp 0.8 0.8 0.5
-fix_modify nvtliq temp Tliq
-WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404)
-
-thermo 10000
-thermo_modify flush yes temp Tliq
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
-
-# dump 1 all atom 10000 dump.lammpstrj
-
-fix fxbal all balance 1000 1.05 shift z 10 1.05
-velocity liquid create $T 47298 dist gaussian rot yes
-velocity liquid create 0.8 47298 dist gaussian rot yes
-run 50000
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4, bins = 7 7 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/cut, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016
- 10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016
- 20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016
- 30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016
- 40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016
- 50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
-Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms
-
-Performance: 531401.825 tau/day, 1230.097 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 28.102 | 28.102 | 28.102 | 0.0 | 69.14
-Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20
-Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25
-Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00
-Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45
-Other | | 0.3879 | | | 0.95
-
-Nlocal: 1255 ave 1255 max 1255 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2268 ave 2268 max 2268 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 40149 ave 40149 max 40149 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 40149
-Ave neighs/atom = 31.9912
-Neighbor list builds = 5714
-Dangerous builds = 0
-# undump 1
-reset_timestep 0
-
-compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
-
-compute liquidStress_ke liquid stress/atom NULL ke
-compute liquidStress_vir liquid stress/atom NULL virial
-fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
-
-compute mopz0 all mop z center kin conf
-fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
-
-compute moppz liquid mop/profile z 0.0 0.1 kin conf
-fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
-
-run 40000
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4, bins = 7 7 16
- 3 neighbor lists, perpetual/occasional/extra = 1 2 0
- (1) pair lj/cut, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
- (2) compute mop, occasional, copy from (1)
- attributes: half, newton on
- pair build: copy
- stencil: none
- bin: none
- (3) compute mop/profile, occasional, copy from (1)
- attributes: half, newton on
- pair build: copy
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
- 10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016
- 20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016
- 30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016
- 40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016
-Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms
-
-Performance: 380198.462 tau/day, 880.089 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 25.456 | 25.456 | 25.456 | 0.0 | 56.01
-Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47
-Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62
-Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00
-Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21
-Other | | 0.3131 | | | 0.69
-
-Nlocal: 1255 ave 1255 max 1255 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2269 ave 2269 max 2269 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 40325 ave 40325 max 40325 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 40325
-Ave neighs/atom = 32.1315
-Neighbor list builds = 4587
-Dangerous builds = 0
-
-Total wall time: 0:01:26
diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.4 b/examples/USER/mop/log.31Aug18.compute_mop.g++.4
deleted file mode 100644
index 16ef8a2ce1..0000000000
--- a/examples/USER/mop/log.31Aug18.compute_mop.g++.4
+++ /dev/null
@@ -1,188 +0,0 @@
-LAMMPS (31 Aug 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
- using 1 OpenMP thread(s) per MPI task
-variable T equal 0.8
-variable p_solid equal 0.05
-
-lattice fcc 1.0
-Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
-region box block 0.0 6.0 0.0 6.0 -2.0 12.0
-create_box 2 box
-Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
- 1 by 1 by 4 MPI processor grid
-
-mass * 1.0
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 2 0.5 1.0
-pair_coeff 2 2 0.0 0.0
-neigh_modify delay 0
-
-region solid_bottom block INF INF INF INF -1.1 0.1
-region liquid block INF INF INF INF 1.1 8.9
-region solid_up block INF INF INF INF 9.9 11.1
-
-create_atoms 1 region liquid
-Created 1080 atoms
- Time spent = 0.000378132 secs
-delete_atoms porosity liquid 0.26 88765
-Deleted 288 atoms, new total = 792
-group liquid region liquid
-792 atoms in group liquid
-
-create_atoms 2 region solid_bottom
-Created 216 atoms
- Time spent = 0.000345945 secs
-group solid_bottom region solid_bottom
-216 atoms in group solid_bottom
-create_atoms 2 region solid_up
-Created 216 atoms
- Time spent = 0.000124454 secs
-group solid_up region solid_up
-216 atoms in group solid_up
-group solid union solid_bottom solid_up
-432 atoms in group solid
-
-variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
-variable faSolid equal 0.05*lx*ly/count(solid_up)
-fix piston_up solid_up aveforce NULL NULL -${faSolid}
-fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
-fix freeze_up solid_up setforce 0.0 0.0 NULL
-fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
-fix nvesol solid nve
-compute Tliq liquid temp
-fix nvtliq liquid nvt temp $T $T 0.5
-fix nvtliq liquid nvt temp 0.8 $T 0.5
-fix nvtliq liquid nvt temp 0.8 0.8 0.5
-fix_modify nvtliq temp Tliq
-WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
-
-thermo 10000
-thermo_modify flush yes temp Tliq
-WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
-
-# dump 1 all atom 10000 dump.lammpstrj
-
-fix fxbal all balance 1000 1.05 shift z 10 1.05
-velocity liquid create $T 47298 dist gaussian rot yes
-velocity liquid create 0.8 47298 dist gaussian rot yes
-run 50000
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4, bins = 7 7 16
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair lj/cut, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.122 | 3.135 | 3.147 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.8 -3.4905808 0 -2.7150906 -0.59565852 2016
- 10000 0.82075861 -3.1822235 0 -2.3866107 0.013840263 2016
- 20000 0.76467575 -3.0955084 0 -2.3542602 -0.076868925 2016
- 30000 0.75803557 -3.1011543 0 -2.3663428 -0.052887049 2016
- 40000 0.81732724 -3.064259 0 -2.2719724 0.070708808 2016
- 50000 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
-Loop time of 22.1566 on 4 procs for 50000 steps with 1224 atoms
-
-Performance: 974879.887 tau/day, 2256.666 timesteps/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 10.732 | 13.012 | 14.39 | 38.0 | 58.73
-Neigh | 2.47 | 3.7351 | 4.3661 | 38.4 | 16.86
-Comm | 1.881 | 3.4383 | 5.8722 | 79.7 | 15.52
-Output | 0.00014567 | 0.0003581 | 0.0009892 | 0.0 | 0.00
-Modify | 1.1006 | 1.5188 | 2.6121 | 51.3 | 6.85
-Other | | 0.4521 | | | 2.04
-
-Nlocal: 306 ave 312 max 295 min
-Histogram: 1 0 0 0 0 0 0 1 1 1
-Nghost: 1242.75 ave 1373 max 944 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Neighs: 9770.25 ave 10807 max 8736 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 39081
-Ave neighs/atom = 31.9289
-Neighbor list builds = 5704
-Dangerous builds = 0
-# undump 1
-reset_timestep 0
-
-compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
-
-compute liquidStress_ke liquid stress/atom NULL ke
-compute liquidStress_vir liquid stress/atom NULL virial
-fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
-
-compute mopz0 all mop z center kin conf
-fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
-
-compute moppz liquid mop/profile z 0.0 0.1 kin conf
-fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
-
-run 40000
-Neighbor list info ...
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4, bins = 7 7 16
- 3 neighbor lists, perpetual/occasional/extra = 1 2 0
- (1) pair lj/cut, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
- (2) compute mop, occasional, copy from (1)
- attributes: half, newton on
- pair build: copy
- stencil: none
- bin: none
- (3) compute mop/profile, occasional, copy from (1)
- attributes: half, newton on
- pair build: copy
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.147 | 4.15 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
- 10000 0.82372476 -3.1299329 0 -2.3314448 -0.14706101 2016
- 20000 0.80692892 -3.1278896 0 -2.3456828 -0.085123604 2016
- 30000 0.78458951 -3.0966006 0 -2.3360488 0.13637007 2016
- 40000 0.80106495 -3.1135836 0 -2.3370611 -0.14404185 2016
-Loop time of 31.4145 on 4 procs for 40000 steps with 1224 atoms
-
-Performance: 550065.249 tau/day, 1273.299 timesteps/s
-92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 10.199 | 12.307 | 13.428 | 35.4 | 39.18
-Neigh | 2.1261 | 3.1416 | 3.6373 | 33.5 | 10.00
-Comm | 3.5381 | 4.476 | 6.229 | 48.9 | 14.25
-Output | 0.00062943 | 0.0031546 | 0.0040004 | 2.6 | 0.01
-Modify | 10.186 | 10.862 | 12.26 | 24.8 | 34.58
-Other | | 0.6247 | | | 1.99
-
-Nlocal: 306 ave 315 max 299 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Nghost: 1221.5 ave 1347 max 912 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Neighs: 9710.25 ave 10301 max 8980 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-
-Total # of neighbors = 38841
-Ave neighs/atom = 31.7328
-Neighbor list builds = 4573
-Dangerous builds = 0
-
-Total wall time: 0:00:53
diff --git a/src/.gitignore b/src/.gitignore
index c7aaa8ab64..3a6ba21426 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -288,10 +288,6 @@
/compute_meso_rho_atom.h
/compute_meso_t_atom.cpp
/compute_meso_t_atom.h
-/compute_mop.cpp
-/compute_mop.h
-/compute_mop_profile.cpp
-/compute_mop_profile.h
/compute_msd_nongauss.cpp
/compute_msd_nongauss.h
/compute_pe_tally.cpp
@@ -306,6 +302,10 @@
/compute_rigid_local.h
/compute_spec_atom.cpp
/compute_spec_atom.h
+/compute_stress_mop.cpp
+/compute_stress_mop.h
+/compute_stress_mop.profile.cpp
+/compute_stress_mop.profile.h
/compute_stress_tally.cpp
/compute_stress_tally.h
/compute_temp_asphere.cpp
diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp
deleted file mode 100644
index ba6b458172..0000000000
--- a/src/USER-MOP/compute_mop.cpp
+++ /dev/null
@@ -1,424 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
- ------------------------------------------------------------------------- */
-
-/*------------------------------------------------------------------------
- Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
- --------------------------------------------------------------------------*/
-
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
-
-#include "compute_mop.h"
-#include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
-#include "neighbor.h"
-#include "force.h"
-#include "pair.h"
-#include "neigh_request.h"
-#include "neigh_list.h"
-#include "error.h"
-#include "memory.h"
-
-using namespace LAMMPS_NS;
-
-enum{X,Y,Z};
-enum{TOTAL,CONF,KIN};
-
-#define BIG 1000000000
-
-/* ---------------------------------------------------------------------- */
-
-ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg)
-{
- if (narg < 6) error->all(FLERR,"Illegal compute mop command");
-
- MPI_Comm_rank(world,&me);
-
- // set compute mode and direction of plane(s) for pressure calculation
-
- if (strcmp(arg[3],"x")==0) {
- dir = X;
- } else if (strcmp(arg[3],"y")==0) {
- dir = Y;
- } else if (strcmp(arg[3],"z")==0) {
- dir = Z;
- } else error->all(FLERR,"Illegal compute mop command");
-
- // Position of the plane
-
- if (strcmp(arg[4],"lower")==0) {
- pos = domain->boxlo[dir];
- } else if (strcmp(arg[4],"upper")==0) {
- pos = domain->boxhi[dir];
- } else if (strcmp(arg[4],"center")==0) {
- pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
- } else pos = force->numeric(FLERR,arg[4]);
-
- if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
- pos1 = pos + domain->prd[dir];
- } else {
- pos1 = pos - domain->prd[dir];
- }
-
- // parse values until one isn't recognized
-
- which = new int[3*(narg-5)];
- nvalues = 0;
- int i;
-
- int iarg=5;
- while (iarg < narg) {
- if (strcmp(arg[iarg],"conf") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = CONF;
- nvalues++;
- }
- } else if (strcmp(arg[iarg],"kin") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = KIN;
- nvalues++;
- }
- } else if (strcmp(arg[iarg],"total") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = TOTAL;
- nvalues++;
- }
- } else error->all(FLERR, "Illegal compute mop command"); //break;
-
- iarg++;
- }
-
- // Error check
- // 3D only
-
- if (domain->dimension < 3)
- error->all(FLERR, "Compute mop incompatible with simulation dimension");
-
- // orthogonal simulation box
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
- // plane inside the box
- if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
- error->all(FLERR, "Plane for compute mop is out of bounds");
-
-
- // Initialize some variables
-
- values_local = values_global = vector = NULL;
-
- // this fix produces a global vector
-
- memory->create(vector,nvalues,"mop:vector");
- memory->create(values_local,nvalues,"mop/spatial:values_local");
- memory->create(values_global,nvalues,"mop/spatial:values_global");
- size_vector = nvalues;
-
- vector_flag = 1;
- extvector = 0;
-
-}
-
-/* ---------------------------------------------------------------------- */
-
-ComputeMop::~ComputeMop()
-{
-
- delete [] which;
-
- memory->destroy(values_local);
- memory->destroy(values_global);
- memory->destroy(vector);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeMop::init()
-{
-
- // Conversion constants
-
- nktv2p = force->nktv2p;
- ftm2v = force->ftm2v;
-
- // Plane area
-
- area = 1;
- int i;
- for (i=0; i<3; i++){
- if (i!=dir) area = area*domain->prd[i];
- }
-
- // Timestep Value
-
- dt = update->dt;
-
- // Error check
-
- // Compute mop requires fixed simulation box
- if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
- error->all(FLERR, "Compute mop requires a fixed simulation box");
-
- // This compute requires a pair style with pair_single method implemented
-
- if (force->pair == NULL)
- error->all(FLERR,"No pair style is defined for compute mop");
- if (force->pair->single_enable == 0)
- error->all(FLERR,"Pair style does not support compute mop");
-
- // Warnings
-
- if (me==0){
-
- //Compute mop only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
-
- if (force->bond!=NULL)
- error->warning(FLERR,"compute mop does not account for bond potentials");
- if (force->angle!=NULL)
- error->warning(FLERR,"compute mop does not account for angle potentials");
- if (force->dihedral!=NULL)
- error->warning(FLERR,"compute mop does not account for dihedral potentials");
- if (force->improper!=NULL)
- error->warning(FLERR,"compute mop does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop does not account for kspace contributions");
- }
-
- // need an occasional half neighbor list
- int irequest = neighbor->request((void *) this);
- neighbor->requests[irequest]->pair = 0;
- neighbor->requests[irequest]->compute = 1;
- neighbor->requests[irequest]->occasional = 1;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeMop::init_list(int id, NeighList *ptr)
-{
- list = ptr;
-}
-
-
-/* ----------------------------------------------------------------------
- compute output vector
- ------------------------------------------------------------------------- */
-
-void ComputeMop::compute_vector()
-{
- invoked_array = update->ntimestep;
-
- //Compute pressures on separate procs
- compute_pairs();
-
- // sum pressure contributions over all procs
- MPI_Allreduce(values_local,values_global,nvalues,
- MPI_DOUBLE,MPI_SUM,world);
-
- int m;
- for (m=0; m<nvalues; m++) {
- vector[m] = values_global[m];
- }
-
-}
-
-
-/*------------------------------------------------------------------------
- compute pressure contribution of local proc
- -------------------------------------------------------------------------*/
-
-void ComputeMop::compute_pairs()
-
-{
- int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
- double delx,dely,delz;
- double rsq,eng,fpair,factor_coul,factor_lj;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- double *mass = atom->mass;
- int *type = atom->type;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- double *special_coul = force->special_coul;
- double *special_lj = force->special_lj;
- int newton_pair = force->newton_pair;
-
-
- // zero out arrays for one sample
-
- for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
-
- // invoke half neighbor list (will copy or build if necessary)
-
- neighbor->build_one(list);
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // loop over neighbors of my atoms
-
- Pair *pair = force->pair;
- double **cutsq = force->pair->cutsq;
-
- // Parse values
-
- double xi[3];
- double vi[3];
- double fi[3];
- double xj[3];
-
- m = 0;
- while (m<nvalues) {
- if (which[m] == CONF || which[m] == TOTAL) {
-
- //Compute configurational contribution to pressure
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
-
- xi[0] = atom->x[i][0];
- xi[1] = atom->x[i][1];
- xi[2] = atom->x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- factor_lj = special_lj[sbmask(j)];
- factor_coul = special_coul[sbmask(j)];
- j &= NEIGHMASK;
-
- // skip if neither I nor J are in group
- if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
-
- xj[0] = atom->x[j][0];
- xj[1] = atom->x[j][1];
- xj[2] = atom->x[j][2];
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
- jtype = type[j];
- if (rsq >= cutsq[itype][jtype]) continue;
-
- if (newton_pair || j < nlocal) {
-
- //check if ij pair is accross plane, add contribution to pressure
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
- }
- else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
- }
-
- } else {
-
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
- }
-
- }
-
- }
-
- }
-
- }
-
-
- // Compute kinetic contribution to pressure
- // counts local particles transfers across the plane
-
- if (which[m] == KIN || which[m] == TOTAL){
- double vcm[3];
- double masstotal,sgn;
-
- for (int i = 0; i < nlocal; i++){
-
- // skip if I is not in group
- if (mask[i] & groupbit){
-
- itype = type[i];
-
- //coordinates at t
- xi[0] = atom->x[i][0];
- xi[1] = atom->x[i][1];
- xi[2] = atom->x[i][2];
-
- //velocities at t
- vi[0] = atom->v[i][0];
- vi[1] = atom->v[i][1];
- vi[2] = atom->v[i][2];
-
- //forces at t
- fi[0] = atom->f[i][0];
- fi[1] = atom->f[i][1];
- fi[2] = atom->f[i][2];
-
- //coordinates at t-dt (based on Velocity-Verlet alg.)
- xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
- xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
- xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
-
- // because LAMMPS does not put atoms back in the box
- // at each timestep, must check atoms going through the
- // image of the plane that is closest to the box
-
- double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir];
- if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
-
- if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)){
-
- //sgn = copysign(1,vi[dir]-vcm[dir]);
- sgn = copysign(1,vi[dir]);
-
- //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
- double vcross[3];
- vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
- vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
- vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
-
- values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
- values_local[m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
- values_local[m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
- }
- }
- }
- }
- m+=3;
- }
-}
-
diff --git a/src/USER-MOP/compute_mop.h b/src/USER-MOP/compute_mop.h
deleted file mode 100644
index 53fa1e9d5c..0000000000
--- a/src/USER-MOP/compute_mop.h
+++ /dev/null
@@ -1,74 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
- ------------------------------------------------------------------------- */
-
-/*------------------------------------------------------------------------
- Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
- --------------------------------------------------------------------------*/
-
-#ifdef COMPUTE_CLASS
-
-ComputeStyle(mop,ComputeMop)
-
-#else
-
-#ifndef LMP_COMPUTE_MOP_H
-#define LMP_COMPUTE_MOP_H
-
-#include "compute.h"
-
-namespace LAMMPS_NS {
-
- class ComputeMop : public Compute {
- public:
- ComputeMop(class LAMMPS *, int, char **);
- virtual ~ComputeMop();
- void init();
- void init_list(int, class NeighList *);
- void compute_vector();
-
- private:
-
- void compute_pairs();
-
- int me,nvalues,dir;
- int *which;
-
- double *values_local,*values_global;
- double pos,pos1,dt,nktv2p,ftm2v;
- double area;
- class NeighList *list;
-
- };
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
- E: Illegal ... command
-
- Self-explanatory. Check the input script syntax and compare to the
- documentation for the command. You can use -echo screen as a
- command-line option when running LAMMPS to see the offending line.
-
- E: Pair style does not support compute mop
-
- The pair style does not have a single() function, so it can
- not be invoked by compute mop/spatial.
-
-
-
-*/
-
diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp
deleted file mode 100644
index df62518c53..0000000000
--- a/src/USER-MOP/compute_mop_profile.cpp
+++ /dev/null
@@ -1,496 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
- ------------------------------------------------------------------------- */
-
-/*------------------------------------------------------------------------
- Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
- --------------------------------------------------------------------------*/
-
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
-
-#include "compute_mop_profile.h"
-#include "atom.h"
-#include "update.h"
-#include "domain.h"
-#include "group.h"
-#include "modify.h"
-#include "fix.h"
-#include "neighbor.h"
-#include "force.h"
-#include "pair.h"
-#include "neigh_request.h"
-#include "neigh_list.h"
-#include "error.h"
-#include "memory.h"
-
-using namespace LAMMPS_NS;
-
-enum{X,Y,Z};
-enum{LOWER,CENTER,UPPER,COORD};
-enum{TOTAL,CONF,KIN};
-
-#define BIG 1000000000
-
-/* ---------------------------------------------------------------------- */
-
-ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg)
-{
- if (narg < 7) error->all(FLERR,"Illegal compute mop/profile command");
-
- MPI_Comm_rank(world,&me);
-
- // set compute mode and direction of plane(s) for pressure calculation
-
- if (strcmp(arg[3],"x")==0) {
- dir = X;
- } else if (strcmp(arg[3],"y")==0) {
- dir = Y;
- } else if (strcmp(arg[3],"z")==0) {
- dir = Z;
- } else error->all(FLERR,"Illegal compute mop/profile command");
-
- // bin parameters
-
- if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
- else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
- else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
- else originflag = COORD;
- if (originflag == COORD)
- origin = force->numeric(FLERR,arg[4]);
- delta = force->numeric(FLERR,arg[5]);
- invdelta = 1.0/delta;
-
- // parse values until one isn't recognized
-
- which = new int[3*(narg-6)];
- nvalues = 0;
- int i;
-
- int iarg=6;
- while (iarg < narg) {
- if (strcmp(arg[iarg],"conf") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = CONF;
- nvalues++;
- }
- } else if (strcmp(arg[iarg],"kin") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = KIN;
- nvalues++;
- }
- } else if (strcmp(arg[iarg],"total") == 0) {
- for (i=0; i<3; i++) {
- which[nvalues] = TOTAL;
- nvalues++;
- }
- } else error->all(FLERR, "Illegal compute mop/profile command"); //break;
-
- iarg++;
- }
-
- // check domain related errors
-
- // 3D only
-
- if (domain->dimension < 3)
- error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
-
- // orthogonal simulation box
-
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
-
- // initialize some variables
-
- nbins = 0;
- coord = coordp = NULL;
- values_local = values_global = array = NULL;
-
- // bin setup
-
- setup_bins();
-
- // this fix produces a global array
-
- memory->create(array,nbins,1+nvalues,"mop/profile:array");
- size_array_rows = nbins;
- size_array_cols = 1 + nvalues;
-
- array_flag = 1;
- extarray = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-ComputeMopProfile::~ComputeMopProfile()
-{
-
- delete [] which;
-
- memory->destroy(coord);
- memory->destroy(coordp);
- memory->destroy(values_local);
- memory->destroy(values_global);
- memory->destroy(array);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeMopProfile::init()
-{
-
- // conversion constants
-
- nktv2p = force->nktv2p;
- ftm2v = force->ftm2v;
-
- // plane area
-
- area = 1;
- int i;
- for (i=0; i<3; i++) {
- if (i!=dir) area = area*domain->prd[i];
- }
-
- // timestep Value
-
- dt = update->dt;
-
- // Error check
- // Compute mop/profile requires fixed simulation box
-
- if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
- error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
-
- //This compute requires a pair style with pair_single method implemented
-
- if (force->pair == NULL)
- error->all(FLERR,"No pair style is defined for compute mop/profile");
- if (force->pair->single_enable == 0)
- error->all(FLERR,"Pair style does not support compute mop/profile");
-
- // Warnings
-
- if (me==0){
-
- //Compute mop/profile only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
-
- if (force->bond!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for bond potentials");
- if (force->angle!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for angle potentials");
- if (force->dihedral!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
- if (force->improper!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
- }
-
- // need an occasional half neighbor list
-
- int irequest = neighbor->request((void *) this);
- neighbor->requests[irequest]->pair = 0;
- neighbor->requests[irequest]->compute = 1;
- neighbor->requests[irequest]->occasional = 1;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeMopProfile::init_list(int id, NeighList *ptr)
-{
- list = ptr;
-}
-
-
-/* ----------------------------------------------------------------------
- compute output array
- ------------------------------------------------------------------------- */
-
-void ComputeMopProfile::compute_array()
-{
- invoked_array = update->ntimestep;
-
- //Compute pressures on separate procs
- compute_pairs();
-
- // sum pressure contributions over all procs
- MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
- MPI_DOUBLE,MPI_SUM,world);
-
- int ibin,m,mo;
- for (ibin=0; ibin<nbins; ibin++) {
- array[ibin][0] = coord[ibin][0];
- mo=1;
-
- m = 0;
- while (m<nvalues) {
- array[ibin][m+mo] = values_global[ibin][m];
- m++;
- }
- }
-}
-
-
-/*------------------------------------------------------------------------
- compute pressure contribution of local proc
- -------------------------------------------------------------------------*/
-
-void ComputeMopProfile::compute_pairs()
-
-{
- int i,j,m,n,ii,jj,inum,jnum,itype,jtype,ibin;
- double delx,dely,delz;
- double rsq,eng,fpair,factor_coul,factor_lj;
- int *ilist,*jlist,*numneigh,**firstneigh;
- double pos,pos1,pos_temp;
-
- double *mass = atom->mass;
- int *type = atom->type;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- double *special_coul = force->special_coul;
- double *special_lj = force->special_lj;
- int newton_pair = force->newton_pair;
-
-
- // zero out arrays for one sample
- for (m = 0; m < nbins; m++) {
- for (i = 0; i < nvalues; i++) values_local[m][i] = 0.0;
- }
-
- // invoke half neighbor list (will copy or build if necessary)
-
- neighbor->build_one(list);
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // loop over neighbors of my atoms
-
- Pair *pair = force->pair;
- double **cutsq = force->pair->cutsq;
-
- // parse values
-
- double xi[3];
- double vi[3];
- double fi[3];
- double xj[3];
-
- m = 0;
- while (m<nvalues) {
- if (which[m] == CONF || which[m] == TOTAL) {
-
- // Compute configurational contribution to pressure
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
-
- xi[0] = atom->x[i][0];
- xi[1] = atom->x[i][1];
- xi[2] = atom->x[i][2];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- factor_lj = special_lj[sbmask(j)];
- factor_coul = special_coul[sbmask(j)];
- j &= NEIGHMASK;
-
- // skip if neither I nor J are in group
-
- if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
-
- xj[0] = atom->x[j][0];
- xj[1] = atom->x[j][1];
- xj[2] = atom->x[j][2];
- delx = xi[0] - xj[0];
- dely = xi[1] - xj[1];
- delz = xi[2] - xj[2];
- rsq = delx*delx + dely*dely + delz*delz;
- jtype = type[j];
- if (rsq >= cutsq[itype][jtype]) continue;
-
- if (newton_pair || j < nlocal) {
-
- for (ibin=0;ibin<nbins;ibin++) {
- pos = coord[ibin][0];
- pos1 = coordp[ibin][0];
-
- //check if ij pair is accross plane, add contribution to pressure
-
- if ( ((xi[dir]>pos) && (xj[dir]<pos))
- || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
-
- } else if ( ((xi[dir]<pos) && (xj[dir]>pos))
- || ((xi[dir]<pos1) && (xj[dir]>pos1)) ) {
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[ibin][m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
- }
- }
- } else {
-
- for (ibin=0;ibin<nbins;ibin++) {
- pos = coord[ibin][0];
- pos1 = coordp[ibin][0];
-
- //check if ij pair is accross plane, add contribution to pressure
-
- if ( ((xi[dir]>pos) && (xj[dir]<pos))
- || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
-
- pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
- values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
- values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
- values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
- }
- }
- }
- }
- }
- }
-
- // compute kinetic contribution to pressure
- // counts local particles transfers across the plane
-
- if (which[m] == KIN || which[m] == TOTAL){
-
- double vcm[3];
- double masstotal,sgn;
-
- for (int i = 0; i < nlocal; i++){
-
- // skip if I is not in group
-
- if (mask[i] & groupbit){
-
- itype = type[i];
-
- //coordinates at t
- xi[0] = atom->x[i][0];
- xi[1] = atom->x[i][1];
- xi[2] = atom->x[i][2];
-
- //velocities at t
- vi[0] = atom->v[i][0];
- vi[1] = atom->v[i][1];
- vi[2] = atom->v[i][2];
-
- //forces at t
- fi[0] = atom->f[i][0];
- fi[1] = atom->f[i][1];
- fi[2] = atom->f[i][2];
-
- //coordinates at t-dt (based on Velocity-Verlet alg.)
- xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
- xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
- xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
-
- for (ibin=0;ibin<nbins;ibin++) {
- pos = coord[ibin][0];
- pos1 = coordp[ibin][0];
-
- if (((xi[dir]-pos)*(xj[dir]-pos)*(xi[dir]-pos1)*(xj[dir]-pos1)<0)){
-
- sgn = copysign(1,vi[dir]);
-
- //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
- double vcross[3];
- vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
- vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
- vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
-
- values_local[ibin][m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
- values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
- values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
- }
- }
- }
- }
- }
- m+=3;
- }
-}
-
-/* ----------------------------------------------------------------------
- setup 1d bins and their extent and coordinates
- called at init()
- ------------------------------------------------------------------------- */
-
-void ComputeMopProfile::setup_bins()
-{
- int i,j,k,m,n;
- double lo,hi,coord1,coord2;
-
- double *boxlo,*boxhi,*prd;
- boxlo = domain->boxlo;
- boxhi = domain->boxhi;
- prd = domain->prd;
-
- if (originflag == LOWER) origin = boxlo[dir];
- else if (originflag == UPPER) origin = boxhi[dir];
- else if (originflag == CENTER)
- origin = 0.5 * (boxlo[dir] + boxhi[dir]);
-
- if (origin < boxlo[dir]) {
- error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" );
- } else {
- n = static_cast<int> ((origin - boxlo[dir]) * invdelta);
- lo = origin - n*delta;
- }
- if (origin < boxhi[dir]) {
- n = static_cast<int> ((boxhi[dir] - origin) * invdelta);
- hi = origin + n*delta;
- } else {
- error->all(FLERR,"Origin of bins for compute mop/profile is out of bounds" );
- }
-
- offset = lo;
- nbins = static_cast<int> ((hi-lo) * invdelta + 1.5);
-
- //allocate bin arrays
- memory->create(coord,nbins,1,"mop/profile:coord");
- memory->create(coordp,nbins,1,"mop/profile:coordp");
- memory->create(values_local,nbins,nvalues,"mop/profile:values_local");
- memory->create(values_global,nbins,nvalues,"mop/profile:values_global");
-
- // set bin coordinates
- for (i = 0; i < nbins; i++) {
- coord[i][0] = offset + i*delta;
- if ( coord[i][0] < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
- coordp[i][0] = coord[i][0] + domain->prd[dir];
- } else {
- coordp[i][0] = coord[i][0] - domain->prd[dir];
- }
- }
-}
diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h
deleted file mode 100644
index 3cb46087ae..0000000000
--- a/src/USER-MOP/compute_mop_profile.h
+++ /dev/null
@@ -1,81 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
- ------------------------------------------------------------------------- */
-
-/*------------------------------------------------------------------------
- Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
- --------------------------------------------------------------------------*/
-
-#ifdef COMPUTE_CLASS
-
-ComputeStyle(mop/profile,ComputeMopProfile)
-
-#else
-
-#ifndef LMP_COMPUTE_MOP_PROFILE_H
-#define LMP_COMPUTE_MOP_PROFILE_H
-
-#include "compute.h"
-
-namespace LAMMPS_NS {
-
- class ComputeMopProfile : public Compute {
- public:
- ComputeMopProfile(class LAMMPS *, int, char **);
- virtual ~ComputeMopProfile();
- void init();
- void init_list(int, class NeighList *);
- void compute_array();
-
- private:
-
- void compute_pairs();
- void setup_bins();
-
- int me,nvalues,dir;
- int *which;
-
- int originflag;
- double origin,delta,offset,invdelta;
- int nbins;
- double **coord,**coordp;
- double **values_local,**values_global;
-
- int ndim;
- double dt,nktv2p,ftm2v;
- double area;
- class NeighList *list;
-
- };
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
- E: Illegal ... command
-
- Self-explanatory. Check the input script syntax and compare to the
- documentation for the command. You can use -echo screen as a
- command-line option when running LAMMPS to see the offending line.
-
- E: Pair style does not support compute mop/profile
-
- The pair style does not have a single() function, so it can
- not be invoked by compute mop/profile.
-
-
-
-*/
-
--
GitLab
From a6dfab6f27573e82a9fc89dbd2899f91f9f770e6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 4 Sep 2018 09:13:22 -0400
Subject: [PATCH 215/332] recover some const'ness in Domain class, that was
lost when merging MESSAGE package. fixes lib/atc compilation issue
---
src/domain.cpp | 10 +++++-----
src/domain.h | 4 ++--
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/domain.cpp b/src/domain.cpp
index 4e9b414050..8238ab7eea 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1176,12 +1176,12 @@ int Domain::closest_image(int i, int j)
if J is not a valid index like -1, just return it
------------------------------------------------------------------------- */
-int Domain::closest_image(double *pos, int j)
+int Domain::closest_image(const double * const pos, int j)
{
if (j < 0) return j;
- int *sametag = atom->sametag;
- double **x = atom->x;
+ const int * const sametag = atom->sametag;
+ const double * const * const x = atom->x;
int closest = j;
double delx = pos[0] - x[j][0];
@@ -1208,10 +1208,10 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
- called by ServerMD class
+ called by ServerMD class and LammpsInterface in lib/atc.
------------------------------------------------------------------------- */
-void Domain::closest_image(double *xi, double *xj, double *xjimage)
+void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];
diff --git a/src/domain.h b/src/domain.h
index ed24116cf4..9ebdd6ae94 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -115,8 +115,8 @@ class Domain : protected Pointers {
void minimum_image(double *);
void minimum_image_once(double *);
int closest_image(int, int);
- int closest_image(double *, int);
- void closest_image(double *, double *, double *);
+ int closest_image(const double * const, int);
+ void closest_image(const double * const, const double * const, double * const);
void remap(double *, imageint &);
void remap(double *);
void remap_near(double *, double *);
--
GitLab
From f18f12d1a6ab2a7cba28ff3eaed16f726d6b9d53 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 4 Sep 2018 09:14:42 -0400
Subject: [PATCH 216/332] Fix NETCDF include and libs in CMake
---
cmake/CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 0d4bab29f1..f1124fc127 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -435,8 +435,8 @@ endif()
if(PKG_USER-NETCDF)
find_package(NetCDF REQUIRED)
- include_directories(NETCDF_INCLUDE_DIR)
- list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
+ include_directories(${NETCDF_INCLUDE_DIRS})
+ list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
--
GitLab
From 842136afc841e90720abae1fa32ef84bf73f8e52 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 4 Sep 2018 12:12:49 -0400
Subject: [PATCH 217/332] Add core tests to CMake
---
cmake/CMakeLists.txt | 39 ++++++++++++++++++++++++++++++++++++---
1 file changed, 36 insertions(+), 3 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 0d4bab29f1..47a4075bcc 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -136,6 +136,7 @@ if(BUILD_EXE)
if(LAMMPS_MACHINE)
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
endif()
+ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
endif()
option(BUILD_LIB "Build LAMMPS library" OFF)
@@ -208,6 +209,38 @@ option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING)
enable_testing()
+
+ if (CMAKE_VERSION VERSION_GREATER "3.10.3") # due to FetchContent
+ include(FetchContent)
+
+
+ FetchContent_Declare(lammps-testing
+ GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+ GIT_TAG master
+ )
+
+ FetchContent_GetProperties(lammps-testing)
+ if(NOT lammps-testing_POPULATED)
+ message(STATUS "Downloading tests...")
+ FetchContent_Populate(lammps-testing)
+ endif()
+ message(STATUS "Running test discovery...")
+
+ file(GLOB_RECURSE TEST_SCRIPTS ${lammps-testing_SOURCE_DIR}/tests/core/*/in.*)
+ foreach(script_path ${TEST_SCRIPTS})
+ get_filename_component(TEST_NAME ${script_path} EXT)
+ get_filename_component(SCRIPT_NAME ${script_path} NAME)
+ get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+ string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+ string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+ string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+ set(TEST_NAME "test_core_${TEST_NAME}_serial")
+ add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+ set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+ endforeach()
+ else()
+ message(WARNING "Full test-suite requires CMake >= 3.11")
+ endif()
endif(ENABLE_TESTING)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
@@ -1119,11 +1152,11 @@ if(BUILD_EXE)
endif()
endif()
- set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+ set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
- install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1)
+ install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(ENABLE_TESTING)
- add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+ add_test(ShowHelp ${LAMMPS_BINARY} -help)
endif()
endif()
--
GitLab
From af4b2b935428b4e7738b17e78bcca96463e212eb Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 4 Sep 2018 15:37:32 -0400
Subject: [PATCH 218/332] Add LAMMPS_TESTING_SOURCE_DIR and
LAMMPS_TESTING_GIT_TAG options
---
cmake/CMakeLists.txt | 23 +++++++++++++++++------
1 file changed, 17 insertions(+), 6 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 47a4075bcc..0d8da8409d 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -209,14 +209,16 @@ option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING)
enable_testing()
+ option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+ option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
+ mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
- if (CMAKE_VERSION VERSION_GREATER "3.10.3") # due to FetchContent
+ if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
include(FetchContent)
-
FetchContent_Declare(lammps-testing
GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
- GIT_TAG master
+ GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
)
FetchContent_GetProperties(lammps-testing)
@@ -224,9 +226,17 @@ if(ENABLE_TESTING)
message(STATUS "Downloading tests...")
FetchContent_Populate(lammps-testing)
endif()
+
+ set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+ elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+ message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+ "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+ endif()
+
+ if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
- file(GLOB_RECURSE TEST_SCRIPTS ${lammps-testing_SOURCE_DIR}/tests/core/*/in.*)
+ file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
foreach(script_path ${TEST_SCRIPTS})
get_filename_component(TEST_NAME ${script_path} EXT)
get_filename_component(SCRIPT_NAME ${script_path} NAME)
@@ -238,8 +248,9 @@ if(ENABLE_TESTING)
add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
- else()
- message(WARNING "Full test-suite requires CMake >= 3.11")
+ list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+ message(STATUS "Found ${NUM_TESTS} tests.")
endif()
endif(ENABLE_TESTING)
--
GitLab
From bcecc0389e0607223383a8fa0713d73045d41ad9 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 4 Sep 2018 14:48:44 -0600
Subject: [PATCH 219/332] add variable option to compute bond/angle/dihedral
local
---
doc/src/compute_angle_local.txt | 66 ++++++--
doc/src/compute_bond_local.txt | 69 +++++++--
doc/src/compute_dihedral_local.txt | 64 +++++++-
src/compute_angle_local.cpp | 205 ++++++++++++++++++-------
src/compute_angle_local.h | 8 +-
src/compute_bond_local.cpp | 111 ++++++++++++--
src/compute_bond_local.h | 9 +-
src/compute_dihedral_local.cpp | 238 ++++++++++++++++++++---------
src/compute_dihedral_local.h | 8 +-
9 files changed, 611 insertions(+), 167 deletions(-)
diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt
index 3a321965ef..8acaec94d5 100644
--- a/doc/src/compute_angle_local.txt
+++ b/doc/src/compute_angle_local.txt
@@ -10,20 +10,27 @@ compute angle/local command :h3
[Syntax:]
-compute ID group-ID angle/local value1 value2 ... :pre
+compute ID group-ID angle/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
angle/local = style name of this compute command :l
one or more values may be appended :l
-value = {theta} or {eng} :l
+value = {theta} or {eng} or {v_name} :l
{theta} = tabulate angles
- {eng} = tabulate angle energies :pre
+ {eng} = tabulate angle energies
+ {v_name} = equal-style variable with name (see below) :pre
+zero or more keyword/args pairs may be appended :l
+keyword = {set} :l
+ {set} args = theta name
+ theta = only currently allowed arg
+ name = name of variable to set with theta :pre
:ule
[Examples:]
compute 1 all angle/local theta
-compute 1 all angle/local eng theta :pre
+compute 1 all angle/local eng theta
+compute 1 all angle/local theta v_cos set theta t :pre
[Description:]
@@ -36,6 +43,47 @@ The value {theta} is the angle for the 3 atoms in the interaction.
The value {eng} is the interaction energy for the angle.
+The value {v_name} can be used together with the {set} keyword to
+compute a user-specified function of the angle theta. The {name}
+specified for the {v_name} value is the name of an "equal-style
+variable"_variable.html which should evaluate a formula based on a
+variable which will store the angle theta. This other variable must
+be an "internal-style variable"_variable.html defined in the input
+script; its initial numeric value can be anything. It must be an
+internal-style variable, because this command resets its value
+directly. The {set} keyword is used to identify the name of this
+other variable associated with theta.
+
+Note that the value of theta for each angle which stored in the
+internal variable is in radians, not degrees.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the cosine and cosine^2 of every angle in the system
+and output the statistics in various ways:
+
+variable t internal 0.0
+variable cos equal cos(v_t)
+variable cossq equal cos(v_t)*cos(v_t) :pre
+
+compute 1 all property/local aatom1 aatom2 aatom3 atype
+compute 2 all angle/local eng theta v_cos v_cossq set theta t
+dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
+
+compute 3 all reduce ave c_2[*]
+thermo_style custom step temp press c_3[*] :pre
+
+fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre
+
+The "dump local"_dump.html command will output the energy, angle,
+cosine(angle), cosine^2(angle) for every angle in the system. The
+"thermo_style"_thermo_style.html command will print the average of
+those quantities via the "compute reduce"_compute_reduce.html command
+with thermo output. And the "fix ave/histo"_fix_ave_histo.html
+command will histogram the cosine(angle) values and write them to a
+file.
+
+:line
+
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
@@ -65,12 +113,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\
[Output info:]
This compute calculates a local vector or local array depending on the
-number of keywords. The length of the vector or number of rows in the
-array is the number of angles. If a single keyword is specified, a
-local vector is produced. If two or more keywords are specified, a
+number of values. The length of the vector or number of rows in the
+array is the number of angles. If a single value is specified, a
+local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
-keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See the "Howto
+values. The vector or array can be accessed by any command that uses
+local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt
index c3dc1cc4af..4afd1aec40 100644
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@@ -10,12 +10,12 @@ compute bond/local command :h3
[Syntax:]
-compute ID group-ID bond/local value1 value2 ... :pre
+compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
bond/local = style name of this compute command :l
one or more values may be appended :l
-value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} :l
+value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
{dist} = bond distance
{engpot} = bond potential energy
{force} = bond force :pre
@@ -23,13 +23,22 @@ value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {
{engrot} = bond kinetic energy of rotation
{engtrans} = bond kinetic energy of translation
{omega} = magnitude of bond angular velocity
- {velvib} = vibrational velocity along the bond length :pre
+ {velvib} = vibrational velocity along the bond length
+ {v_name} = equal-style variable with name (see below) :pre
+zero or more keyword/args pairs may be appended :l
+keyword = {set} :l
+ {set} args = dist name
+ dist = only currently allowed arg
+ name = name of variable to set with distance (dist) :pre
+:ule
+
:ule
[Examples:]
compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force :pre
+compute 1 all angle/local dist v_distsq set dist d :pre
[Description:]
@@ -38,6 +47,10 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified by the
group parameter as explained below.
+All these properties are computed for the pair of atoms in a bond,
+whether the 2 atoms represent a simple diatomic molecule, or are part
+of some larger molecule.
+
The value {dist} is the current length of the bond.
The value {engpot} is the potential energy for the bond,
@@ -79,9 +92,41 @@ two atoms in the bond towards each other. A negative value means the
2 atoms are moving toward each other; a positive value means they are
moving apart.
-Note that all these properties are computed for the pair of atoms in a
-bond, whether the 2 atoms represent a simple diatomic molecule, or are
-part of some larger molecule.
+The value {v_name} can be used together with the {set} keyword to
+compute a user-specified function of the bond distance. The {name}
+specified for the {v_name} value is the name of an "equal-style
+variable"_variable.html which should evaluate a formula based on a
+variable which will store the bond distance. This other variable must
+be an "internal-style variable"_variable.html defined in the input
+script; its initial numeric value can be anything. It must be an
+internal-style variable, because this command resets its value
+directly. The {set} keyword is used to identify the name of this
+other variable associated with theta.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the distance^2 of every bond in the system and
+output the statistics in various ways:
+
+variable d internal 0.0
+variable dsq equal v_d*v_d :pre
+
+compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local engpot dist v_dsq set dist d
+dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
+
+compute 3 all reduce ave c_2[*]
+thermo_style custom step temp press c_3[*] :pre
+
+fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre
+
+The "dump local"_dump.html command will output the energy, distance,
+distance^2 for every bond in the system. The
+"thermo_style"_thermo_style.html command will print the average of
+those quantities via the "compute reduce"_compute_reduce.html command
+with thermo output. And the "fix ave/histo"_fix_ave_histo.html
+command will histogram the distance^2 values and write them to a file.
+
+:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
@@ -111,12 +156,12 @@ dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
-number of keywords. The length of the vector or number of rows in the
-array is the number of bonds. If a single keyword is specified, a
-local vector is produced. If two or more keywords are specified, a
-local array is produced where the number of columns = the number of
-keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See the "Howto
+number of values. The length of the vector or number of rows in the
+array is the number of bonds. If a single value is specified, a local
+vector is produced. If two or more values are specified, a local
+array is produced where the number of columns = the number of values.
+The vector or array can be accessed by any command that uses local
+values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt
index 77812699d3..951b360f19 100644
--- a/doc/src/compute_dihedral_local.txt
+++ b/doc/src/compute_dihedral_local.txt
@@ -10,18 +10,25 @@ compute dihedral/local command :h3
[Syntax:]
-compute ID group-ID dihedral/local value1 value2 ... :pre
+compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
dihedral/local = style name of this compute command :l
one or more values may be appended :l
-value = {phi} :l
- {phi} = tabulate dihedral angles :pre
+value = {phi} or {v_name} :l
+ {phi} = tabulate dihedral angles
+ {v_name} = equal-style variable with name (see below) :pre
+zero or more keyword/args pairs may be appended :l
+keyword = {set} :l
+ {set} args = phi name
+ phi = only currently allowed arg
+ name = name of variable to set with phi :pre
:ule
[Examples:]
compute 1 all dihedral/local phi :pre
+compute 1 all dihedral/local phi v_cos set phi p :pre
[Description:]
@@ -33,6 +40,47 @@ by the group parameter as explained below.
The value {phi} is the dihedral angle, as defined in the diagram on
the "dihedral_style"_dihedral_style.html doc page.
+The value {v_name} can be used together with the {set} keyword to
+compute a user-specified function of the dihedral angle phi. The
+{name} specified for the {v_name} value is the name of an "equal-style
+variable"_variable.html which should evaluate a formula based on a
+variable which will store the angle phi. This other variable must
+be an "internal-style variable"_variable.html defined in the input
+script; its initial numeric value can be anything. It must be an
+internal-style variable, because this command resets its value
+directly. The {set} keyword is used to identify the name of this
+other variable associated with phi.
+
+Note that the value of phi for each angle which stored in the internal
+variable is in radians, not degrees.
+
+As an example, these commands can be added to the bench/in.rhodo
+script to compute the cosine and cosine^2 of every dihedral angle in
+the system and output the statistics in various ways:
+
+variable p internal 0.0
+variable cos equal cos(v_p)
+variable cossq equal cos(v_p)*cos(v_p) :pre
+
+compute 1 all property/local datom1 datom2 datom3 datom4 dtype
+compute 2 all dihedral/local phi v_cos v_cossq set phi p
+dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
+
+compute 3 all reduce ave c_2[*]
+thermo_style custom step temp press c_3[*] :pre
+
+fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre
+
+The "dump local"_dump.html command will output the angle,
+cosine(angle), cosine^2(angle) for every dihedral in the system. The
+"thermo_style"_thermo_style.html command will print the average of
+those quantities via the "compute reduce"_compute_reduce.html command
+with thermo output. And the "fix ave/histo"_fix_ave_histo.html
+command will histogram the cosine(angle) values and write them to a
+file.
+
+:line
+
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
@@ -57,12 +105,12 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\
[Output info:]
This compute calculates a local vector or local array depending on the
-number of keywords. The length of the vector or number of rows in the
-array is the number of dihedrals. If a single keyword is specified, a
-local vector is produced. If two or more keywords are specified, a
+number of values. The length of the vector or number of rows in the
+array is the number of dihedrals. If a single value is specified, a
+local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
-keywords. The vector or array can be accessed by any command that
-uses local values from a compute as input. See the "Howto
+values. The vector or array can be accessed by any command that uses
+local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index 7137077158..95faad54ad 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -21,6 +21,8 @@
#include "domain.h"
#include "force.h"
#include "angle.h"
+#include "input.h"
+#include "variable.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -30,11 +32,13 @@ using namespace MathConst;
#define DELTA 10000
+enum{THETA,ENG,VARIABLE};
+
/* ---------------------------------------------------------------------- */
ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- vlocal(NULL), alocal(NULL)
+ bstyle(NULL), vstr(NULL), vvar(NULL), tstr(NULL), vlocal(NULL), alocal(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute angle/local command");
@@ -42,19 +46,82 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Compute angle/local used when angles are not allowed");
local_flag = 1;
- nvalues = narg - 3;
- if (nvalues == 1) size_local_cols = 0;
- else size_local_cols = nvalues;
- tflag = eflag = -1;
+ // style args
+
+ nvalues = narg - 3;
+ bstyle = new int[nvalues];
+ vstr = new char*[nvalues];
+ vvar = new int[nvalues];
+
nvalues = 0;
+ tflag = 0;
+ nvar = 0;
+
+ int iarg;
+ for (iarg = 3; iarg < narg; iarg++) {
+ if (strcmp(arg[iarg],"theta") == 0) {
+ bstyle[nvalues++] = THETA;
+ tflag = 1;
+ } else if (strcmp(arg[iarg],"eng") == 0) {
+ bstyle[nvalues++] = ENG;
+ } else if (strncmp(arg[iarg],"v_",2) == 0) {
+ bstyle[nvalues++] = VARIABLE;
+ int n = strlen(arg[iarg]);
+ vstr[nvar] = new char[n];
+ strcpy(vstr[nvar],&arg[iarg][2]);
+ nvar++;
+ } else break;
+ }
- for (int iarg = 3; iarg < narg; iarg++) {
- if (strcmp(arg[iarg],"theta") == 0) tflag = nvalues++;
- else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++;
- else error->all(FLERR,"Invalid keyword in compute angle/local command");
+ // optional args
+
+ setflag = 0;
+ tstr = NULL;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"set") == 0) {
+ setflag = 1;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal compute angle/local command");
+ if (strcmp(arg[iarg+1],"theta") == 0) {
+ delete [] tstr;
+ int n = strlen(arg[iarg+2]) + 1;
+ tstr = new char[n];
+ strcpy(tstr,arg[iarg+2]);
+ tflag = 1;
+ } else error->all(FLERR,"Illegal compute angle/local command");
+ iarg += 3;
+ } else error->all(FLERR,"Illegal compute angle/local command");
}
+ // error check
+
+ if (nvar) {
+ if (!setflag)
+ error->all(FLERR,"Compute angle/local variable requires a set variable");
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,"Variable name for copute angle/local does not exist");
+ if (!input->variable->equalstyle(vvar[i]))
+ error->all(FLERR,"Variable for compute angle/local is invalid style");
+ }
+
+ if (tstr) {
+ tvar = input->variable->find(tstr);
+ if (tvar < 0)
+ error->all(FLERR,"Variable name for compute angle/local does not exist");
+ if (!input->variable->internalstyle(tvar))
+ error->all(FLERR,"Variable for compute angle/local is invalid style");
+ }
+ } else if (setflag)
+ error->all(FLERR,"Compute angle/local set with no variable");
+
+ // initialize output
+
+ if (nvalues == 1) size_local_cols = 0;
+ else size_local_cols = nvalues;
+
nmax = 0;
vlocal = NULL;
alocal = NULL;
@@ -64,6 +131,13 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeAngleLocal::~ComputeAngleLocal()
{
+ delete [] bstyle;
+ for (int i = 0; i < nvar; i++) delete [] vstr[i];
+ delete [] vstr;
+ delete [] vvar;
+
+ delete [] tstr;
+
memory->destroy(vlocal);
memory->destroy(alocal);
}
@@ -75,6 +149,20 @@ void ComputeAngleLocal::init()
if (force->angle == NULL)
error->all(FLERR,"No angle style is defined for compute angle/local");
+ if (nvar) {
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,"Variable name for compute angle/local does not exist");
+ }
+
+ if (tstr) {
+ tvar = input->variable->find(tstr);
+ if (tvar < 0)
+ error->all(FLERR,"Variable name for compute angle/local does not exist");
+ }
+ }
+
// do initial memory allocation so that memory_usage() is correct
ncount = compute_angles(0);
@@ -109,11 +197,11 @@ void ComputeAngleLocal::compute_local()
int ComputeAngleLocal::compute_angles(int flag)
{
- int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype;
+ int i,m,n,na,atom1,atom2,atom3,imol,iatom,atype,ivar;
tagint tagprev;
double delx1,dely1,delz1,delx2,dely2,delz2;
- double rsq1,rsq2,r1,r2,c;
- double *tbuf,*ebuf;
+ double rsq1,rsq2,r1,r2,c,theta;
+ double *ptr;
double **x = atom->x;
tagint *tag = atom->tag;
@@ -131,17 +219,7 @@ int ComputeAngleLocal::compute_angles(int flag)
int nlocal = atom->nlocal;
int molecular = atom->molecular;
- if (flag) {
- if (nvalues == 1) {
- if (tflag >= 0) tbuf = vlocal;
- if (eflag >= 0) ebuf = vlocal;
- } else {
- if (tflag >= 0 && alocal) tbuf = &alocal[0][tflag];
- else tbuf = NULL;
- if (eflag >= 0 && alocal) ebuf = &alocal[0][eflag];
- else ebuf = NULL;
- }
- }
+ // loop over all atoms and their angles
Angle *angle = force->angle;
@@ -175,39 +253,62 @@ int ComputeAngleLocal::compute_angles(int flag)
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
if (atype == 0) continue;
- if (flag) {
- if (tflag >= 0) {
- delx1 = x[atom1][0] - x[atom2][0];
- dely1 = x[atom1][1] - x[atom2][1];
- delz1 = x[atom1][2] - x[atom2][2];
- domain->minimum_image(delx1,dely1,delz1);
-
- rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
- r1 = sqrt(rsq1);
-
- delx2 = x[atom3][0] - x[atom2][0];
- dely2 = x[atom3][1] - x[atom2][1];
- delz2 = x[atom3][2] - x[atom2][2];
- domain->minimum_image(delx2,dely2,delz2);
-
- rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
- r2 = sqrt(rsq2);
+ if (!flag) {
+ m++;
+ continue;
+ }
- // c = cosine of angle
+ // theta needed by one or more outputs
+
+ if (tflag) {
+ delx1 = x[atom1][0] - x[atom2][0];
+ dely1 = x[atom1][1] - x[atom2][1];
+ delz1 = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(delx1,dely1,delz1);
+
+ rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+ r1 = sqrt(rsq1);
+
+ delx2 = x[atom3][0] - x[atom2][0];
+ dely2 = x[atom3][1] - x[atom2][1];
+ delz2 = x[atom3][2] - x[atom2][2];
+ domain->minimum_image(delx2,dely2,delz2);
+
+ rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+ r2 = sqrt(rsq2);
+
+ // c = cosine of angle
+ // theta = angle in radians
+
+ c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ theta = acos(c);
+ }
- c = delx1*delx2 + dely1*dely2 + delz1*delz2;
- c /= r1*r2;
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- tbuf[n] = 180.0*acos(c)/MY_PI;
- }
+ if (nvalues == 1) ptr = &vlocal[m];
+ else ptr = alocal[m];
+
+ if (nvar) {
+ ivar = 0;
+ if (tstr) input->variable->internal_set(tvar,theta);
+ }
- if (eflag >= 0) {
- if (atype > 0)
- ebuf[n] = angle->single(atype,atom1,atom2,atom3);
- else ebuf[n] = 0.0;
+ for (n = 0; n < nvalues; n++) {
+ switch (bstyle[n]) {
+ case THETA:
+ ptr[n] = 180.0*theta/MY_PI;
+ break;
+ case ENG:
+ if (atype > 0) ptr[n] = angle->single(atype,atom1,atom2,atom3);
+ else ptr[n] = 0.0;
+ break;
+ case VARIABLE:
+ ptr[n] = input->variable->compute_equal(vvar[ivar]);
+ ivar++;
+ break;
}
- n += nvalues;
}
m++;
diff --git a/src/compute_angle_local.h b/src/compute_angle_local.h
index 6f59d7f097..a95e23206d 100644
--- a/src/compute_angle_local.h
+++ b/src/compute_angle_local.h
@@ -33,8 +33,12 @@ class ComputeAngleLocal : public Compute {
double memory_usage();
private:
- int nvalues,tflag,eflag;
- int ncount;
+ int nvalues,nvar,ncount,setflag,tflag;
+
+ int tvar;
+ int *bstyle,*vvar;
+ char *tstr;
+ char **vstr;
int nmax;
double *vlocal;
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 56abb9b071..6a179cf1b4 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -21,8 +21,10 @@
#include "domain.h"
#include "force.h"
#include "bond.h"
-#include "math_extra.h"
#include "comm.h"
+#include "input.h"
+#include "variable.h"
+#include "math_extra.h"
#include "memory.h"
#include "error.h"
@@ -31,13 +33,13 @@ using namespace LAMMPS_NS;
#define DELTA 10000
#define EPSILON 1.0e-12
-enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE};
+enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,VARIABLE};
/* ---------------------------------------------------------------------- */
ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- bstyle(NULL), vlocal(NULL), alocal(NULL)
+ bstyle(NULL), vstr(NULL), vvar(NULL), dstr(NULL), vlocal(NULL), alocal(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute bond/local command");
@@ -47,14 +49,18 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
local_flag = 1;
comm_forward = 3;
- nvalues = narg - 3;
- if (nvalues == 1) size_local_cols = 0;
- else size_local_cols = nvalues;
+ // style args
+ nvalues = narg - 3;
bstyle = new int[nvalues];
-
+ vstr = new char*[nvalues];
+ vvar = new int[nvalues];
+
nvalues = 0;
- for (int iarg = 3; iarg < narg; iarg++) {
+ nvar = 0;
+
+ int iarg;
+ for (iarg = 3; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST;
else if (strcmp(arg[iarg],"engpot") == 0) bstyle[nvalues++] = ENGPOT;
else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE;
@@ -63,9 +69,58 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"engtrans") == 0) bstyle[nvalues++] = ENGTRANS;
else if (strcmp(arg[iarg],"omega") == 0) bstyle[nvalues++] = OMEGA;
else if (strcmp(arg[iarg],"velvib") == 0) bstyle[nvalues++] = VELVIB;
- else error->all(FLERR,"Invalid keyword in compute bond/local command");
+ else if (strncmp(arg[iarg],"v_",2) == 0) {
+ bstyle[nvalues++] = VARIABLE;
+ int n = strlen(arg[iarg]);
+ vstr[nvar] = new char[n];
+ strcpy(vstr[nvar],&arg[iarg][2]);
+ nvar++;
+ } else break;
+ }
+
+ // optional args
+
+ setflag = 0;
+ dstr = NULL;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"set") == 0) {
+ setflag = 1;
+ if (iarg+3 > narg) error->all(FLERR,"Illegal compute bond/local command");
+ if (strcmp(arg[iarg+1],"dist") == 0) {
+ delete [] dstr;
+ int n = strlen(arg[iarg+2]) + 1;
+ dstr = new char[n];
+ strcpy(dstr,arg[iarg+2]);
+ } else error->all(FLERR,"Illegal compute bond/local command");
+ iarg += 3;
+ } else error->all(FLERR,"Illegal compute bond/local command");
}
+ // error check
+
+ if (nvar) {
+ if (!setflag)
+ error->all(FLERR,"Compute bond/local variable requires a set variable");
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,"Variable name for copute bond/local does not exist");
+ if (!input->variable->equalstyle(vvar[i]))
+ error->all(FLERR,"Variable for compute bond/local is invalid style");
+ }
+
+ if (dstr) {
+ dvar = input->variable->find(dstr);
+ if (dvar < 0)
+ error->all(FLERR,"Variable name for compute bond/local does not exist");
+ if (!input->variable->internalstyle(dvar))
+ error->all(FLERR,"Variable for compute bond/local is invalid style");
+ }
+ } else if (setflag)
+ error->all(FLERR,"Compute bond/local set with no variable");
+
+
// set singleflag if need to call bond->single()
// set velflag if compute any quantities based on velocities
@@ -77,6 +132,11 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1;
}
+ // initialize output
+
+ if (nvalues == 1) size_local_cols = 0;
+ else size_local_cols = nvalues;
+
nmax = 0;
vlocal = NULL;
alocal = NULL;
@@ -86,9 +146,15 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeBondLocal::~ComputeBondLocal()
{
+ delete [] bstyle;
+ for (int i = 0; i < nvar; i++) delete [] vstr[i];
+ delete [] vstr;
+ delete [] vvar;
+
+ delete [] dstr;
+
memory->destroy(vlocal);
memory->destroy(alocal);
- delete [] bstyle;
}
/* ---------------------------------------------------------------------- */
@@ -98,6 +164,20 @@ void ComputeBondLocal::init()
if (force->bond == NULL)
error->all(FLERR,"No bond style is defined for compute bond/local");
+ if (nvar) {
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,"Variable name for compute bond/local does not exist");
+ }
+
+ if (dstr) {
+ dvar = input->variable->find(dstr);
+ if (dvar < 0)
+ error->all(FLERR,"Variable name for compute bond/local does not exist");
+ }
+ }
+
// set ghostvelflag if need to acquire ghost atom velocities
if (velflag && !comm->ghost_velocity) ghostvelflag = 1;
@@ -140,7 +220,7 @@ void ComputeBondLocal::compute_local()
int ComputeBondLocal::compute_bonds(int flag)
{
- int i,m,n,nb,atom1,atom2,imol,iatom,btype;
+ int i,m,n,nb,atom1,atom2,imol,iatom,btype,ivar;
tagint tagprev;
double dx,dy,dz,rsq;
double mass1,mass2,masstotal,invmasstotal;
@@ -297,6 +377,11 @@ int ComputeBondLocal::compute_bonds(int flag)
if (nvalues == 1) ptr = &vlocal[m];
else ptr = alocal[m];
+ if (nvar) {
+ ivar = 0;
+ if (dstr) input->variable->internal_set(dvar,sqrt(rsq));
+ }
+
for (n = 0; n < nvalues; n++) {
switch (bstyle[n]) {
case DIST:
@@ -323,6 +408,10 @@ int ComputeBondLocal::compute_bonds(int flag)
case VELVIB:
ptr[n] = vvib;
break;
+ case VARIABLE:
+ ptr[n] = input->variable->compute_equal(vvar[ivar]);
+ ivar++;
+ break;
}
}
}
diff --git a/src/compute_bond_local.h b/src/compute_bond_local.h
index b3e99fc61b..17111a941c 100644
--- a/src/compute_bond_local.h
+++ b/src/compute_bond_local.h
@@ -35,10 +35,13 @@ class ComputeBondLocal : public Compute {
double memory_usage();
private:
- int nvalues;
- int ncount;
- int *bstyle;
+ int nvalues,nvar,ncount,setflag;
+
int singleflag,velflag,ghostvelflag,initflag;
+ int dvar;
+ int *bstyle,*vvar;
+ char *dstr;
+ char **vstr;
int nmax;
double *vlocal;
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index 42d1476ad2..7444630090 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -21,6 +21,9 @@
#include "domain.h"
#include "force.h"
#include "dihedral.h"
+#include "input.h"
+#include "variable.h"
+
#include "math_const.h"
#include "memory.h"
#include "error.h"
@@ -31,11 +34,13 @@ using namespace MathConst;
#define DELTA 10000
#define SMALL 0.001
+enum{PHI,VARIABLE};
+
/* ---------------------------------------------------------------------- */
ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- vlocal(NULL), alocal(NULL)
+ bstyle(NULL), vstr(NULL), vvar(NULL), pstr(NULL), vlocal(NULL), alocal(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command");
@@ -44,18 +49,80 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
"Compute dihedral/local used when dihedrals are not allowed");
local_flag = 1;
- nvalues = narg - 3;
- if (nvalues == 1) size_local_cols = 0;
- else size_local_cols = nvalues;
- pflag = -1;
+ // style args
+
+ nvalues = narg - 3;
+ bstyle = new int[nvalues];
+ vstr = new char*[nvalues];
+ vvar = new int[nvalues];
+
nvalues = 0;
+ nvar = 0;
+
+ int iarg;
+ for (iarg = 3; iarg < narg; iarg++) {
+ if (strcmp(arg[iarg],"phi") == 0) {
+ bstyle[nvalues++] = PHI;
+ } else if (strncmp(arg[iarg],"v_",2) == 0) {
+ bstyle[nvalues++] = VARIABLE;
+ int n = strlen(arg[iarg]);
+ vstr[nvar] = new char[n];
+ strcpy(vstr[nvar],&arg[iarg][2]);
+ nvar++;
+ } else break;
+ }
- for (int iarg = 3; iarg < narg; iarg++) {
- if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++;
- else error->all(FLERR,"Invalid keyword in compute dihedral/local command");
+ // optional args
+
+ setflag = 0;
+ pstr = NULL;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"set") == 0) {
+ setflag = 1;
+ if (iarg+3 > narg)
+ error->all(FLERR,"Illegal compute dihedral/local command");
+ if (strcmp(arg[iarg+1],"phi") == 0) {
+ delete [] pstr;
+ int n = strlen(arg[iarg+2]) + 1;
+ pstr = new char[n];
+ strcpy(pstr,arg[iarg+2]);
+ } else error->all(FLERR,"Illegal compute dihedral/local command");
+ iarg += 3;
+ } else error->all(FLERR,"Illegal compute dihedral/local command");
}
+ // error check
+
+ if (nvar) {
+ if (!setflag)
+ error->all(FLERR,"Compute dihedral/local variable requires a set variable");
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,
+ "Variable name for copute dihedral/local does not exist");
+ if (!input->variable->equalstyle(vvar[i]))
+ error->all(FLERR,"Variable for compute dihedral/local is invalid style");
+ }
+
+ if (pstr) {
+ pvar = input->variable->find(pstr);
+ if (pvar < 0)
+ error->all(FLERR,
+ "Variable name for compute dihedral/local does not exist");
+ if (!input->variable->internalstyle(pvar))
+ error->all(FLERR,"Variable for compute dihedral/local is invalid style");
+ }
+ } else if (setflag)
+ error->all(FLERR,"Compute dihedral/local set with no variable");
+
+ // initialize output
+
+ if (nvalues == 1) size_local_cols = 0;
+ else size_local_cols = nvalues;
+
nmax = 0;
vlocal = NULL;
alocal = NULL;
@@ -65,6 +132,13 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeDihedralLocal::~ComputeDihedralLocal()
{
+ delete [] bstyle;
+ for (int i = 0; i < nvar; i++) delete [] vstr[i];
+ delete [] vstr;
+ delete [] vvar;
+
+ delete [] pstr;
+
memory->destroy(vlocal);
memory->destroy(alocal);
}
@@ -76,6 +150,22 @@ void ComputeDihedralLocal::init()
if (force->dihedral == NULL)
error->all(FLERR,"No dihedral style is defined for compute dihedral/local");
+ if (nvar) {
+ for (int i = 0; i < nvar; i++) {
+ vvar[i] = input->variable->find(vstr[i]);
+ if (vvar[i] < 0)
+ error->all(FLERR,
+ "Variable name for compute dihedral/local does not exist");
+ }
+
+ if (pstr) {
+ pvar = input->variable->find(pstr);
+ if (pvar < 0)
+ error->all(FLERR,
+ "Variable name for compute dihedral/local does not exist");
+ }
+ }
+
// do initial memory allocation so that memory_usage() is correct
ncount = compute_dihedrals(0);
@@ -107,12 +197,12 @@ void ComputeDihedralLocal::compute_local()
int ComputeDihedralLocal::compute_dihedrals(int flag)
{
- int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom;
+ int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom,ivar;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;
- double s,c;
- double *pbuf;
+ double s,c,phi;
+ double *ptr;
double **x = atom->x;
tagint *tag = atom->tag;
@@ -130,14 +220,7 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
int nlocal = atom->nlocal;
int molecular = atom->molecular;
- if (flag) {
- if (nvalues == 1) {
- if (pflag >= 0) pbuf = vlocal;
- } else {
- if (pflag >= 0 && alocal) pbuf = &alocal[0][pflag];
- else pbuf = NULL;
- }
- }
+ // loop over all atoms and their dihedrals
m = n = 0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
@@ -169,56 +252,75 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
- if (flag) {
-
- // phi calculation from dihedral style harmonic
-
- if (pflag >= 0) {
- vb1x = x[atom1][0] - x[atom2][0];
- vb1y = x[atom1][1] - x[atom2][1];
- vb1z = x[atom1][2] - x[atom2][2];
- domain->minimum_image(vb1x,vb1y,vb1z);
-
- vb2x = x[atom3][0] - x[atom2][0];
- vb2y = x[atom3][1] - x[atom2][1];
- vb2z = x[atom3][2] - x[atom2][2];
- domain->minimum_image(vb2x,vb2y,vb2z);
-
- vb2xm = -vb2x;
- vb2ym = -vb2y;
- vb2zm = -vb2z;
- domain->minimum_image(vb2xm,vb2ym,vb2zm);
-
- vb3x = x[atom4][0] - x[atom3][0];
- vb3y = x[atom4][1] - x[atom3][1];
- vb3z = x[atom4][2] - x[atom3][2];
- domain->minimum_image(vb3x,vb3y,vb3z);
-
- ax = vb1y*vb2zm - vb1z*vb2ym;
- ay = vb1z*vb2xm - vb1x*vb2zm;
- az = vb1x*vb2ym - vb1y*vb2xm;
- bx = vb3y*vb2zm - vb3z*vb2ym;
- by = vb3z*vb2xm - vb3x*vb2zm;
- bz = vb3x*vb2ym - vb3y*vb2xm;
-
- rasq = ax*ax + ay*ay + az*az;
- rbsq = bx*bx + by*by + bz*bz;
- rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
- rg = sqrt(rgsq);
-
- ra2inv = rb2inv = 0.0;
- if (rasq > 0) ra2inv = 1.0/rasq;
- if (rbsq > 0) rb2inv = 1.0/rbsq;
- rabinv = sqrt(ra2inv*rb2inv);
-
- c = (ax*bx + ay*by + az*bz)*rabinv;
- s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
-
- if (c > 1.0) c = 1.0;
- if (c < -1.0) c = -1.0;
- pbuf[n] = 180.0*atan2(s,c)/MY_PI;
+ if (!flag) {
+ m++;
+ continue;
+ }
+
+ // phi calculation from dihedral style harmonic
+
+ vb1x = x[atom1][0] - x[atom2][0];
+ vb1y = x[atom1][1] - x[atom2][1];
+ vb1z = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(vb1x,vb1y,vb1z);
+
+ vb2x = x[atom3][0] - x[atom2][0];
+ vb2y = x[atom3][1] - x[atom2][1];
+ vb2z = x[atom3][2] - x[atom2][2];
+ domain->minimum_image(vb2x,vb2y,vb2z);
+
+ vb2xm = -vb2x;
+ vb2ym = -vb2y;
+ vb2zm = -vb2z;
+ domain->minimum_image(vb2xm,vb2ym,vb2zm);
+
+ vb3x = x[atom4][0] - x[atom3][0];
+ vb3y = x[atom4][1] - x[atom3][1];
+ vb3z = x[atom4][2] - x[atom3][2];
+ domain->minimum_image(vb3x,vb3y,vb3z);
+
+ ax = vb1y*vb2zm - vb1z*vb2ym;
+ ay = vb1z*vb2xm - vb1x*vb2zm;
+ az = vb1x*vb2ym - vb1y*vb2xm;
+ bx = vb3y*vb2zm - vb3z*vb2ym;
+ by = vb3z*vb2xm - vb3x*vb2zm;
+ bz = vb3x*vb2ym - vb3y*vb2xm;
+
+ rasq = ax*ax + ay*ay + az*az;
+ rbsq = bx*bx + by*by + bz*bz;
+ rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
+ rg = sqrt(rgsq);
+
+ ra2inv = rb2inv = 0.0;
+ if (rasq > 0) ra2inv = 1.0/rasq;
+ if (rbsq > 0) rb2inv = 1.0/rbsq;
+ rabinv = sqrt(ra2inv*rb2inv);
+
+ c = (ax*bx + ay*by + az*bz)*rabinv;
+ s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ phi = atan2(s,c);
+
+ if (nvalues == 1) ptr = &vlocal[m];
+ else ptr = alocal[m];
+
+ if (nvar) {
+ ivar = 0;
+ if (pstr) input->variable->internal_set(pvar,phi);
+ }
+
+ for (n = 0; n < nvalues; n++) {
+ switch (bstyle[n]) {
+ case PHI:
+ ptr[n] = 180.0*phi/MY_PI;
+ break;
+ case VARIABLE:
+ ptr[n] = input->variable->compute_equal(vvar[ivar]);
+ ivar++;
+ break;
}
- n += nvalues;
}
m++;
diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h
index c077e52dbd..d5f6a64183 100644
--- a/src/compute_dihedral_local.h
+++ b/src/compute_dihedral_local.h
@@ -33,8 +33,12 @@ class ComputeDihedralLocal : public Compute {
double memory_usage();
private:
- int nvalues,pflag;
- int ncount;
+ int nvalues,nvar,ncount,setflag,tflag;
+
+ int pvar;
+ int *bstyle,*vvar;
+ char *pstr;
+ char **vstr;
int nmax;
double *vlocal;
--
GitLab
From 037420b611979f5fca9a1aeb360824294cb8ae64 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Tue, 4 Sep 2018 14:59:30 -0600
Subject: [PATCH 220/332] cmake: only add tests if exe is build
---
cmake/CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 0d8da8409d..d4701102f7 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -207,7 +207,7 @@ endif()
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
option(ENABLE_TESTING "Enable testing" OFF)
-if(ENABLE_TESTING)
+if(ENABLE_TESTING AND BUILD_EXE)
enable_testing()
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
@@ -252,7 +252,7 @@ if(ENABLE_TESTING)
message(STATUS "Found ${NUM_TESTS} tests.")
endif()
-endif(ENABLE_TESTING)
+endif()
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
--
GitLab
From db7c2549d064c61c6f8b6a62acea5f04aa33e470 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <christoph.junghans@gmail.com>
Date: Tue, 4 Sep 2018 17:05:59 -0600
Subject: [PATCH 221/332] cmake: inject with-pic into Scafacos
---
cmake/CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index b7bbd6e1ba..fcc547c5b1 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -416,6 +416,7 @@ if(PKG_USER-SCAFACOS)
--with-internal-fftw
--with-internal-pfft
--with-internal-pnfft
+ $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>
FC=${CMAKE_MPI_Fortran_COMPILER}
CXX=${CMAKE_MPI_CXX_COMPILER}
CC=${CMAKE_MPI_C_COMPILER}
--
GitLab
From 8608b4f93c8e66d3e518c2ba783b775d978d6034 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 4 Sep 2018 21:31:08 -0400
Subject: [PATCH 222/332] Remove extra libm in LAMMPS_LINK_LIBS
---
cmake/CMakeLists.txt | 1 -
1 file changed, 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index fcc547c5b1..e0f8d08a25 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -434,7 +434,6 @@ if(PKG_USER-SCAFACOS)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
- list(APPEND LAMMPS_LINK_LIBS m)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
--
GitLab
From a5f7b418dea73439d6cb4a56ccec4f312b582263 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 4 Sep 2018 22:06:49 -0600
Subject: [PATCH 223/332] bond/react: efficient competing reactions
---
src/USER-MISC/fix_bond_react.cpp | 25 ++++++++++++++++++-------
src/comm.h | 3 +++
src/comm_brick.cpp | 31 ++++++++++++++++++++++++++++++-
src/comm_brick.h | 2 ++
4 files changed, 53 insertions(+), 8 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 5ce1f11475..f369a9a10f 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1858,16 +1858,27 @@ if so, flag for broadcasting for perusal by all processors
void FixBondReact::glove_ghostcheck()
{
- // it appears this little loop was deemed important enough for its own function!
- // noteworthy: it's only relevant for parallel
-
// here we add glove to either local_mega_glove or ghostly_mega_glove
+ // ghostly_mega_glove includes atoms that are ghosts, either of this proc or another
+ // 'ghosts of another' indication taken from comm->sendlist
+
int ghostly = 0;
- for (int i = 0; i < onemol->natoms; i++) {
- if (atom->map(glove[i][1]) >= atom->nlocal) {
- ghostly = 1;
- break;
+ if (comm->style == 0) {
+ int tmp;
+ int *localsendlist = (int *) comm->extract("localsendlist",tmp);
+
+ // create an indexed sendlist
+ for (int i = 0; i < onemol->natoms; i++) {
+ int ilocal = atom->map(glove[i][1]);
+ if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
+ ghostly = 1;
+ break;
+ }
}
+ } else {
+ #if !defined(MPI_STUBS)
+ ghostly = 1;
+ #endif
}
if (ghostly == 1) {
diff --git a/src/comm.h b/src/comm.h
index 298f435c3d..2579f9b283 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -112,6 +112,9 @@ class Comm : protected Pointers {
int read_lines_from_file(FILE *, int, int, char *);
int read_lines_from_file_universe(FILE *, int, int, char *);
+ // extract data useful to other classes
+ virtual void *extract(const char *, int &) {return NULL;}
+
protected:
int bordergroup; // only communicate this group in borders
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 3aa6d7748c..d179475345 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -55,7 +55,8 @@ CommBrick::CommBrick(LAMMPS *lmp) :
size_reverse_send(NULL), size_reverse_recv(NULL),
slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL),
- sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
+ sendlist(NULL), localsendlist(NULL), maxsendlist(NULL),
+ buf_send(NULL), buf_recv(NULL)
{
style = 0;
layout = Comm::LAYOUT_UNIFORM;
@@ -74,6 +75,7 @@ CommBrick::~CommBrick()
}
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
+ if (localsendlist) memory->destroy(localsendlist);
memory->sfree(sendlist);
memory->destroy(maxsendlist);
@@ -1469,6 +1471,33 @@ void CommBrick::free_multi()
multilo = multihi = NULL;
}
+/* ----------------------------------------------------------------------
+ extract data potentially useful to other classes
+------------------------------------------------------------------------- */
+
+void *CommBrick::extract(const char *str, int &dim)
+{
+ if (strcmp(str,"localsendlist") == 0) {
+ int i, iswap, isend;
+ if (!localsendlist)
+ memory->create(localsendlist,atom->nlocal,"comm:localsendlist");
+ else
+ memory->grow(localsendlist,atom->nlocal,"comm:localsendlist");
+
+ for (i = 0; i < atom->nlocal; i++)
+ localsendlist[i] = 0;
+
+ for (iswap = 0; iswap < nswap; iswap++)
+ for (isend = 0; isend < sendnum[iswap]; isend++)
+ if (sendlist[iswap][isend] < atom->nlocal)
+ localsendlist[sendlist[iswap][isend]] = 1;
+
+ return (void *) localsendlist;
+ }
+
+ return NULL;
+}
+
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
diff --git a/src/comm_brick.h b/src/comm_brick.h
index 461ee84b40..b3a3a7e094 100644
--- a/src/comm_brick.h
+++ b/src/comm_brick.h
@@ -46,6 +46,7 @@ class CommBrick : public Comm {
void forward_comm_array(int, double **); // forward comm of array
int exchange_variable(int, double *, double *&); // exchange on neigh stencil
+ void *extract(const char *,int &);
virtual bigint memory_usage();
protected:
@@ -67,6 +68,7 @@ class CommBrick : public Comm {
int *firstrecv; // where to put 1st recv atom in each swap
int **sendlist; // list of atoms to send in each swap
+ int *localsendlist; // indexed list of local sendlist atoms
int *maxsendlist; // max size of send list for each swap
double *buf_send; // send buffer for all comm
--
GitLab
From ae7b18fb772c17c6df105ba7f1f76fac420e998d Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Wed, 5 Sep 2018 00:11:50 -0600
Subject: [PATCH 224/332] only one call to extract needed
---
src/USER-MISC/fix_bond_react.cpp | 8 ++++----
src/USER-MISC/fix_bond_react.h | 1 +
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 469e1d6347..a6f08a7376 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -961,6 +961,10 @@ void FixBondReact::superimpose_algorithm()
local_num_mega = 0;
ghostly_num_mega = 0;
+ // indicates local ghosts of other procs
+ int tmp;
+ localsendlist = (int *) comm->extract("localsendlist",tmp);
+
// quick description of important global indices you'll see floating about:
// 'pion' is the pioneer loop index
// 'neigh' in the first neighbor index
@@ -1863,10 +1867,6 @@ void FixBondReact::glove_ghostcheck()
int ghostly = 0;
if (comm->style == 0) {
- int tmp;
- int *localsendlist = (int *) comm->extract("localsendlist",tmp);
-
- // create an indexed sendlist
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index 8ff71141f8..08756f8131 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -122,6 +122,7 @@ class FixBondReact : public Fix {
tagint **local_mega_glove; // consolidation local of reaction instances
tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances
tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
+ int *localsendlist; // indicates ghosts of other procs
int local_num_mega; // num of local reaction instances
int ghostly_num_mega; // num of ghostly reaction instances
int global_megasize; // num of reaction instances in global_mega_glove
--
GitLab
From d3d16882ca562b51476e7037949c6fdbfc260da5 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Wed, 5 Sep 2018 08:12:19 -0600
Subject: [PATCH 225/332] remove note for Rene
---
examples/USER/scafacos/README | 10 ----------
1 file changed, 10 deletions(-)
delete mode 100644 examples/USER/scafacos/README
diff --git a/examples/USER/scafacos/README b/examples/USER/scafacos/README
deleted file mode 100644
index 0ddd19d3ee..0000000000
--- a/examples/USER/scafacos/README
+++ /dev/null
@@ -1,10 +0,0 @@
-RENE: this dir needs a few short-running examples,
-for both 1 and 4 procs, of using different Scafacos methods.
-with sample log file outputs - so users can verify
-they are running it correctly
-
-For each input script, there should be files like
-
-in.scafacos.fmm
-log.20Jul18.scafacos.fmm.g++.1
-log.20Jul18.scafacos.fmm.g++.4
--
GitLab
From 4a5e28af81ff62f33ca603fda26ebf609f3c4a2e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 5 Sep 2018 10:32:11 -0400
Subject: [PATCH 226/332] Avoid unnecessary sorting in print_columns
std::map is a sorted associative container. We don't need to
first copy it into a vector and sort that one.
print_columns has been refactored as a template function and
makes use of this property.
---
src/info.cpp | 156 ++++++++++-----------------------------------------
1 file changed, 30 insertions(+), 126 deletions(-)
diff --git a/src/info.cpp b/src/info.cpp
index 748354e878..672ce72b74 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -44,7 +44,7 @@
#include "error.h"
#include <ctime>
-#include <vector>
+#include <map>
#include <string>
#include <algorithm>
@@ -117,7 +117,8 @@ static const char bstyles[] = "pfsm";
using namespace LAMMPS_NS;
using namespace std;
-static void print_columns(FILE* fp, vector<string> & styles);
+template<typename ValueType>
+static void print_columns(FILE* fp, map<string, ValueType> * styles);
/* ---------------------------------------------------------------------- */
@@ -686,196 +687,98 @@ void Info::available_styles(FILE * out, int flags)
void Info::atom_styles(FILE * out)
{
fprintf(out, "\nAtom styles:\n");
-
- vector<string> styles;
-
- for(Atom::AtomVecCreatorMap::iterator it = atom->avec_map->begin(); it != atom->avec_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, atom->avec_map);
fprintf(out, "\n\n\n");
}
void Info::integrate_styles(FILE * out)
{
fprintf(out, "\nIntegrate styles:\n");
-
- vector<string> styles;
-
- for(Update::IntegrateCreatorMap::iterator it = update->integrate_map->begin(); it != update->integrate_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, update->integrate_map);
fprintf(out, "\n\n\n");
}
void Info::minimize_styles(FILE * out)
{
fprintf(out, "\nMinimize styles:\n");
-
- vector<string> styles;
-
- for(Update::MinimizeCreatorMap::iterator it = update->minimize_map->begin(); it != update->minimize_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, update->minimize_map);
fprintf(out, "\n\n\n");
}
void Info::pair_styles(FILE * out)
{
fprintf(out, "\nPair styles:\n");
-
- vector<string> styles;
-
- for(Force::PairCreatorMap::iterator it = force->pair_map->begin(); it != force->pair_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->pair_map);
fprintf(out, "\n\n\n");
}
void Info::bond_styles(FILE * out)
{
fprintf(out, "\nBond styles:\n");
-
- vector<string> styles;
-
- for(Force::BondCreatorMap::iterator it = force->bond_map->begin(); it != force->bond_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->bond_map);
fprintf(out, "\n\n\n");
}
void Info::angle_styles(FILE * out)
{
fprintf(out, "\nAngle styles:\n");
-
- vector<string> styles;
-
- for(Force::AngleCreatorMap::iterator it = force->angle_map->begin(); it != force->angle_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->angle_map);
fprintf(out, "\n\n\n");
}
void Info::dihedral_styles(FILE * out)
{
fprintf(out, "\nDihedral styles:\n");
-
- vector<string> styles;
-
- for(Force::DihedralCreatorMap::iterator it = force->dihedral_map->begin(); it != force->dihedral_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->dihedral_map);
fprintf(out, "\n\n\n");
}
void Info::improper_styles(FILE * out)
{
fprintf(out, "\nImproper styles:\n");
-
- vector<string> styles;
-
- for(Force::ImproperCreatorMap::iterator it = force->improper_map->begin(); it != force->improper_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->improper_map);
fprintf(out, "\n\n\n");
}
void Info::kspace_styles(FILE * out)
{
fprintf(out, "\nKSpace styles:\n");
-
- vector<string> styles;
-
- for(Force::KSpaceCreatorMap::iterator it = force->kspace_map->begin(); it != force->kspace_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, force->kspace_map);
fprintf(out, "\n\n\n");
}
void Info::fix_styles(FILE * out)
{
fprintf(out, "\nFix styles:\n");
-
- vector<string> styles;
-
- for(Modify::FixCreatorMap::iterator it = modify->fix_map->begin(); it != modify->fix_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, modify->fix_map);
fprintf(out, "\n\n\n");
}
void Info::compute_styles(FILE * out)
{
fprintf(out, "\nCompute styles:\n");
-
- vector<string> styles;
-
- for(Modify::ComputeCreatorMap::iterator it = modify->compute_map->begin(); it != modify->compute_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, modify->compute_map);
fprintf(out, "\n\n\n");
}
void Info::region_styles(FILE * out)
{
fprintf(out, "\nRegion styles:\n");
-
- vector<string> styles;
-
- for(Domain::RegionCreatorMap::iterator it = domain->region_map->begin(); it != domain->region_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, domain->region_map);
fprintf(out, "\n\n\n");
}
void Info::dump_styles(FILE * out)
{
fprintf(out, "\nDump styles:\n");
-
- vector<string> styles;
-
- for(Output::DumpCreatorMap::iterator it = output->dump_map->begin(); it != output->dump_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, output->dump_map);
fprintf(out, "\n\n\n");
}
void Info::command_styles(FILE * out)
{
fprintf(out, "\nCommand styles (add-on input script commands):\n");
-
- vector<string> styles;
-
- for(Input::CommandCreatorMap::iterator it = input->command_map->begin(); it != input->command_map->end(); ++it) {
- styles.push_back(it->first);
- }
-
- print_columns(out, styles);
+ print_columns(out, input->command_map);
fprintf(out, "\n\n\n");
}
@@ -1110,41 +1013,42 @@ bool Info::is_defined(const char *category, const char *name)
return false;
}
-static void print_columns(FILE* fp, vector<string> & styles)
+template<typename ValueType>
+static void print_columns(FILE* fp, map<string, ValueType> * styles)
{
- if (styles.size() == 0) {
+ if (styles->empty()) {
fprintf(fp, "\nNone");
return;
}
- std::sort(styles.begin(), styles.end());
-
+ // std::map keys are already sorted
int pos = 80;
- for (int i = 0; i < styles.size(); ++i) {
+ for(typename map<string, ValueType>::iterator it = styles->begin(); it != styles->end(); ++it) {
+ const string & style_name = it->first;
// skip "secret" styles
- if (isupper(styles[i][0])) continue;
+ if (isupper(style_name[0])) continue;
- int len = styles[i].length();
+ int len = style_name.length();
if (pos + len > 80) {
fprintf(fp,"\n");
pos = 0;
}
if (len < 16) {
- fprintf(fp,"%-16s",styles[i].c_str());
+ fprintf(fp,"%-16s", style_name.c_str());
pos += 16;
} else if (len < 32) {
- fprintf(fp,"%-32s",styles[i].c_str());
+ fprintf(fp,"%-32s", style_name.c_str());
pos += 32;
} else if (len < 48) {
- fprintf(fp,"%-48s",styles[i].c_str());
+ fprintf(fp,"%-48s", style_name.c_str());
pos += 48;
} else if (len < 64) {
- fprintf(fp,"%-64s",styles[i].c_str());
+ fprintf(fp,"%-64s", style_name.c_str());
pos += 64;
} else {
- fprintf(fp,"%-80s",styles[i].c_str());
+ fprintf(fp,"%-80s", style_name.c_str());
pos += 80;
}
}
--
GitLab
From 0c92c22755c8b101022e7f5907ff10bacee3076d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 5 Sep 2018 10:56:12 -0400
Subject: [PATCH 227/332] moved contents of USER-MOP package to USER-MISC as
suggested by @sjplimp
---
cmake/CMakeLists.txt | 2 +-
doc/src/Packages_details.txt | 24 -------------
doc/src/Packages_user.txt | 1 -
doc/src/compute_stress_mop.txt | 4 +--
.../USER/{ => misc}/mop/in.compute_stress_mop | 0
.../USER/{ => misc}/mop/moppz.time.reference | 0
.../USER/{ => misc}/mop/mopz0.time.reference | 0
.../USER/{ => misc}/mop/profile.z.reference | 0
src/Makefile | 2 +-
src/USER-MISC/README | 2 ++
.../compute_stress_mop.cpp | 0
.../compute_stress_mop.h | 0
.../compute_stress_mop_profile.cpp | 0
.../compute_stress_mop_profile.h | 0
src/USER-MOP/README | 35 -------------------
15 files changed, 6 insertions(+), 64 deletions(-)
rename examples/USER/{ => misc}/mop/in.compute_stress_mop (100%)
rename examples/USER/{ => misc}/mop/moppz.time.reference (100%)
rename examples/USER/{ => misc}/mop/mopz0.time.reference (100%)
rename examples/USER/{ => misc}/mop/profile.z.reference (100%)
rename src/{USER-MOP => USER-MISC}/compute_stress_mop.cpp (100%)
rename src/{USER-MOP => USER-MISC}/compute_stress_mop.h (100%)
rename src/{USER-MOP => USER-MISC}/compute_stress_mop_profile.cpp (100%)
rename src/{USER-MOP => USER-MISC}/compute_stress_mop_profile.h (100%)
delete mode 100644 src/USER-MOP/README
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 190ef3b2e0..eecdc6d132 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -215,7 +215,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
- USER-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
+ USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 36071064c0..381dc2e995 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -84,7 +84,6 @@ as contained in the file name.
"USER-MGPT"_#PKG-USER-MGPT,
"USER-MISC"_#PKG-USER-MISC,
"USER-MOFFF"_#PKG-USER-MOFFF,
-"USER-MOP"_#PKG-USER-MOP,
"USER-MOLFILE"_#PKG-USER-MOLFILE,
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
@@ -1573,29 +1572,6 @@ examples/USER/mofff :ul
:line
-USER-MOP package :link(PKG-USER-MOP),h4
-
-[Contents:]
-
-This package contains two compute styles: compute stress/mop and compute stress/mop/profile.
-
-compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
-
-compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
-
-[Author:] Laurent Joly (University of Lyon 1)
-Romain Vermorel at (University of Pau and Pays de l'Adour)
-
-[Supporting info:]
-
-src/USER-MOP: filenames -> commands
-src/USER-MOP/README
-"compute stress/mop"_compute_stress_mop.html
-"compute stress/mop/profile"_compute_stress_mop.html
-examples/USER/mop :ul
-
-:line
-
USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 5b9b8734b3..7db2fa895c 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -57,7 +57,6 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
-"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt
index 8d95ef42e2..1006463179 100644
--- a/doc/src/compute_stress_mop.txt
+++ b/doc/src/compute_stress_mop.txt
@@ -86,8 +86,8 @@ The values produced by this compute can be accessed by various "output commands"
[Restrictions:]
-This style is part of the USER-MOP package. It is only enabled if LAMMPS
-is built with that package. See the "Build package"_Build_package.html
+These styles are part of the USER-MISC package. They are only enabled if
+LAMMPS is built with that package. See the "Build package"_Build_package.html
doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
diff --git a/examples/USER/mop/in.compute_stress_mop b/examples/USER/misc/mop/in.compute_stress_mop
similarity index 100%
rename from examples/USER/mop/in.compute_stress_mop
rename to examples/USER/misc/mop/in.compute_stress_mop
diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/misc/mop/moppz.time.reference
similarity index 100%
rename from examples/USER/mop/moppz.time.reference
rename to examples/USER/misc/mop/moppz.time.reference
diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/misc/mop/mopz0.time.reference
similarity index 100%
rename from examples/USER/mop/mopz0.time.reference
rename to examples/USER/misc/mop/mopz0.time.reference
diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/misc/mop/profile.z.reference
similarity index 100%
rename from examples/USER/mop/profile.z.reference
rename to examples/USER/misc/mop/profile.z.reference
diff --git a/src/Makefile b/src/Makefile
index 6b1a2bdb98..948d203cfe 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
- user-mgpt user-misc user-mop user-mofff user-molfile \
+ user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 0f9e7bf383..eb221c07db 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -30,6 +30,8 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
+compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
+compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
diff --git a/src/USER-MOP/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp
similarity index 100%
rename from src/USER-MOP/compute_stress_mop.cpp
rename to src/USER-MISC/compute_stress_mop.cpp
diff --git a/src/USER-MOP/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h
similarity index 100%
rename from src/USER-MOP/compute_stress_mop.h
rename to src/USER-MISC/compute_stress_mop.h
diff --git a/src/USER-MOP/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp
similarity index 100%
rename from src/USER-MOP/compute_stress_mop_profile.cpp
rename to src/USER-MISC/compute_stress_mop_profile.cpp
diff --git a/src/USER-MOP/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h
similarity index 100%
rename from src/USER-MOP/compute_stress_mop_profile.h
rename to src/USER-MISC/compute_stress_mop_profile.h
diff --git a/src/USER-MOP/README b/src/USER-MOP/README
deleted file mode 100644
index 15fcb3701a..0000000000
--- a/src/USER-MOP/README
+++ /dev/null
@@ -1,35 +0,0 @@
-USER-MOP
-============
-
-This package provides the stress/mop and stress/mop/profile compute styles.
-See the doc page for compute stress/mop or compute stress/mop/profile command for how to use
-them.
-
-PACKAGE DESCRIPTION
--------------------
-
-These are LAMMPS (http://lammps.sandia.gov/) compute styles that calculate
-components of the local stress tensor using the method of planes as described in
-the paper by Todd et al. (B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure
-tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995)).
-
-This package contains the source files of two compute styles:
-* compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
-* compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
-
-The persons who created these files are Laurent Joly at University of Lyon 1 and Romain Vermorel at University of Pau and Pays de l'Adour.
-Contact them directly if you have questions.
-
-Laurent Joly
-Institut Lumière Matière
-Université Lyon 1 et CNRS
-43 boulevard du 11 novembre 1918
-69622 Villeurbanne Cedex
-e-mail: laurent.joly@univ-lyon1.fr
-
-Romain Vermorel
-Laboratory of Complex Fluids and their Reservoirs (LFCR)
-Université de Pau et des Pays de l'Adour
-Avenue de l'Université
-64012 Pau
-e-mail: romain.vermorel@univ-pau.fr
--
GitLab
From 779f1bd0b1c45d622982759c578446694b8e2872 Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Wed, 5 Sep 2018 11:27:10 -0400
Subject: [PATCH 228/332] Fixes a bug in pair_morse_smooth_linear where the
cutoff was not properly initialized.
---
cmake/CMakeLists.txt | 84 +-
cmake/FindLAMMPS.cmake.in | 48 +
cmake/Modules/FindZMQ.cmake | 8 +
cmake/pkgconfig/liblammps.pc.in | 6 +-
doc/src/Build_extras.txt | 34 +
doc/src/Build_package.txt | 1 +
doc/src/Commands_all.txt | 2 +
doc/src/Howto.txt | 4 +-
doc/src/Howto_client_server.txt | 131 +
doc/src/Howto_couple.txt | 14 +-
doc/src/Manual.txt | 4 +-
doc/src/Packages_details.txt | 29 +-
doc/src/Packages_standard.txt | 1 +
doc/src/Run_options.txt | 25 +
doc/src/commands_list.txt | 2 +
doc/src/fix_client_md.txt | 106 +
doc/src/lammps.book | 5 +
doc/src/message.txt | 162 +
doc/src/server.txt | 71 +
doc/src/server_mc.txt | 116 +
doc/src/server_md.txt | 147 +
examples/COUPLE/README | 5 +
examples/COUPLE/lammps_mc/Makefile | 33 +
examples/COUPLE/lammps_mc/README | 128 +
examples/COUPLE/lammps_mc/in.mc | 7 +
examples/COUPLE/lammps_mc/in.mc.server | 36 +
.../COUPLE/lammps_mc/log.28Aug18.file.g++.1 | 254 +
.../COUPLE/lammps_mc/log.28Aug18.file.g++.4 | 254 +
.../COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 | 254 +
.../COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 | 254 +
examples/COUPLE/lammps_mc/mc.cpp | 263 +
examples/COUPLE/lammps_mc/mc.h | 40 +
examples/COUPLE/lammps_mc/random_park.cpp | 72 +
examples/COUPLE/lammps_mc/random_park.h | 28 +
examples/COUPLE/lammps_vasp/INCAR | 53 +
examples/COUPLE/lammps_vasp/KPOINTS | 6 +
examples/COUPLE/lammps_vasp/POSCAR_W | 11 +
examples/COUPLE/lammps_vasp/README | 149 +
examples/COUPLE/lammps_vasp/data.W | 15 +
examples/COUPLE/lammps_vasp/in.client.W | 34 +
examples/COUPLE/lammps_vasp/log.client.output | 76 +
examples/COUPLE/lammps_vasp/vasp_wrap.py | 300 +
examples/COUPLE/lammps_vasp/vasprun.xml | 12329 ++++++++++++++++
examples/README | 1 +
examples/USER/diffraction/BulkNi.in | 5 +-
examples/USER/diffraction/Output/BulkNi.in | 35 -
examples/message/README | 117 +
examples/message/Script.sh | 55 +
examples/message/in.message | 29 +
examples/message/in.message.client | 41 +
examples/message/in.message.server | 29 +
examples/message/in.message.tilt | 30 +
examples/message/in.message.tilt.client | 42 +
examples/message/in.message.tilt.server | 31 +
.../log.28Aug18.message.client.file.g++.1 | 79 +
.../log.28Aug18.message.client.file.g++.2 | 79 +
.../log.28Aug18.message.client.mpione.g++.1 | 79 +
.../log.28Aug18.message.client.mpione.g++.2 | 79 +
.../log.28Aug18.message.client.mpitwo.g++.1 | 79 +
.../log.28Aug18.message.client.mpitwo.g++.2 | 79 +
.../log.28Aug18.message.client.zmq.g++.1 | 79 +
.../log.28Aug18.message.client.zmq.g++.2 | 79 +
examples/message/log.28Aug18.message.g++.1 | 85 +
examples/message/log.28Aug18.message.g++.4 | 85 +
.../log.28Aug18.message.server.file.g++.1 | 44 +
.../log.28Aug18.message.server.file.g++.4 | 44 +
.../log.28Aug18.message.server.mpione.g++.1 | 44 +
.../log.28Aug18.message.server.mpione.g++.4 | 44 +
.../log.28Aug18.message.server.mpitwo.g++.1 | 44 +
.../log.28Aug18.message.server.mpitwo.g++.4 | 44 +
.../log.28Aug18.message.server.zmq.g++.1 | 44 +
.../log.28Aug18.message.server.zmq.g++.4 | 44 +
...g.28Aug18.message.tilt.client.mpione.g++.1 | 130 +
...g.28Aug18.message.tilt.client.mpione.g++.2 | 130 +
...g.28Aug18.message.tilt.client.mpitwo.g++.1 | 130 +
...g.28Aug18.message.tilt.client.mpitwo.g++.2 | 130 +
.../log.28Aug18.message.tilt.client.zmq.g++.1 | 130 +
.../log.28Aug18.message.tilt.client.zmq.g++.2 | 130 +
.../message/log.28Aug18.message.tilt.g++.1 | 129 +
.../message/log.28Aug18.message.tilt.g++.4 | 129 +
...g.28Aug18.message.tilt.server.mpione.g++.1 | 48 +
...g.28Aug18.message.tilt.server.mpione.g++.4 | 48 +
...g.28Aug18.message.tilt.server.mpitwo.g++.1 | 48 +
...g.28Aug18.message.tilt.server.mpitwo.g++.4 | 48 +
.../log.28Aug18.message.tilt.server.zmq.g++.1 | 48 +
.../log.28Aug18.message.tilt.server.zmq.g++.4 | 48 +
lib/README | 2 +
lib/message/Install.py | 118 +
lib/message/Makefile.lammps.nozmq | 5 +
lib/message/Makefile.lammps.zmq | 5 +
lib/message/README | 51 +
lib/message/cslib/LICENSE | 32 +
lib/message/cslib/README | 23 +
lib/message/cslib/src/Makefile | 107 +
lib/message/cslib/src/STUBS_MPI/mpi.h | 96 +
lib/message/cslib/src/STUBS_ZMQ/zmq.h | 36 +
lib/message/cslib/src/cslib.cpp | 768 +
lib/message/cslib/src/cslib.h | 87 +
lib/message/cslib/src/cslib.py | 362 +
lib/message/cslib/src/cslib_wrap.cpp | 239 +
lib/message/cslib/src/cslib_wrap.f90 | 147 +
lib/message/cslib/src/cslib_wrap.h | 54 +
lib/message/cslib/src/msg.cpp | 110 +
lib/message/cslib/src/msg.h | 52 +
lib/message/cslib/src/msg_file.cpp | 143 +
lib/message/cslib/src/msg_file.h | 40 +
lib/message/cslib/src/msg_mpi_one.cpp | 82 +
lib/message/cslib/src/msg_mpi_one.h | 38 +
lib/message/cslib/src/msg_mpi_two.cpp | 81 +
lib/message/cslib/src/msg_mpi_two.h | 35 +
lib/message/cslib/src/msg_zmq.cpp | 140 +
lib/message/cslib/src/msg_zmq.h | 38 +
src/MESSAGE/Install.sh | 67 +
src/MESSAGE/fix_client_md.cpp | 325 +
src/MESSAGE/fix_client_md.h | 65 +
src/MESSAGE/message.cpp | 90 +
src/MESSAGE/message.h | 40 +
src/MESSAGE/server.cpp | 50 +
src/MESSAGE/server.h | 40 +
src/MESSAGE/server_mc.cpp | 148 +
src/MESSAGE/server_mc.h | 29 +
src/MESSAGE/server_md.cpp | 389 +
src/MESSAGE/server_md.h | 38 +
src/Makefile | 6 +-
src/USER-MISC/pair_morse_smooth_linear.cpp | 17 +-
src/atom.cpp | 3 +-
src/domain.cpp | 13 +-
src/domain.h | 5 +-
src/fix_tmd.cpp | 2 +-
src/lammps.cpp | 225 +-
src/lammps.h | 4 +
src/library.cpp | 3 +-
src/version.h | 2 +-
133 files changed, 22779 insertions(+), 169 deletions(-)
create mode 100644 cmake/FindLAMMPS.cmake.in
create mode 100644 cmake/Modules/FindZMQ.cmake
create mode 100644 doc/src/Howto_client_server.txt
create mode 100644 doc/src/fix_client_md.txt
create mode 100644 doc/src/message.txt
create mode 100644 doc/src/server.txt
create mode 100644 doc/src/server_mc.txt
create mode 100644 doc/src/server_md.txt
create mode 100644 examples/COUPLE/lammps_mc/Makefile
create mode 100644 examples/COUPLE/lammps_mc/README
create mode 100644 examples/COUPLE/lammps_mc/in.mc
create mode 100644 examples/COUPLE/lammps_mc/in.mc.server
create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
create mode 100644 examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
create mode 100644 examples/COUPLE/lammps_mc/mc.cpp
create mode 100644 examples/COUPLE/lammps_mc/mc.h
create mode 100644 examples/COUPLE/lammps_mc/random_park.cpp
create mode 100644 examples/COUPLE/lammps_mc/random_park.h
create mode 100644 examples/COUPLE/lammps_vasp/INCAR
create mode 100644 examples/COUPLE/lammps_vasp/KPOINTS
create mode 100644 examples/COUPLE/lammps_vasp/POSCAR_W
create mode 100644 examples/COUPLE/lammps_vasp/README
create mode 100644 examples/COUPLE/lammps_vasp/data.W
create mode 100644 examples/COUPLE/lammps_vasp/in.client.W
create mode 100644 examples/COUPLE/lammps_vasp/log.client.output
create mode 100644 examples/COUPLE/lammps_vasp/vasp_wrap.py
create mode 100644 examples/COUPLE/lammps_vasp/vasprun.xml
delete mode 100644 examples/USER/diffraction/Output/BulkNi.in
create mode 100644 examples/message/README
create mode 100644 examples/message/Script.sh
create mode 100644 examples/message/in.message
create mode 100644 examples/message/in.message.client
create mode 100644 examples/message/in.message.server
create mode 100644 examples/message/in.message.tilt
create mode 100644 examples/message/in.message.tilt.client
create mode 100644 examples/message/in.message.tilt.server
create mode 100644 examples/message/log.28Aug18.message.client.file.g++.1
create mode 100644 examples/message/log.28Aug18.message.client.file.g++.2
create mode 100644 examples/message/log.28Aug18.message.client.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.client.mpione.g++.2
create mode 100644 examples/message/log.28Aug18.message.client.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.client.mpitwo.g++.2
create mode 100644 examples/message/log.28Aug18.message.client.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.client.zmq.g++.2
create mode 100644 examples/message/log.28Aug18.message.g++.1
create mode 100644 examples/message/log.28Aug18.message.g++.4
create mode 100644 examples/message/log.28Aug18.message.server.file.g++.1
create mode 100644 examples/message/log.28Aug18.message.server.file.g++.4
create mode 100644 examples/message/log.28Aug18.message.server.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.server.mpione.g++.4
create mode 100644 examples/message/log.28Aug18.message.server.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.server.mpitwo.g++.4
create mode 100644 examples/message/log.28Aug18.message.server.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.server.zmq.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
create mode 100644 examples/message/log.28Aug18.message.tilt.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
create mode 100644 examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
create mode 100644 lib/message/Install.py
create mode 100644 lib/message/Makefile.lammps.nozmq
create mode 100644 lib/message/Makefile.lammps.zmq
create mode 100644 lib/message/README
create mode 100644 lib/message/cslib/LICENSE
create mode 100644 lib/message/cslib/README
create mode 100644 lib/message/cslib/src/Makefile
create mode 100644 lib/message/cslib/src/STUBS_MPI/mpi.h
create mode 100644 lib/message/cslib/src/STUBS_ZMQ/zmq.h
create mode 100644 lib/message/cslib/src/cslib.cpp
create mode 100644 lib/message/cslib/src/cslib.h
create mode 100644 lib/message/cslib/src/cslib.py
create mode 100644 lib/message/cslib/src/cslib_wrap.cpp
create mode 100644 lib/message/cslib/src/cslib_wrap.f90
create mode 100644 lib/message/cslib/src/cslib_wrap.h
create mode 100644 lib/message/cslib/src/msg.cpp
create mode 100644 lib/message/cslib/src/msg.h
create mode 100644 lib/message/cslib/src/msg_file.cpp
create mode 100644 lib/message/cslib/src/msg_file.h
create mode 100644 lib/message/cslib/src/msg_mpi_one.cpp
create mode 100644 lib/message/cslib/src/msg_mpi_one.h
create mode 100644 lib/message/cslib/src/msg_mpi_two.cpp
create mode 100644 lib/message/cslib/src/msg_mpi_two.h
create mode 100644 lib/message/cslib/src/msg_zmq.cpp
create mode 100644 lib/message/cslib/src/msg_zmq.h
create mode 100644 src/MESSAGE/Install.sh
create mode 100644 src/MESSAGE/fix_client_md.cpp
create mode 100644 src/MESSAGE/fix_client_md.h
create mode 100644 src/MESSAGE/message.cpp
create mode 100644 src/MESSAGE/message.h
create mode 100644 src/MESSAGE/server.cpp
create mode 100644 src/MESSAGE/server.h
create mode 100644 src/MESSAGE/server_mc.cpp
create mode 100644 src/MESSAGE/server_mc.h
create mode 100644 src/MESSAGE/server_md.cpp
create mode 100644 src/MESSAGE/server_md.h
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 3ef3e8d7f4..0d4bab29f1 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -43,6 +43,29 @@ function(validate_option name values)
endif()
endfunction(validate_option)
+function(get_lammps_version version_header variable)
+ file(READ ${version_header} line)
+ set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+ string(STRIP ${day} day)
+ string(STRIP ${month} month)
+ string(STRIP ${year} year)
+ list(FIND MONTHS "${month}" month)
+ string(LENGTH ${day} day_length)
+ string(LENGTH ${month} month_length)
+ if(day_length EQUAL 1)
+ set(day "0${day}")
+ endif()
+ if(month_length EQUAL 1)
+ set(month "0${month}")
+ endif()
+ set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
+
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
@@ -121,10 +144,10 @@ if(BUILD_LIB)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
- set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
- mark_as_advanced(LIB_SUFFIX)
- if(LIB_SUFFIX)
- set(LIB_SUFFIX "_${LIB_SUFFIX}")
+ set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
+ mark_as_advanced(LAMMPS_LIB_SUFFIX)
+ if(LAMMPS_LIB_SUFFIX)
+ set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
endif()
endif()
@@ -188,7 +211,7 @@ if(ENABLE_TESTING)
endif(ENABLE_TESTING)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
+ KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
@@ -481,6 +504,39 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
+if(PKG_MESSAGE)
+ option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+
+ if(BUILD_SHARED_LIBS)
+ add_library(cslib SHARED ${cslib_SOURCES})
+ else()
+ add_library(cslib STATIC ${cslib_SOURCES})
+ endif()
+
+ if(BUILD_MPI)
+ target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+ else()
+ target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+ endif()
+
+ if(MESSAGE_ZMQ)
+ target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+ find_package(ZMQ REQUIRED)
+ target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+ target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+ else()
+ target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+ target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ endif()
+
+ list(APPEND LAMMPS_LINK_LIBS cslib)
+ include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()
+
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
@@ -1040,14 +1096,14 @@ if(BUILD_LIB)
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
- set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
- if(BUILD_SHARED_LIBS)
- set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
- install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
- configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
- endif()
+ set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
+ set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+ install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+ configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
@@ -1177,7 +1233,7 @@ endif()
###############################################################################
# Print package summary
###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
new file mode 100644
index 0000000000..586df83c2d
--- /dev/null
+++ b/cmake/FindLAMMPS.cmake.in
@@ -0,0 +1,48 @@
+# - Find liblammps
+# Find the native liblammps headers and libraries.
+#
+# The following variables will set:
+# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
+# LAMMPS_LIBRARIES - List of libraries when using lammps.
+# LAMMPS_API_DEFINES - lammps library api defines
+# LAMMPS_VERSION - lammps library version
+# LAMMPS_FOUND - True if liblammps found.
+#
+# In addition a LAMMPS::LAMMPS imported target is getting created.
+#
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright (2003) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software. This software is distributed under
+# the GNU General Public License.
+#
+# See the README file in the top-level LAMMPS directory.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
+find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
+
+set(LAMMPS_VERSION @LAMMPS_VERSION@)
+set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
+
+find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+
+set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
+set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
+
+mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
+
+if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
+ add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
+ set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
+endif()
diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake
new file mode 100644
index 0000000000..608ccda777
--- /dev/null
+++ b/cmake/Modules/FindZMQ.cmake
@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index 400b7593cf..7850972f3b 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -4,15 +4,15 @@
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
Requires:
-Libs: -L${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 088ffd8972..1e3744b7fb 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -31,6 +31,7 @@ This is the list of packages that may require additional steps.
"KOKKOS"_#kokkos,
"LATTE"_#latte,
"MEAM"_#meam,
+"MESSAGE"_#message,
"MSCG"_#mscg,
"OPT"_#opt,
"POEMS"_#poems,
@@ -361,6 +362,10 @@ make lib-meam args="-m mpi" # build with default Fortran compiler compatible
make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
+NOTE: You should test building the MEAM library with both the Intel
+and GNU compilers to see if a simulation runs faster with one versus
+the other on your system.
+
The build should produce two files: lib/meam/libmeam.a and
lib/meam/Makefile.lammps. The latter is copied from an existing
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
@@ -373,6 +378,35 @@ file.
:line
+MESSAGE package :h4,link(message)
+
+This package can optionally include support for messaging via sockets,
+using the open-source "ZeroMQ library"_http://zeromq.org, which must
+be installed on your system.
+
+[CMake build]:
+
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the CSlib library in
+lib/message. You can build the CSlib library manually if you prefer;
+follow the instructions in lib/message/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/message/Install.py script with the specified args:
+
+make lib-message # print help message
+make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
+make lib-message args="-s" # build as serial lib with no ZMQ support
+
+The build should produce two files: lib/message/cslib/src/libmessage.a
+and lib/message/Makefile.lammps. The latter is copied from an
+existing Makefile.lammps.* and has settings to link with the ZeroMQ
+library if requested in the build.
+
+:line
+
MSCG package :h4,link(mscg)
To build with this package, you must download and build the MS-CG
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 4f71e9eb18..aaa340f302 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -42,6 +42,7 @@ packages:
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MEAM"_Build_extras.html#meam,
+"MESSAGE"_#Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index aec5a9db8b..6f54681342 100644
--- a/doc/src/Commands_all.txt
+++ b/doc/src/Commands_all.txt
@@ -71,6 +71,7 @@ An alphabetic list of all LAMMPS commands.
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
+"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
@@ -103,6 +104,7 @@ An alphabetic list of all LAMMPS commands.
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
+"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index 438ea561a1..730b492699 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -54,6 +54,7 @@ General howto :h3
Howto_replica
Howto_library
Howto_couple
+ Howto_client_server
END_RST -->
@@ -64,7 +65,8 @@ END_RST -->
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
-"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+"Couple LAMMPS to other codes"_Howto_couple.html
+"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
new file mode 100644
index 0000000000..714c23f066
--- /dev/null
+++ b/doc/src/Howto_client_server.txt
@@ -0,0 +1,131 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Using LAMMPS in client/server mode
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages to a "server" code. The server responds to
+each request with a reply message. This enables the two codes to work
+in tandem to perform a simulation. LAMMPS can act as either a client
+or server code.
+
+Some advantages of client/server coupling are that the two codes run
+as stand-alone executables; they are not linked together. Thus
+neither code needs to have a library interface. This often makes it
+easier to run the two codes on different numbers of processors. If a
+message protocol (format and content) is defined for a particular kind
+of simulation, then in principle any code that implements the
+client-side protocol can be used in tandem with any code that
+implements the server-side protocol, without the two codes needing to
+know anything more specific about each other.
+
+A simple example of client/server coupling is where LAMMPS is the
+client code performing MD timestepping. Each timestep it sends a
+message to a server quantum code containing current coords of all the
+atoms. The quantum code computes energy and forces based on the
+coords. It returns them as a message to LAMMPS, which completes the
+timestep.
+
+Alternate methods for code coupling with LAMMPS are described on
+the "Howto couple"_Howto_couple.html doc page.
+
+LAMMPS support for client/server coupling is in its "MESSAGE
+package"_Packages_details.html#PKG-MESSAGE which implements several
+commands that enable LAMMPS to act as a client or server, as discussed
+below. The MESSAGE package also wraps a client/server library called
+CSlib which enables two codes to exchange messages in different ways,
+either via files, sockets, or MPI. The CSlib is provided with LAMMPS
+in the lib/message dir. The CSlib has its own
+"website"_http://cslib.sandia.gov with documentation and test
+programs.
+
+NOTE: For client/server coupling to work between LAMMPS and another
+code, the other code also has to use the CSlib. This can sometimes be
+done without any modifications to the other code by simply wrapping it
+with a Python script that exchanges CSlib messages with LAMMPS and
+prepares input for or processes output from the other code. The other
+code also has to implement a matching protocol for the format and
+content of messages that LAMMPS exchanges with it.
+
+These are the commands currently in the MESSAGE package for two
+protocols, MD and MC (Monte Carlo). New protocols can easily be
+defined and added to this directory, where LAMMPS acts as either the
+client or server.
+
+"message"_message.html
+"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
+"server md"_server_md.html = LAMMPS is a server for computing MD forces
+"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
+
+The server doc files give details of the message protocols
+for data that is exchanged bewteen the client and server.
+
+These example directories illustrate how to use LAMMPS as either a
+client or server code:
+
+examples/message
+examples/COUPLE/README
+examples/COUPLE/lammps_mc
+examples/COUPLE/lammps_vasp :ul
+
+The examples/message dir couples a client instance of LAMMPS to a
+server instance of LAMMPS.
+
+The lammps_mc dir shows how to couple LAMMPS as a server to a simple
+Monte Carlo client code as the driver.
+
+The lammps_vasp dir shows how to couple LAMMPS as a client code
+running MD timestepping to VASP acting as a server providing quantum
+DFT forces, thru a Python wrapper script on VASP.
+
+Here is how to launch a client and server code together for any of the
+4 modes of message exchange that the "message"_message.html command
+and the CSlib support. Here LAMMPS is used as both the client and
+server code. Another code could be subsitituted for either.
+
+The examples below show launching both codes from the same window (or
+batch script), using the "&" character to launch the first code in the
+background. For all modes except {mpi/one}, you could also launch the
+codes in separate windows on your desktop machine. It does not
+matter whether you launch the client or server first.
+
+In these examples either code can be run on one or more processors.
+If running in a non-MPI mode (file or zmq) you can launch a code on a
+single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch both codes via
+mpirun, even if one or both of them runs on a single processor. This
+is so that MPI can figure out how to connect both MPI processes
+together to exchange MPI messages between them.
+
+For message exchange in {file}, {zmq}, or {mpi/two} modes:
+
+% mpirun -np 1 lmp_mpi -log log.client < in.client &
+% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 4 lmp_mpi -log log.client < in.client &
+% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 2 lmp_mpi -log log.client < in.client &
+% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
+
+For message exchange in {mpi/one} mode:
+
+Launch both codes in a single mpirun command:
+
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as their its option, where color is an integer
+label that will be used to distinguish one executable from another in
+the multiple executables that the mpirun command launches. In this
+example the client was colored with a 0, and the server with a 1.
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index d7b4924d8c..0214db1ece 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
-LAMMPS can be coupled to other codes in at least 3 ways. Each has
+LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
+:line
+
(1) Define a new "fix"_fix.html command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
@@ -32,6 +34,8 @@ LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
+:line
+
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
@@ -52,6 +56,8 @@ command writes and reads.
See the "Modify command"_Modify_command.html doc page for info on how
to add a new command to LAMMPS.
+:line
+
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
@@ -102,3 +108,9 @@ on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
+
+:line
+
+(4) Couple LAMMPS with another code in a client/server mode. This is
+described on the "Howto client/server"_Howto_client_server.html doc
+page.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ad3e66a4b2..e442aa1808 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Aug 2018 version">
+<META NAME="docnumber" CONTENT="31 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-22 Aug 2018 version :c,h2
+31 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 381dc2e995..a4ed1e3ff4 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -549,10 +549,6 @@ This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
extras"_Build_extras.html doc page.
-NOTE: You should test building the MEAM library with both the Intel
-and GNU compilers to see if a simulation runs faster with one versus
-the other on your system.
-
[Supporting info:]
src/MEAM: filenames -> commands
@@ -563,6 +559,31 @@ examples/meam :ul
:line
+MESSAGE package :link(PKG-MESSAGE),h4
+
+[Contents:]
+
+Commands to use LAMMPS as either a client or server and couple it to
+another application.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#message on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/MESSAGE: filenames -> commands
+lib/message/README
+"message"_message.html
+"fix client/md"_fix_client_md.html
+"server md"_server_md.html
+"server mc"_server_mc.html
+examples/message :ul
+
+:line
+
MISC package :link(PKG-MISC),h4
[Contents:]
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 2feb4e142d..583ecf39fe 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index 9c862d7b8e..27f436ed55 100644
--- a/doc/src/Run_options.txt
+++ b/doc/src/Run_options.txt
@@ -18,6 +18,7 @@ letter abbreviation can be used:
"-i or -in"_#file
"-k or -kokkos"_#run-kokkos
"-l or -log"_#log
+"-m or -mpicolor"_#mpicolor
"-nc or -nocite"_#nocite
"-pk or -package"_#package
"-p or -partition"_#partition
@@ -175,6 +176,30 @@ Option -plog will override the name of the partition log files file.N.
:line
+[-mpicolor] color :link(mpi)
+
+If used, this must be the first command-line argument after the LAMMPS
+executable name. It is only used when LAMMPS is launched by an mpirun
+command which also launches another executable(s) at the same time.
+(The other executable could be LAMMPS as well.) The color is an
+integer value which should be different for each executable (another
+application may set this value in a different way). LAMMPS and the
+other executable(s) perform an MPI_Comm_split() with their own colors
+to shrink the MPI_COMM_WORLD communication to be the subset of
+processors they are actually running on.
+
+Currently, this is only used in LAMMPS to perform client/server
+messaging with another application. LAMMPS can act as either a client
+or server (or both). More details are given on the "Howto
+client/server"_Howto_client_server.html doc page.
+
+Specifically, this refers to the "mpi/one" mode of messaging provided
+by the "message"_message.html command and the CSlib library LAMMPS
+links with from the lib/message directory. See the
+"message"_message.html command for more details.
+
+:line
+
[-nocite] :link(nocite)
Disable writing the log.cite file which is normally written to list
diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt
index 62b973e3a4..8fae57a718 100644
--- a/doc/src/commands_list.txt
+++ b/doc/src/commands_list.txt
@@ -56,6 +56,7 @@ Commands :h1
lattice
log
mass
+ message
min_modify
min_style
minimize
@@ -87,6 +88,7 @@ Commands :h1
restart
run
run_style
+ server
set
shell
special_bonds
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
new file mode 100644
index 0000000000..5b62d5617d
--- /dev/null
+++ b/doc/src/fix_client_md.txt
@@ -0,0 +1,106 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix client/md command :h3
+
+[Syntax:]
+
+fix ID group-ID client/md :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+client/md = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all client/md :pre
+
+[Description:]
+
+This fix style enables LAMMPS to run as a "client" code and
+communicate each timestep with a separate "server" code to perform an
+MD simulation together.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When using this fix, LAMMPS (as the client code) passes the current
+coordinates of all particles to the server code each timestep, which
+computes their interaction, and returns the energy, forces, and virial
+for the interacting particles to LAMMPS, so it can complete the
+timestep.
+
+The server code could be a quantum code, or another classical MD code
+which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
+does not have. In the quantum case, this fix is a mechanism for
+running {ab initio} MD with quantum forces.
+
+The group associated with this fix is ignored.
+
+The protocol and "units"_units.html for message format and content
+that LAMMPS exchanges with the server code is defined on the "server
+md"_server_md.html doc page.
+
+Note that when using LAMMPS as an MD client, your LAMMPS input script
+should not normally contain force field commands, like a
+"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
+"kspace_style"_kspace_style.html commmand. However it is possible for
+a server code to only compute a portion of the full force-field, while
+LAMMPS computes the remaining part. Your LAMMPS script can also
+specify boundary conditions or force constraints in the usual way,
+which will be added to the per-atom forces returned by the server
+code.
+
+See the examples/message dir for example scripts where LAMMPS is both
+the "client" and/or "server" code for this kind of client/server MD
+simulation. The examples/message/README file explains how to launch
+LAMMPS and another code in tandem to perform a coupled simulation.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential energy computed by the server application to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the server application's contribution to the system's
+virial as part of "thermodynamic output"_thermo_style.html. The
+default is {virial yes}
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the MESSAGE package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other server code.
+
+[Related commands:]
+
+"message"_message.html, "server"_server.html
+
+[Default:] none
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c296ff4039..72a07945e7 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -167,6 +167,7 @@ label.html
lattice.html
log.html
mass.html
+message.html
min_modify.html
min_style.html
minimize.html
@@ -194,6 +195,9 @@ reset_timestep.html
restart.html
run.html
run_style.html
+server.html
+server_mc.html
+server_md.html
set.html
shell.html
special_bonds.html
@@ -241,6 +245,7 @@ fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
+fix_client_md.html
fix_cmap.html
fix_colvars.html
fix_controller.html
diff --git a/doc/src/message.txt b/doc/src/message.txt
new file mode 100644
index 0000000000..cca1a5b369
--- /dev/null
+++ b/doc/src/message.txt
@@ -0,0 +1,162 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Command_all.html)
+
+:line
+
+message command :h3
+
+[Syntax:]
+
+message which protocol mode arg :pre
+
+which = {client} or {server} :ulb,l
+protocol = {md} or {mc} :l
+mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
+ {file} arg = filename
+ filename = file used for message exchanges
+ {zmq} arg = socket-ID
+ socket-ID for client = localhost:5555, see description below
+ socket-ID for server = *:5555, see description below
+ {mpi/one} arg = none
+ {mpi/two} arg = filename
+ filename = file used to establish communication bewteen 2 MPI jobs :pre
+:ule
+
+[Examples:]
+
+message client md file tmp.couple
+message server md file tmp.couple :pre
+
+message client md zmq localhost:5555
+message server md zmq *:5555 :pre
+
+message client md mpi/one
+message server md mpi/one :pre
+
+message client md mpi/two tmp.couple
+message server md mpi/two tmp.couple :pre
+
+[Description:]
+
+Establish a messaging protocol between LAMMPS and another code for the
+purpose of client/server coupling.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+:line
+
+The {which} argument defines LAMMPS to be the client or the server.
+
+:line
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+md = run dynamics with another code
+mc = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client or server. See the
+"server md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+The {mode} argument specifies how messages are exchanged between the
+client and server codes. Both codes must use the same mode and use
+consistent parameters.
+
+For mode {file}, the 2 codes communicate via binary files. They must
+use the same filename, which is actually a file prefix. Several files
+with that prefix will be created and deleted as a simulation runs.
+The filename can include a path. Both codes must be able to access
+the path/file in a common filesystem.
+
+For mode {zmq}, the 2 codes communicate via a socket on the server
+code's machine. Support for socket messaging is provided by the
+open-source "ZeroMQ library"_http://zeromq.org, which must be
+installed on your system. The client specifies an IP address (IPv4
+format) or the DNS name of the machine the server code is running on,
+followed by a 4-digit port ID for the socket, separated by a colon.
+E.g.
+
+localhost:5555 # client and server running on same machine
+192.168.1.1:5555 # server is 192.168.1.1
+deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre
+
+The server specifes "*:5555" where "*" represents all available
+interfaces on the server's machine, and the port ID must match
+what the client specifies.
+
+NOTE: What are allowed port IDs?
+
+NOTE: Additional explanation is needed here about how to use the {zmq}
+mode on a parallel machine, e.g. a cluster with many nodes.
+
+For mode {mpi/one}, the 2 codes communicate via MPI and are launched
+by the same mpirun command, e.g. with this syntax for OpenMPI:
+
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
+mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre
+
+Note the use of the "-mpicolor color" command-line argument with
+LAMMPS. See the "command-line args"_Run_options.html doc page for
+further explanation.
+
+For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
+be 2 separate mpirun commands. The specified {filename} argument is a
+file the 2 MPI processes will use to exchange info so that an MPI
+inter-communicator can be established to enable the 2 codes to send
+MPI messages to each other. Both codes must be able to access the
+path/file in a common filesystem.
+
+:line
+
+Normally, the message command should be used at the top of a LAMMPS
+input script. It performs an initial handshake with the other code to
+setup messaging and to verify that both codes are using the same
+message protocol and mode. Assuming both codes are launched at
+(nearly) the same time, the other code should perform the same kind of
+initialization.
+
+If LAMMPS is the client code, it will begin sending messages when a
+LAMMPS client command begins its operation. E.g. for the "fix
+client/md"_fix_client_md.html command, it is when a "run"_run.html
+command is executed.
+
+If LAMMPS is the server code, it will begin receiving messages when
+the "server"_server.html command is invoked.
+
+A fix client command will terminate its messaging with the server when
+LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
+server command will terminate its messaging with the client when the
+client signals it. Then the remainder of the LAMMPS input script will
+be processed.
+
+If both codes do something similar, this means a new round of
+client/server messaging can be initiated after termination by re-using
+a 2nd message command in your LAMMPS input script, followed by a new
+fix client or server command.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"server"_server.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/server.txt b/doc/src/server.txt
new file mode 100644
index 0000000000..86fb68d012
--- /dev/null
+++ b/doc/src/server.txt
@@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server command :h3
+
+[Syntax:]
+
+server protocol :pre
+
+protocol = {md} or {mc} :ul
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it receives
+messages from a separate "client" code and responds by sending a reply
+message back to the client. The specified {protocol} determines the
+format and content of messages LAMMPS expects to receive and how it
+responds.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+"md"_server_md.html = run dynamics with another code
+"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client (via the "fix
+client/md"_fix_client_md.html command) or server. See the "server
+md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
new file mode 100644
index 0000000000..53ccfc8ecd
--- /dev/null
+++ b/doc/src/server_mc.txt
@@ -0,0 +1,116 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server mc command :h3
+
+[Syntax:]
+
+server mc :pre
+
+mc = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server mc :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {mc}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The "server"_server.html doc page gives other options for using LAMMPS
+See an example of how this command is used in
+examples/COUPLE/lammps_mc/in.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives
+instructions from a Monte Carlo (MC) driver to displace random atoms,
+compute the energy before and after displacement, and run dynamics to
+equilibrate the system.
+
+The MC driver performs the random displacements on random atoms,
+accepts or rejects the move in an MC sense, and orchestrates the MD
+runs.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
+these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
+example of how an MC driver code can use these messages.
+
+Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
+
+[Client sends one of these kinds of message]:
+
+cs->send(NATOMS,0) # msgID = 1 with no fields :pre
+
+cs->send(EINIT,0) # msgID = 2 with no fields :pre
+
+cs->send(DISPLACE,2) # msgID = 3 with 2 fields
+cs->pack_int(1,ID) # 1st field = ID of atom to displace
+cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
+
+cs->send(ACCEPT,1) # msgID = 4 with 1 field
+cs->pack_int(1,flag) # 1st field = accept/reject flag :pre
+
+cs->send(RUN,1) # msgID = 5 with 1 field
+cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
+
+[Server replies]:
+
+cs->send(NATOMS,1) # msgID = 1 with 1 field
+cs->pack_int(1,natoms) # 1st field = number of atoms :pre
+
+cs->send(EINIT,2) # msgID = 2 with 2 fields
+cs->pack_double(1,poteng) # 1st field = potential energy of system
+cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
+
+cs->send(DISPLACE,1) # msgID = 3 with 1 field
+cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
+
+cs->send(ACCEPT,0) # msgID = 4 with no fields
+
+cs->send(RUN,0) # msgID = 5 with no fields
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
+
+[Related commands:]
+
+"message"_message.html
+
+[Default:] none
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
new file mode 100644
index 0000000000..0db7bbe16b
--- /dev/null
+++ b/doc/src/server_md.txt
@@ -0,0 +1,147 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server md command :h3
+
+[Syntax:]
+
+server md :pre
+
+md = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {md}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The "server"_server.html doc page gives other options for using LAMMPS
+in server mode. See an example of how this command is used in
+examples/message/in.message.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives the
+current coordinates of all particles from the client code each
+timestep, computes their interaction, and returns the energy, forces,
+and pressure for the interacting particles to the client code, so it
+can complete the timestep. This command could also be used with a
+client code that performs energy minimization, using the server to
+compute forces and energy each iteration of its minimizer.
+
+When using the "fix client/md" command, LAMMPS (as the client code)
+does the timestepping and receives needed energy, forces, and pressure
+values from the server code.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
+files for details on how LAMMPS uses these messages. See the
+examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
+a quantum code (VASP) can use use these messages.
+
+The following pseudo-code uses these values, defined as enums.
+
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre
+
+[Client sends 2 kinds of messages]:
+
+# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+# optional fields: UNITS, CHARGE :pre
+
+cs->send(SETUP,nfields) # msgID with nfields :pre
+
+cs->pack_int(DIM,dim) # dimension (2,3) of simulation
+cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+cs->pack_int(NATOMS,natoms) # total number of atoms
+cs->pack_int(NTYPES,ntypes) # number of atom types
+cs->pack(TYPES,natoms,type) # vector of per-atom types
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
+cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
+
+# required fields: COORDS
+# optional fields: ORIGIN, BOX :pre
+
+cs->send(STEP,nfields) # msgID with nfields :pre
+
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+
+[Server replies to either kind of message]:
+
+# required fields: FORCES, ENERGY, PRESSURE
+# optional fields: ERROR :pre
+
+cs->send(msgID,nfields) # msgID with nfields
+cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
+cs->pack(ENERGY,1,poteng) # total potential energy of system
+cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
+cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre
+
+:line
+
+The units for various quantities that are sent and received iva
+messages are defined for atomic-scale simulations in the table below.
+The client and server codes (including LAMMPS) can use internal units
+different than these (e.g. "real units"_units.html in LAMMPS), so long
+as they convert to these units for meesaging.
+
+COORDS, ORIGIN, BOX = Angstroms
+CHARGE = multiple of electron charge (1.0 is a proton)
+ENERGY = eV
+FORCES = eV/Angstrom
+PRESSURE = bars :ul
+
+Note that these are "metal units"_units.html in LAMMPS.
+
+If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
+units"_units.html, then the client and server should exchange a UNITS
+message as indicated above, and both the client and server should
+agree on the units for the data they exchange.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index 83e7463531..0e611befbd 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
+6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
In all of the examples included here, LAMMPS must first be built as a
library. Basically, in the src dir you type one of
@@ -33,9 +34,13 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
+lammps_mc client/server coupling of Monte Carlo client
+ with LAMMPS server for energy evaluation
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
+lammps_vasp client/server coupling of LAMMPS client with
+ VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile
new file mode 100644
index 0000000000..c75bd08c73
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/Makefile
@@ -0,0 +1,33 @@
+# Makefile for MC
+
+SHELL = /bin/sh
+
+SRC = mc.cpp random_park.cpp
+OBJ = $(SRC:.cpp=.o)
+
+# change this line for your machine to path for CSlib src dir
+
+CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
+
+# compiler/linker settings
+
+CC = g++
+CCFLAGS = -g -O3 -I$(CSLIB)
+LINK = g++
+LINKFLAGS = -g -O -L$(CSLIB)
+
+# targets
+
+mc: $(OBJ)
+# first line if built the CSlib within lib/message with ZMQ support
+# second line if built the CSlib without ZMQ support
+ $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
+# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
+
+clean:
+ @rm -f *.o mc
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) -c $<
diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README
new file mode 100644
index 0000000000..c201a6351c
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/README
@@ -0,0 +1,128 @@
+Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE)
+and Section_howto.html#howto10 for more details on how
+client/server coupling works in LAMMPS.
+
+In this dir, the mc.cpp/h files are a standalone "client" MC code. It
+should be run on a single processor, though it could become a parallel
+program at some point. LAMMPS is also run as a standalone executable
+as a "server" on as many processors as desired using its "server mc"
+command; see it's doc page for details.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the MC
+program became parallel, data could also be exchanged via MPI.
+
+The MC code makes simple MC moves, by displacing a single random atom
+by a small random amount. It uses LAMMPS to calculate the energy
+change, and to run dynamics between MC moves.
+
+----------------
+
+Build LAMMPS with its MESSAGE package installed:
+
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
+
+% cd lammps/lib/message
+% python Install.py -m -z # build CSlib with MPI and ZMQ support
+% cd lammps/src
+% make yes-message
+% make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+----------------
+
+Build the MC client code
+
+The source files for the MC code are in this dir. It links with the
+CSlib library in lib/message/cslib.
+
+You must first build the CSlib in serial mode, e.g.
+
+% cd lammps/lib/message/cslib/src
+% make lib # build serial and parallel lib with ZMQ support
+% make lib zmq=no # build serial and parallel lib without ZMQ support
+
+Then edit the Makefile in this dir. The CSLIB variable should be the
+path to where the LAMMPS lib/message/cslib/src dir is on your system.
+If you built the CSlib without ZMQ support you will also need to
+comment/uncomment one line. Then you can just type
+
+% make
+
+and you should get an "mc" executable.
+
+----------------
+
+To run in client/server mode:
+
+Both the client (MC) and server (LAMMPS) must use the same messaging
+mode, namely file or zmq. This is an argument to the MC code; it can
+be selected by setting the "mode" variable when you run LAMMPS. The
+default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The MC code is always run in serial.
+
+When you run, the server should print out thermodynamic info
+for every MD run it performs (between MC moves). The client
+will print nothing until the simulation ends, then it will
+print stats about the accepted MC moves.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
+
+--------------
+
+The input script for the MC program is in.mc. You can edit it to run
+longer simulations.
+
+500 nsteps = total # of steps of MD
+100 ndynamics = # of MD steps between MC moves
+0.1 delta = displacement size of MC move
+1.0 temperature = used in MC Boltzman factor
+12345 seed = random number seed
+
+--------------
+
+The problem size that LAMMPS is computing the MC energy for and
+running dynamics on is set by the x,y,z variables in the LAMMPS
+in.mc.server script. The default size is 500 particles. You can
+adjust the size as follows:
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
diff --git a/examples/COUPLE/lammps_mc/in.mc b/examples/COUPLE/lammps_mc/in.mc
new file mode 100644
index 0000000000..85052d09f1
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc
@@ -0,0 +1,7 @@
+# MC params
+
+500 nsteps
+100 ndynamics
+0.1 delta
+1.0 temperature
+12345 seed
diff --git a/examples/COUPLE/lammps_mc/in.mc.server b/examples/COUPLE/lammps_mc/in.mc.server
new file mode 100644
index 0000000000..8b10bb0f7b
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc.server
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server mc file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server mc zmq *:5555" &
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
new file mode 100644
index 0000000000..0d67c89cf1
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000649929 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
new file mode 100644
index 0000000000..2ae51d2461
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000592947 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
+
+59.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.815e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
+
+106.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.04e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
+
+113.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.755e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
+
+117.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.563e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
+
+93.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.994e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
+
+111.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.576e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
new file mode 100644
index 0000000000..0565487bc6
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000741005 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
+
+83.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+104.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
new file mode 100644
index 0000000000..e74d03235d
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000576019 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
+
+89.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 4.768e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
+
+94.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.457e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
+
+115.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.04e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
+
+125.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.384e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
+
+112.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.444e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp
new file mode 100644
index 0000000000..7c2e2ce039
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.cpp
@@ -0,0 +1,263 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+// MC code used with LAMMPS in client/server mode
+// MC is the client, LAMMPS is the server
+
+// Syntax: mc infile mode modearg
+// mode = file, zmq
+// modearg = filename for file, localhost:5555 for zmq
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "mc.h"
+#include "random_park.h"
+
+#include "cslib.h"
+using namespace CSLIB_NS;
+
+void error(const char *);
+CSlib *cs_create(char *, char *);
+
+#define MAXLINE 256
+
+/* ---------------------------------------------------------------------- */
+
+// main program
+
+int main(int narg, char **arg)
+{
+ if (narg != 4) {
+ error("Syntax: mc infile mode modearg");
+ exit(1);
+ }
+
+ // initialize CSlib
+
+ CSlib *cs = cs_create(arg[2],arg[3]);
+
+ // create MC class and perform run
+
+ MC *mc = new MC(arg[1],cs);
+ mc->run();
+
+ // final MC stats
+
+ int naccept = mc->naccept;
+ int nattempt = mc->nattempt;
+
+ printf("------ MC stats ------\n");
+ printf("MC attempts = %d\n",nattempt);
+ printf("MC accepts = %d\n",naccept);
+ printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
+
+ // clean up
+
+ delete cs;
+ delete mc;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void error(const char *str)
+{
+ printf("ERROR: %s\n",str);
+ exit(1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib *cs_create(char *mode, char *arg)
+{
+ CSlib *cs = new CSlib(0,mode,arg,NULL);
+
+ // initial handshake to agree on protocol
+
+ cs->send(0,1);
+ cs->pack_string(1,(char *) "mc");
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ return cs;
+}
+
+// ----------------------------------------------------------------------
+// MC class
+// ----------------------------------------------------------------------
+
+MC::MC(char *mcfile, void *cs_caller)
+//MC::MC(char *mcfile, CSlib *cs_caller)
+{
+ cs_void = cs_caller;
+
+ // setup MC params
+
+ options(mcfile);
+
+ // random # generator
+
+ random = new RanPark(seed);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MC::~MC()
+{
+ free(x);
+ delete random;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::run()
+{
+ int iatom,accept,msgID,nfield;
+ double pe_initial,pe_final,edelta;
+ double dx,dy,dz;
+ double xold[3],xnew[3];
+ int *fieldID,*fieldtype,*fieldlen;
+
+ enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+ CSlib *cs = (CSlib *) cs_void;
+
+ // one-time request for atom count from MD
+ // allocate 1d coord buffer
+
+ cs->send(NATOMS,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ natoms = cs->unpack_int(1);
+
+ x = (double *) malloc(3*natoms*sizeof(double));
+
+ // loop over MC moves
+
+ naccept = nattempt = 0;
+
+ for (int iloop = 0; iloop < nloop; iloop++) {
+
+ // request current energy from MD
+ // recv energy, coords from MD
+
+ cs->send(EINIT,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_initial = cs->unpack_double(1);
+ double *x = (double *) cs->unpack(2);
+
+ // perform simple MC event
+ // displace a single atom by random amount
+
+ iatom = (int) natoms*random->uniform();
+ xold[0] = x[3*iatom+0];
+ xold[1] = x[3*iatom+1];
+ xold[2] = x[3*iatom+2];
+
+ dx = 2.0*delta*random->uniform() - delta;
+ dy = 2.0*delta*random->uniform() - delta;
+ dz = 2.0*delta*random->uniform() - delta;
+
+ xnew[0] = xold[0] + dx;
+ xnew[1] = xold[1] + dx;
+ xnew[2] = xold[2] + dx;
+
+ // send atom ID and its new coords to MD
+ // recv new energy
+
+ cs->send(DISPLACE,2);
+ cs->pack_int(1,iatom+1);
+ cs->pack(2,4,3,xnew);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_final = cs->unpack_double(1);
+
+ // decide whether to accept/reject MC event
+
+ if (pe_final <= pe_initial) accept = 1;
+ else if (temperature == 0.0) accept = 0;
+ else if (random->uniform() >
+ exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
+ else accept = 1;
+
+ nattempt++;
+ if (accept) naccept++;
+
+ // send accept (1) or reject (0) flag to MD
+
+ cs->send(ACCEPT,1);
+ cs->pack_int(1,accept);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // send dynamics timesteps
+
+ cs->send(RUN,1);
+ cs->pack_int(1,ndynamics);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ }
+
+ // send exit message to MD
+
+ cs->send(-1,0);
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::options(char *filename)
+{
+ // default params
+
+ nsteps = 0;
+ ndynamics = 100;
+ delta = 0.1;
+ temperature = 1.0;
+ seed = 12345;
+
+ // read and parse file
+
+ FILE *fp = fopen(filename,"r");
+ if (fp == NULL) error("Could not open MC file");
+
+ char line[MAXLINE];
+ char *keyword,*value;
+ char *eof = fgets(line,MAXLINE,fp);
+
+ while (eof) {
+ if (line[0] == '#') { // comment line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ value = strtok(line," \t\n\r\f");
+ if (value == NULL) { // blank line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ keyword = strtok(NULL," \t\n\r\f");
+ if (keyword == NULL) error("Missing keyword in MC file");
+
+ if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
+ else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
+ else if (strcmp(keyword,"delta") == 0) delta = atof(value);
+ else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
+ else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
+ else error("Unknown param in MC file");
+
+ eof = fgets(line,MAXLINE,fp);
+ }
+
+ // derived params
+
+ nloop = nsteps/ndynamics;
+}
diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h
new file mode 100644
index 0000000000..e9d88523fc
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+#ifndef MC_H
+#define MC_H
+
+/* ---------------------------------------------------------------------- */
+
+class MC {
+ public:
+ int naccept; // # of accepted MC events
+ int nattempt; // # of attempted MC events
+
+ MC(char *, void *);
+ ~MC();
+ void run();
+
+ private:
+ int nsteps; // total # of MD steps
+ int ndynamics; // steps in one short dynamics run
+ int nloop; // nsteps/ndynamics
+ int natoms; // # of MD atoms
+
+ double delta; // MC displacement distance
+ double temperature; // MC temperature for Boltzmann criterion
+ double *x; // atom coords as 3N 1d vector
+ double energy; // global potential energy
+
+ int seed; // RNG seed
+ class RanPark *random;
+
+ void *cs_void; // messaging library
+
+ void options(char *);
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp
new file mode 100644
index 0000000000..61ac18c6c0
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.cpp
@@ -0,0 +1,72 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+// Park/Miller RNG
+
+#include <math.h>
+#include "random_park.h"
+//#include "error.h"
+
+#define IA 16807
+#define IM 2147483647
+#define AM (1.0/IM)
+#define IQ 127773
+#define IR 2836
+
+/* ---------------------------------------------------------------------- */
+
+RanPark::RanPark(int seed_init)
+{
+ //if (seed_init <= 0)
+ // error->one(FLERR,"Invalid seed for Park random # generator");
+ seed = seed_init;
+ save = 0;
+}
+
+/* ----------------------------------------------------------------------
+ uniform RN
+------------------------------------------------------------------------- */
+
+double RanPark::uniform()
+{
+ int k = seed/IQ;
+ seed = IA*(seed-k*IQ) - IR*k;
+ if (seed < 0) seed += IM;
+ double ans = AM*seed;
+ return ans;
+}
+
+/* ----------------------------------------------------------------------
+ gaussian RN
+------------------------------------------------------------------------- */
+
+double RanPark::gaussian()
+{
+ double first,v1,v2,rsq,fac;
+
+ if (!save) {
+ do {
+ v1 = 2.0*uniform()-1.0;
+ v2 = 2.0*uniform()-1.0;
+ rsq = v1*v1 + v2*v2;
+ } while ((rsq >= 1.0) || (rsq == 0.0));
+ fac = sqrt(-2.0*log(rsq)/rsq);
+ second = v1*fac;
+ first = v2*fac;
+ save = 1;
+ } else {
+ first = second;
+ save = 0;
+ }
+ return first;
+}
diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h
new file mode 100644
index 0000000000..0dc2081768
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.h
@@ -0,0 +1,28 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef RANPARK_H
+#define RANPARK_H
+
+class RanPark {
+ public:
+ RanPark(int);
+ double uniform();
+ double gaussian();
+
+ private:
+ int seed,save;
+ double second;
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_vasp/INCAR b/examples/COUPLE/lammps_vasp/INCAR
new file mode 100644
index 0000000000..ac2358e5fb
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/INCAR
@@ -0,0 +1,53 @@
+# Startparameter for this run:
+ NWRITE = 2 write-flag & timer
+ PREC = normal normal or accurate (medium, high low for compatibility)
+ ISTART = 0 job : 0-new 1-cont 2-samecut
+ ICHARG = 2 charge: 1-file 2-atom 10-const
+ ISPIN = 1 spin polarized calculation?
+ LSORBIT = F spin-orbit coupling
+ INIWAV = 1 electr: 0-lowe 1-rand 2-diag
+
+# Electronic Relaxation 1
+ ENCUT = 600.0 eV #Plane wave energy cutoff
+ ENINI = 600.0 initial cutoff
+ NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
+ EDIFF = 0.1E-05 stopping-criterion for ELM
+# Ionic relaxation
+ EDIFFG = 0.1E-02 stopping-criterion for IOM
+ NSW = 0 number of steps for IOM
+ NBLOCK = 1; KBLOCK = 1 inner block; outer block
+ IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
+ NFREE = 0 steps in history (QN), initial steepest desc. (CG)
+ ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
+ IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
+
+ POTIM = 0.5000 time-step for ionic-motion
+ TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
+ SMASS = -3.00 Nose mass-parameter (am)
+ estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
+ PSTRESS= 0.0 pullay stress
+
+# DOS related values:
+ EMIN = 10.00; EMAX =-10.00 energy-range for DOS
+ EFERMI = 0.00
+ ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
+
+# Electronic relaxation 2 (details)
+ IALGO = 48 algorithm
+
+# Write flags
+ LWAVE = T write WAVECAR
+ LCHARG = T write CHGCAR
+ LVTOT = F write LOCPOT, total local potential
+ LVHAR = F write LOCPOT, Hartree potential only
+ LELF = F write electronic localiz. function (ELF)
+
+# Dipole corrections
+ LMONO = F monopole corrections only (constant potential shift)
+ LDIPOL = F correct potential (dipole corrections)
+ IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
+ EPSILON= 1.0000000 bulk dielectric constant
+
+# Exchange correlation treatment:
+ GGA = -- GGA type
+
diff --git a/examples/COUPLE/lammps_vasp/KPOINTS b/examples/COUPLE/lammps_vasp/KPOINTS
new file mode 100644
index 0000000000..322509da30
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/KPOINTS
@@ -0,0 +1,6 @@
+K-Points
+ 0
+Monkhorst Pack
+ 15 15 15
+ 0 0 0
+
diff --git a/examples/COUPLE/lammps_vasp/POSCAR_W b/examples/COUPLE/lammps_vasp/POSCAR_W
new file mode 100644
index 0000000000..aba5df54a0
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/POSCAR_W
@@ -0,0 +1,11 @@
+W unit cell
+1.0
+3.16 0.00000000 0.00000000
+0.00000000 3.16 0.00000000
+0.00000000 0.00000000 3.16
+W
+2
+Direct
+ 0.00000000 0.00000000 0.00000000
+ 0.50000000 0.50000000 0.50000000
+
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
new file mode 100644
index 0000000000..e942d52535
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/README
@@ -0,0 +1,149 @@
+Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
+coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
+Section_howto.html#howto10 for more details on how client/server
+coupling works in LAMMPS.
+
+In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
+code so it can work as a "server" code which LAMMPS drives as a
+"client" code to perform ab initio MD. LAMMPS performs the MD
+timestepping, sends VASP a current set of coordinates each timestep,
+VASP computes forces and energy and virial and returns that info to
+LAMMPS.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the
+vasp_wrap.py program became parallel, or the CSlib library calls were
+integrated into VASP directly, then data could also be exchanged via
+MPI.
+
+----------------
+
+Build LAMMPS with its MESSAGE package installed:
+
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
+
+cd lammps/lib/message
+python Install.py -m -z # build CSlib with MPI and ZMQ support
+cd lammps/src
+make yes-message
+make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+----------------
+
+Build the CSlib in a form usable by the vasp_wrapper.py script:
+
+% cd lammps/lib/message/cslib/src
+% make shlib # build serial and parallel shared lib with ZMQ support
+% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
+
+This will make a shared library versions of the CSlib, which Python
+requires. Python must be able to find both the cslib.py script and
+the libcsnompi.so library in your lammps/lib/message/cslib/src
+directory. If it is not able to do this, you will get an error when
+you run vasp_wrapper.py.
+
+You can do this by augmenting two environment variables, either
+from the command line, or in your shell start-up script.
+Here is the sample syntax for the csh or tcsh shells:
+
+setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
+
+----------------
+
+Prepare to use VASP and the vasp_wrapper.py script
+
+You can run the vasp_wrap.py script as-is to test that the coupling
+between it and LAMMPS is functional. This will use the included
+vasprun.xml file output by a previous VASP run.
+
+But note that the as-is version of vasp_wrap.py will not attempt to
+run VASP.
+
+To do this, you must edit the 1st vaspcmd line at the top of
+vasp_wrapper.py to be the launch command needed to run VASP on your
+system. It can be a command to run VASP in serial or in parallel,
+e.g. an mpirun command. Then comment out the 2nd vaspcmd line
+immediately following it.
+
+Insure you have the necessary VASP input files in this
+directory, suitable for the VASP calculation you want to perform:
+
+INCAR
+KPOINTS
+POSCAR_template
+POTCAR
+
+Examples of all but the POTCAR file are provided. As explained below,
+POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
+be used to test the LAMMPS/VASP coupling. The POTCAR file is a
+proprietary VASP file, so use one from your VASP installation.
+
+Note that the POSCAR_template file should be matched to the LAMMPS
+input script (# of atoms and atom types, box size, etc). The provided
+POSCAR_W matches in.client.W.
+
+Once you run VASP yourself, the vasprun.xml file will be overwritten.
+
+----------------
+
+To run in client/server mode:
+
+NOTE: The vasp_wrap.py script must be run with Python version 2, not
+3. This is because it used the CSlib python wrapper, which only
+supports version 2. We plan to upgrade CSlib to support Python 3.
+
+Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
+messaging mode, namely file or zmq. This is an argument to the
+vasp_wrap.py code; it can be selected by setting the "mode" variable
+when you run LAMMPS. The default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The vasp_wrap.py code is always run in serial, but it
+launches VASP from Python via an mpirun command which can run VASP
+itself in parallel.
+
+When you run, the server should print out thermodynamic info every
+timestep which corresponds to the forces and virial computed by VASP.
+VASP will also generate output files each timestep. The vasp_wrapper.py
+script could be generalized to archive these.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
diff --git a/examples/COUPLE/lammps_vasp/data.W b/examples/COUPLE/lammps_vasp/data.W
new file mode 100644
index 0000000000..8accd9ca79
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/data.W
@@ -0,0 +1,15 @@
+LAMMPS W data file
+
+2 atoms
+
+1 atom types
+
+0.0 3.16 xlo xhi
+0.0 3.16 ylo yhi
+0.0 3.16 zlo zhi
+
+Atoms
+
+1 1 0.000 0.000 0.000
+2 1 1.58 1.58 1.58
+
diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W
new file mode 100644
index 0000000000..3eaf99dcbb
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/in.client.W
@@ -0,0 +1,34 @@
+# small W unit cell for use with VASP
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+mass 1 183.85
+
+replicate $x $y $z
+
+velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 1
+run 3
+
diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output
new file mode 100644
index 0000000000..fa8f4f920a
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/log.client.output
@@ -0,0 +1,76 @@
+LAMMPS (22 Aug 2018)
+# small W unit cell for use with VASP
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
+message client md zmq localhost:5555
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 2 atoms
+mass 1 183.85
+
+replicate $x $y $z
+replicate 1 $y $z
+replicate 1 1 $z
+replicate 1 1 1
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 2 MPI processor grid
+ 2 atoms
+ Time spent = 0.000148058 secs
+
+velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 1
+run 3
+Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 0 0 -48.030793 -78159.503
+ 1 298.24318 0 0 -48.03102 -78167.19
+ 2 296.85584 0 0 -48.031199 -78173.26
+ 3 295.83795 0 0 -48.031331 -78177.714
+Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
+
+Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
+Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
+Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
+Other | | 1.204e-05 | | | 0.00
+
+Nlocal: 1 ave 1 max 1 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 4 ave 4 max 4 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds not checked
+
+Total wall time: 0:01:21
diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py
new file mode 100644
index 0000000000..1e2c52aa46
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py
@@ -0,0 +1,300 @@
+#!/usr/bin/env python
+
+# ----------------------------------------------------------------------
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+# ----------------------------------------------------------------------
+
+# Syntax: vasp_wrap.py file/zmq POSCARfile
+
+# wrapper on VASP to act as server program using CSlib
+# receives message with list of coords from client
+# creates VASP inputs
+# invokes VASP to calculate self-consistent energy of that config
+# reads VASP outputs
+# sends message with energy, forces, pressure to client
+
+# NOTES:
+# check to insure basic VASP input files are in place?
+# could archive VASP input/output in special filenames or dirs?
+# need to check that POTCAR file is consistent with atom ordering?
+# could make syntax for launching VASP more flexible
+# e.g. command-line arg for # of procs
+# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
+
+from __future__ import print_function
+import sys
+
+version = sys.version_info[0]
+if version == 3:
+ sys.exit("The CSlib python wrapper does not yet support python 3")
+
+import subprocess
+import xml.etree.ElementTree as ET
+from cslib import CSlib
+
+# comment out 2nd line once 1st line is correct for your system
+
+vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
+ "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
+vaspcmd = "touch tmp"
+
+# enums matching FixClientMD class in LAMMPS
+
+SETUP,STEP = range(1,2+1)
+DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
+FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
+
+# -------------------------------------
+# functions
+
+# error message and exit
+
+def error(txt):
+ print("ERROR:",txt)
+ sys.exit(1)
+
+# -------------------------------------
+# read initial VASP POSCAR file to setup problem
+# return natoms,ntypes,box
+
+def vasp_setup(poscar):
+
+ ps = open(poscar,'r').readlines()
+
+ # box size
+
+ words = ps[2].split()
+ xbox = float(words[0])
+ words = ps[3].split()
+ ybox = float(words[1])
+ words = ps[4].split()
+ zbox = float(words[2])
+ box = [xbox,ybox,zbox]
+
+ ntypes = 0
+ natoms = 0
+ words = ps[6].split()
+ for word in words:
+ if word == '#': break
+ ntypes += 1
+ natoms += int(word)
+
+ return natoms,ntypes,box
+
+# -------------------------------------
+# write a new POSCAR file for VASP
+
+def poscar_write(poscar,natoms,ntypes,types,coords,box):
+
+ psold = open(poscar,'r').readlines()
+ psnew = open("POSCAR",'w')
+
+ # header, including box size
+
+ psnew.write(psold[0])
+ psnew.write(psold[1])
+ psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
+ psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
+ psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
+ psnew.write(psold[5])
+ psnew.write(psold[6])
+
+ # per-atom coords
+ # grouped by types
+
+ psnew.write("Cartesian\n")
+
+ for itype in range(1,ntypes+1):
+ for i in range(natoms):
+ if types[i] != itype: continue
+ x = coords[3*i+0]
+ y = coords[3*i+1]
+ z = coords[3*i+2]
+ aline = " %g %g %g\n" % (x,y,z)
+ psnew.write(aline)
+
+ psnew.close()
+
+# -------------------------------------
+# read a VASP output vasprun.xml file
+# uses ElementTree module
+# see https://docs.python.org/2/library/xml.etree.elementtree.html
+
+def vasprun_read():
+ tree = ET.parse('vasprun.xml')
+ root = tree.getroot()
+
+ #fp = open("vasprun.xml","r")
+ #root = ET.parse(fp)
+
+ scsteps = root.findall('calculation/scstep')
+ energy = scsteps[-1].find('energy')
+ for child in energy:
+ if child.attrib["name"] == "e_0_energy":
+ eout = float(child.text)
+
+ fout = []
+ sout = []
+
+ varrays = root.findall('calculation/varray')
+ for varray in varrays:
+ if varray.attrib["name"] == "forces":
+ forces = varray.findall("v")
+ for line in forces:
+ fxyz = line.text.split()
+ fxyz = [float(value) for value in fxyz]
+ fout += fxyz
+ if varray.attrib["name"] == "stress":
+ tensor = varray.findall("v")
+ stensor = []
+ for line in tensor:
+ sxyz = line.text.split()
+ sxyz = [float(value) for value in sxyz]
+ stensor.append(sxyz)
+ sxx = stensor[0][0]
+ syy = stensor[1][1]
+ szz = stensor[2][2]
+ # symmetrize off-diagonal components
+ sxy = 0.5 * (stensor[0][1] + stensor[1][0])
+ sxz = 0.5 * (stensor[0][2] + stensor[2][0])
+ syz = 0.5 * (stensor[1][2] + stensor[2][1])
+ sout = [sxx,syy,szz,sxy,sxz,syz]
+
+ #fp.close()
+
+ return eout,fout,sout
+
+# -------------------------------------
+# main program
+
+# command-line args
+
+if len(sys.argv) != 3:
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
+ sys.exit(1)
+
+mode = sys.argv[1]
+poscar_template = sys.argv[2]
+
+if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
+elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
+else:
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
+ sys.exit(1)
+
+natoms,ntypes,box = vasp_setup(poscar_template)
+
+# initial message for MD protocol
+
+msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+if msgID != 0: error("Bad initial client/server handshake")
+protocol = cs.unpack_string(1)
+if protocol != "md": error("Mismatch in client/server protocol")
+cs.send(0,0)
+
+# endless server loop
+
+while 1:
+
+ # recv message from client
+ # msgID = 0 = all-done message
+
+ msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+ if msgID < 0: break
+
+ # SETUP receive at beginning of each run
+ # required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ # NATOMS, NTYPES, TYPES, COORDS
+ # optional fields: others in enum above, but VASP ignores them
+
+ if msgID == SETUP:
+
+ origin = []
+ box = []
+ natoms_recv = ntypes_recv = 0
+ types = []
+ coords = []
+
+ for field in fieldID:
+ if field == DIM:
+ dim = cs.unpack_int(DIM)
+ if dim != 3: error("VASP only performs 3d simulations")
+ elif field == PERIODICITY:
+ periodicity = cs.unpack(PERIODICITY,1)
+ if not periodicity[0] or not periodicity[1] or not periodicity[2]:
+ error("VASP wrapper only currently supports fully periodic systems")
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+ elif field == NATOMS:
+ natoms_recv = cs.unpack_int(NATOMS)
+ if natoms != natoms_recv:
+ error("VASP wrapper mis-match in number of atoms")
+ elif field == NTYPES:
+ ntypes_recv = cs.unpack_int(NTYPES)
+ if ntypes != ntypes_recv:
+ error("VASP wrapper mis-match in number of atom types")
+ elif field == TYPES:
+ types = cs.unpack(TYPES,1)
+ elif field == COORDS:
+ coords = cs.unpack(COORDS,1)
+
+ if not origin or not box or not natoms or not ntypes or \
+ not types or not coords:
+ error("Required VASP wrapper setup field not received");
+
+ # STEP receive at each timestep of run or minimization
+ # required fields: COORDS
+ # optional fields: ORIGIN, BOX
+
+ elif msgID == STEP:
+
+ coords = []
+
+ for field in fieldID:
+ if field == COORDS:
+ coords = cs.unpack(COORDS,1)
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+
+ if not coords: error("Required VASP wrapper step field not received");
+
+ else: error("VASP wrapper received unrecognized message")
+
+ # create POSCAR file
+
+ poscar_write(poscar_template,natoms,ntypes,types,coords,box)
+
+ # invoke VASP
+
+ print("\nLaunching VASP ...")
+ print(vaspcmd)
+ subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
+
+ # process VASP output
+
+ energy,forces,virial = vasprun_read()
+
+ # convert VASP kilobars to bars
+
+ for i,value in enumerate(virial): virial[i] *= 1000.0
+
+ # return forces, energy, pressure to client
+
+ cs.send(msgID,3);
+ cs.pack(FORCES,4,3*natoms,forces)
+ cs.pack_double(ENERGY,energy)
+ cs.pack(VIRIAL,4,6,virial)
+
+# final reply to client
+
+cs.send(0,0)
+
+# clean-up
+
+del cs
diff --git a/examples/COUPLE/lammps_vasp/vasprun.xml b/examples/COUPLE/lammps_vasp/vasprun.xml
new file mode 100644
index 0000000000..0f15c871b4
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasprun.xml
@@ -0,0 +1,12329 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<modeling>
+ <generator>
+ <i name="program" type="string">vasp </i>
+ <i name="version" type="string">5.4.4.18Apr17-6-g9f103f2a35 </i>
+ <i name="subversion" type="string">(build Aug 01 2017 10:32:50) complex parallel </i>
+ <i name="platform" type="string">LinuxIFC </i>
+ <i name="date" type="string">2017 12 19 </i>
+ <i name="time" type="string">15:22:45 </i>
+ </generator>
+ <incar>
+ <i type="int" name="ISTART"> 0</i>
+ <i type="string" name="PREC">normal normal or accurate (medium, h</i>
+ <i type="int" name="IALGO"> 48</i>
+ <i type="logical" name="LSORBIT"> F </i>
+ <i type="int" name="ISPIN"> 1</i>
+ <i type="int" name="ICHARG"> 2</i>
+ <i type="int" name="INIWAV"> 1</i>
+ <i type="int" name="NELM"> 100</i>
+ <i type="int" name="NELMDL"> -5</i>
+ <i type="int" name="NELMIN"> 2</i>
+ <i type="int" name="IBRION"> -1</i>
+ <i type="int" name="NFREE"> 0</i>
+ <i name="EDIFF"> 0.00000100</i>
+ <i name="EDIFFG"> 0.00100000</i>
+ <i type="int" name="NSW"> 0</i>
+ <i type="int" name="ISIF"> 2</i>
+ <i type="int" name="IWAVPR"> 10</i>
+ <i type="int" name="NBLOCK"> 1</i>
+ <i type="int" name="KBLOCK"> 1</i>
+ <i name="ENCUT"> 600.00000000</i>
+ <i name="ENINI"> 600.00000000</i>
+ <i name="POTIM"> 0.50000000</i>
+ <i name="TEBEG"> 3500.00000000</i>
+ <i name="TEEND"> 3500.00000000</i>
+ <i name="SMASS"> -3.00000000</i>
+ <i name="EMIN"> 10.00000000</i>
+ <i name="EMAX"> -10.00000000</i>
+ <i name="EFERMI"> 0.00000000</i>
+ <i type="int" name="ISMEAR"> 0</i>
+ <i name="SIGMA"> 0.10000000</i>
+ <i type="int" name="NWRITE"> 2</i>
+ <i name="PSTRESS"> 0.00000000</i>
+ <i type="logical" name="LWAVE"> T </i>
+ <i type="logical" name="LCHARG"> T </i>
+ <i type="logical" name="LVTOT"> F </i>
+ <i type="logical" name="LVHAR"> F </i>
+ <i type="logical" name="LELF"> F </i>
+ <v type="int" name="KPOINT_BSE"> -1 0 0 0</v>
+ <i type="int" name="NELM"> 100</i>
+ <i type="string" name="GGA"> -- GGA type</i>
+ <i type="logical" name="LDIPOL"> F </i>
+ <i type="logical" name="LMONO"> F </i>
+ <i type="int" name="IDIPOL"> 0</i>
+ <i name="EPSILON"> 1.00000000</i>
+ </incar>
+ <structure name="primitive_cell" >
+ <crystal>
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+ <v> 0.00000000 3.55744000 0.00000000 </v>
+ <v> 0.00000000 0.00000000 3.17678100 </v>
+ </varray>
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+ <v> 0.00000000 0.28110102 0.00000000 </v>
+ <v> 0.00000000 0.00000000 0.31478405 </v>
+ </varray>
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+ </varray>
+ </structure>
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+ <v type="int" > 2 </v>
+ <v type="int" > 3 </v>
+ <v type="int" > 4 </v>
+ </varray>
+ <kpoints>
+ <generation param="Monkhorst-Pack">
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+ <r> 45.7886 0.0094 36.0000 </r>
+ <r> 46.2923 0.0000 36.0000 </r>
+ <r> 46.7959 0.0000 36.0000 </r>
+ <r> 47.2995 0.0000 36.0000 </r>
+ <r> 47.8031 0.0000 36.0000 </r>
+ <r> 48.3067 0.0000 36.0000 </r>
+ <r> 48.8103 0.0000 36.0000 </r>
+ <r> 49.3140 0.0000 36.0000 </r>
+ <r> 49.8176 0.0000 36.0000 </r>
+ <r> 50.3212 0.0000 36.0000 </r>
+ <r> 50.8248 0.0000 36.0000 </r>
+ <r> 51.3284 0.0000 36.0000 </r>
+ <r> 51.8320 0.0000 36.0000 </r>
+ <r> 52.3357 0.0000 36.0000 </r>
+ </set>
+ </set>
+ </array>
+ </total>
+ </dos>
+ </calculation>
+ <structure name="finalpos" >
+ <crystal>
+ <varray name="basis" >
+ <v> 3.66961100 0.00000000 0.00000000 </v>
+ <v> 0.00000000 3.55744000 0.00000000 </v>
+ <v> 0.00000000 0.00000000 3.17678100 </v>
+ </varray>
+ <i name="volume"> 41.47103646 </i>
+ <varray name="rec_basis" >
+ <v> 0.27250845 0.00000000 0.00000000 </v>
+ <v> 0.00000000 0.28110102 0.00000000 </v>
+ <v> 0.00000000 0.00000000 0.31478405 </v>
+ </varray>
+ </crystal>
+ <varray name="positions" >
+ <v> 0.00000000 0.00000000 0.00000000 </v>
+ <v> 0.00000000 0.50000000 0.50000000 </v>
+ <v> 0.50000000 0.00000000 0.50000000 </v>
+ <v> 0.50000000 0.50000000 0.00000000 </v>
+ </varray>
+ </structure>
+</modeling>
diff --git a/examples/README b/examples/README
index d6c946725f..3c9c299819 100644
--- a/examples/README
+++ b/examples/README
@@ -83,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
+message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in
index 0fa9c1b74c..8315e57750 100644
--- a/examples/USER/diffraction/BulkNi.in
+++ b/examples/USER/diffraction/BulkNi.in
@@ -17,8 +17,9 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.05 echo manual
+compute SAED all saed 0.0251 Ni Kmax 0.85 &
+ Zone 0 0 0 c 0.025 0.025 0.025 &
+ dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
diff --git a/examples/USER/diffraction/Output/BulkNi.in b/examples/USER/diffraction/Output/BulkNi.in
deleted file mode 100644
index 8315e57750..0000000000
--- a/examples/USER/diffraction/Output/BulkNi.in
+++ /dev/null
@@ -1,35 +0,0 @@
-variable A string bulkNi
-log $A.log
-
-boundary p p p
-
-units metal
-timestep 0.001
-
-lattice fcc 3.52
-region box block 0 20 0 20 0 20
-create_box 1 box
-create_atoms 1 box
-
-pair_style none
-mass * 58.71
-atom_modify sort 0 0
-
-compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-
-compute SAED all saed 0.0251 Ni Kmax 0.85 &
- Zone 0 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.01 echo manual
-
-fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
- mode vector file $A.hist.xrd
-
-fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
-
-dump 1 all custom 1 $A.dump id x y z
-run 0
-
-unfix 1
-unfix 2
-uncompute XRD
-uncompute SAED
diff --git a/examples/message/README b/examples/message/README
new file mode 100644
index 0000000000..6cd99d5c09
--- /dev/null
+++ b/examples/message/README
@@ -0,0 +1,117 @@
+This dir contains scripts that demonstrate how to use LAMMPS as both a
+client and server code to run a simple MD simulation. LAMMPS as a
+client performs the MD timestepping. LAMMPS as a server provides the
+energy and forces between interacting particles. Every timestep the
+LAMMPS client sends a message to the LAMMPS server and receives a
+response message in return.
+
+Another code could replace LAMMPS as the client, e.g. another MD code
+which wants to use a LAMMPS potential. Another code could replace
+LAMMPS as the server, e.g. a quantum code computing quantum forces, so
+that ab initio MD could be performed. See an example of the latter in
+examples/COUPLE/lammps_vasp.
+
+See the doc pages for the "MESSAGE package"
+(Package_details.html#PKG-MESSAGE) and "Howto client/server"
+(Howto_client_server.html) for more details on how client/server
+coupling works in LAMMPS.
+
+--------------
+
+Note that you can adjust the problem size run by these scripts by
+setting "x,y,z" variables when you run LAMMPS. The default problem size
+is x = y = z = 5, which is 500 particles.
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
+
+This applies to either in.message or in.message.client
+
+You can also run the in.message scripts with an NPT integrator
+instead of NVE, if you comment/uncomment the correct lines.
+
+The client and server script define a "mode" variable
+which can be set to file, zmq, mpi/one, or mpi/two,
+as illustrated below.
+
+--------------
+
+To run this problem in the traditional way (no client/server coupling)
+do one of these:
+
+% lmp_serial < in.message
+% mpirun -np 4 lmp_mpi < in.message
+
+Or run with in.message.tilt.
+
+--------------
+
+To run in client/server mode:
+
+Both the client and server script must use the same messaging mode.
+This can be selected by setting the "mode" variable when you run
+LAMMPS. The default mode = file. The other options for the mode
+variable are zmq, mpione, mpitwo.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means any of
+the 4 messaging modes can be used.
+
+The next sections illustrate how to launch LAMMPS twice, once as a
+client, once as a server, for each of the messaging modes.
+
+In all cases, the client should print out thermodynamic info for 50
+steps. The server should print out setup info, print nothing until
+the client exits, at which point the server should also exit.
+
+The examples below show launching LAMMPS twice from the same window
+(or batch script), using the "&" character to launch the first time in
+the background. For all modes except {mpi/one}, you could also launch
+twice in separate windows on your desktop machine. It does not matter
+whether you launch the client or server first.
+
+In these examples either the client or server can be run on one or
+more processors. If running in a non-MPI mode (file or zmq) you can
+launch LAMMPS on a single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both
+times via mpirun, even if one or both of them runs on a single
+processor. This is so that MPI can figure out how to connect both MPI
+processes together to exchange MPI messages between them.
+
+--------------
+
+NOTE: the Script.sh file has comands to perform all the
+runs listed below.
+
+--------------
+
+File or ZMQ or mpi/two modes of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
+% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
+
+% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client &
+% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server
+
+% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
+% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
+
+Or run with in.message.tilt.client/server.
+Don't run the tilt files with the "file" mode; they run too slow.
+
+--------------
+
+Mpi/one mode of messaging:
+
+Launch LAMMPS twice in a single mpirun command:
+
+% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server
+
+Or run with in.message.tilt.client/server.
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as its first option, where color is set to one
+integer value for the 1st app, and another value for the 2nd app.
diff --git a/examples/message/Script.sh b/examples/message/Script.sh
new file mode 100644
index 0000000000..fdcd6f1188
--- /dev/null
+++ b/examples/message/Script.sh
@@ -0,0 +1,55 @@
+# sample launch script
+
+# message on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message
+
+mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
+
+# message on 2/4 procs each
+
+mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message
+
+mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
+
+# message.tilt on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
+
+# message.tilt on 2/4 procs each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
diff --git a/examples/message/in.message b/examples/message/in.message
new file mode 100644
index 0000000000..7fbbffc355
--- /dev/null
+++ b/examples/message/in.message
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.client b/examples/message/in.message.client
new file mode 100644
index 0000000000..f1ec644a80
--- /dev/null
+++ b/examples/message/in.message.client
@@ -0,0 +1,41 @@
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.server b/examples/message/in.message.server
new file mode 100644
index 0000000000..2fedd2ae00
--- /dev/null
+++ b/examples/message/in.message.server
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 1 0 1 0 1
+create_box 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/in.message.tilt b/examples/message/in.message.tilt
new file mode 100644
index 0000000000..51126eae1e
--- /dev/null
+++ b/examples/message/in.message.tilt
@@ -0,0 +1,30 @@
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client
new file mode 100644
index 0000000000..b55bc6585b
--- /dev/null
+++ b/examples/message/in.message.tilt.client
@@ -0,0 +1,42 @@
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.server b/examples/message/in.message.tilt.server
new file mode 100644
index 0000000000..ba211ed15f
--- /dev/null
+++ b/examples/message/in.message.tilt.server
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/log.28Aug18.message.client.file.g++.1 b/examples/message/log.28Aug18.message.client.file.g++.1
new file mode 100644
index 0000000000..bca1d37dd5
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.file.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000752926 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms
+
+Performance: 4298.421 tau/day, 9.950 timesteps/s
+0.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
+Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00
+Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
+Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98
+Other | | 0.0004668 | | | 0.01
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.client.file.g++.2 b/examples/message/log.28Aug18.message.client.file.g++.2
new file mode 100644
index 0000000000..1c868dde37
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.file.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000613928 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms
+
+Performance: 4299.499 tau/day, 9.953 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00
+Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00
+Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01
+Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92
+Other | | 0.003203 | | | 0.06
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.1 b/examples/message/log.28Aug18.message.client.mpione.g++.1
new file mode 100644
index 0000000000..78bee72fdf
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000540018 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms
+
+Performance: 534798.272 tau/day, 1237.959 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01
+Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16
+Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24
+Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17
+Other | | 0.0001726 | | | 0.43
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.2 b/examples/message/log.28Aug18.message.client.mpione.g++.2
new file mode 100644
index 0000000000..7d7af866e3
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000475883 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms
+
+Performance: 1035997.740 tau/day, 2398.143 timesteps/s
+99.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02
+Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60
+Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38
+Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15
+Other | | 0.0001761 | | | 0.84
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
new file mode 100644
index 0000000000..ee97e7bd1a
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000603914 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms
+
+Performance: 312504.627 tau/day, 723.390 timesteps/s
+42.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01
+Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15
+Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20
+Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25
+Other | | 0.0002651 | | | 0.38
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
new file mode 100644
index 0000000000..72db0198d5
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000667095 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms
+
+Performance: 1135563.588 tau/day, 2628.619 timesteps/s
+58.5% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02
+Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95
+Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81
+Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58
+Other | | 0.0005029 | | | 2.64
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.1 b/examples/message/log.28Aug18.message.client.zmq.g++.1
new file mode 100644
index 0000000000..23fa70c1be
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000734091 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms
+
+Performance: 277513.222 tau/day, 642.392 timesteps/s
+11.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01
+Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11
+Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15
+Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37
+Other | | 0.0002885 | | | 0.37
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.2 b/examples/message/log.28Aug18.message.client.zmq.g++.2
new file mode 100644
index 0000000000..7833befd21
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000570059 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms
+
+Performance: 518489.499 tau/day, 1200.207 timesteps/s
+56.5% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01
+Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33
+Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27
+Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49
+Other | | 0.0003769 | | | 0.90
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.g++.1 b/examples/message/log.28Aug18.message.g++.1
new file mode 100644
index 0000000000..c06af4e0d1
--- /dev/null
+++ b/examples/message/log.28Aug18.message.g++.1
@@ -0,0 +1,85 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000682831 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms
+
+Performance: 544341.699 tau/day, 1260.050 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59
+Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41
+Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21
+Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32
+Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34
+Other | | 0.000448 | | | 1.13
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18820 ave 18820 max 18820 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.g++.4 b/examples/message/log.28Aug18.message.g++.4
new file mode 100644
index 0000000000..695b51f166
--- /dev/null
+++ b/examples/message/log.28Aug18.message.g++.4
@@ -0,0 +1,85 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000656843 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms
+
+Performance: 1642350.242 tau/day, 3801.737 timesteps/s
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71
+Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82
+Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41
+Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98
+Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14
+Other | | 0.0003865 | | | 2.94
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 1091 ave 1094 max 1089 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs: 4705 ave 4849 max 4648 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.file.g++.1 b/examples/message/log.28Aug18.message.server.file.g++.1
new file mode 100644
index 0000000000..cf1418d3c5
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.file.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.server.file.g++.4 b/examples/message/log.28Aug18.message.server.file.g++.4
new file mode 100644
index 0000000000..c233bad692
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.file.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.1 b/examples/message/log.28Aug18.message.server.mpione.g++.1
new file mode 100644
index 0000000000..81e04aa923
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.4 b/examples/message/log.28Aug18.message.server.mpione.g++.4
new file mode 100644
index 0000000000..a185cb1c29
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
new file mode 100644
index 0000000000..973a08eb6a
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
new file mode 100644
index 0000000000..9e76e52d90
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.1 b/examples/message/log.28Aug18.message.server.zmq.g++.1
new file mode 100644
index 0000000000..ce5729878b
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.4 b/examples/message/log.28Aug18.message.server.zmq.g++.4
new file mode 100644
index 0000000000..b3201da4da
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
new file mode 100644
index 0000000000..a290ec307b
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000485897 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 12374053.445 tau/day, 28643.642 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12
+Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89
+Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03
+Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15
+Other | | 0.04905 | | | 2.81
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
new file mode 100644
index 0000000000..0089732355
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000453949 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 7638300.565 tau/day, 17681.251 timesteps/s
+100.0% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04
+Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89
+Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02
+Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41
+Other | | 0.07465 | | | 2.64
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
new file mode 100644
index 0000000000..814b3df1aa
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000543118 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 4497356.047 tau/day, 10410.546 timesteps/s
+50.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07
+Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70
+Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02
+Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25
+Other | | 0.09449 | | | 1.97
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
new file mode 100644
index 0000000000..7c172d3727
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000574827 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 3812643.232 tau/day, 8825.563 timesteps/s
+48.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03
+Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67
+Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01
+Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27
+Other | | 0.1146 | | | 2.02
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
new file mode 100644
index 0000000000..f5e2f220cd
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000530005 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 1666000.147 tau/day, 3856.482 timesteps/s
+23.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01
+Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16
+Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00
+Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28
+Other | | 0.07062 | | | 0.54
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
new file mode 100644
index 0000000000..8fc570f5da
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000673056 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 1586733.497 tau/day, 3672.994 timesteps/s
+59.3% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01
+Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21
+Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00
+Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04
+Other | | 0.0994 | | | 0.73
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/message/log.28Aug18.message.tilt.g++.1 b/examples/message/log.28Aug18.message.tilt.g++.1
new file mode 100644
index 0000000000..3f7cfc9da0
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.1
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000437021 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 18673426.371 tau/day, 43225.524 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66
+Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10
+Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85
+Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05
+Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42
+Other | | 0.05684 | | | 4.91
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.g++.4 b/examples/message/log.28Aug18.message.tilt.g++.4
new file mode 100644
index 0000000000..74061463f6
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.4
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000396967 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 23312793.646 tau/day, 53964.800 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26
+Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81
+Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87
+Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07
+Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98
+Other | | 0.0465 | | | 5.02
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
new file mode 100644
index 0000000000..428ff346ad
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000438929 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
new file mode 100644
index 0000000000..3da50163ed
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000455141 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
new file mode 100644
index 0000000000..fc29a6da63
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000521898 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
new file mode 100644
index 0000000000..758b84fe9d
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000378847 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
new file mode 100644
index 0000000000..78526ba748
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000557184 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
new file mode 100644
index 0000000000..b1ad768470
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000586987 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:13
diff --git a/lib/README b/lib/README
index 3c8f46dd0a..12c27b2a39 100644
--- a/lib/README
+++ b/lib/README
@@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
meam modified embedded atom method (MEAM) potential, MEAM package
from Greg Wagner (Sandia)
+message client/server communication library via MPI, sockets, files
+ from Steve Plimpton (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
diff --git a/lib/message/Install.py b/lib/message/Install.py
new file mode 100644
index 0000000000..d3f31c986f
--- /dev/null
+++ b/lib/message/Install.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+# Install.py tool to build the CSlib library
+# used to automate the steps described in the README file in this dir
+
+from __future__ import print_function
+import sys,os,re,subprocess
+
+# help message
+
+help = """
+Syntax from src dir: make lib-message args="-m"
+ or: make lib-message args="-s -z"
+Syntax from lib dir: python Install.py -m
+ or: python Install.py -s -z
+
+specify zero or more options, order does not matter
+
+ -m = parallel build of CSlib library
+ -s = serial build of CSlib library
+ -z = build CSlib library with ZMQ socket support, default = no ZMQ support
+
+Example:
+
+make lib-message args="-m -z" # build parallel CSlib with ZMQ support
+make lib-message args="-s" # build serial CSlib with no ZMQ support
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print(help)
+ else: print("ERROR",str)
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+mpiflag = False
+serialflag = False
+zmqflag = False
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ mpiflag = True
+ iarg += 1
+ elif args[iarg] == "-s":
+ serialflag = True
+ iarg += 1
+ elif args[iarg] == "-z":
+ zmqflag = True
+ iarg += 1
+ else: error()
+
+if (not mpiflag and not serialflag):
+ error("Must use either -m or -s flag")
+
+if (mpiflag and serialflag):
+ error("Cannot use -m and -s flag at the same time")
+
+# build CSlib
+# copy resulting lib to cslib/src/libmessage.a
+# copy appropriate Makefile.lammps.* to Makefile.lammps
+
+print("Building CSlib ...")
+srcdir = fullpath("./cslib/src")
+
+if mpiflag and zmqflag:
+ cmd = "cd %s; make lib_parallel" % srcdir
+elif mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_parallel zmq=no" % srcdir
+elif not mpiflag and zmqflag:
+ cmd = "cd %s; make lib_serial" % srcdir
+elif not mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_serial zmq=no" % srcdir
+
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir
+else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps"
+else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps"
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
diff --git a/lib/message/Makefile.lammps.nozmq b/lib/message/Makefile.lammps.nozmq
new file mode 100644
index 0000000000..1bb10cc988
--- /dev/null
+++ b/lib/message/Makefile.lammps.nozmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB =
+message_SYSPATH =
diff --git a/lib/message/Makefile.lammps.zmq b/lib/message/Makefile.lammps.zmq
new file mode 100644
index 0000000000..759f2ce04b
--- /dev/null
+++ b/lib/message/Makefile.lammps.zmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB = -lzmq
+message_SYSPATH =
diff --git a/lib/message/README b/lib/message/README
new file mode 100644
index 0000000000..dafb94e9ef
--- /dev/null
+++ b/lib/message/README
@@ -0,0 +1,51 @@
+This directory contains the CSlib library which is required
+to use the MESSAGE package and its client/server commands
+in a LAMMPS input script.
+
+The CSlib libary is included in the LAMMPS distribution. A fuller
+version including documentation and test programs is available at
+http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia
+National Laboratories.
+
+You can type "make lib-message" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
+The CSlib can be optionally built with support for sockets using
+the open-source ZeroMQ (ZMQ) library. If it is not installed
+on your system, it is easy to download and install.
+
+Go to the ZMQ website for details: http://zeromq.org
+
+-----------------
+
+Instructions:
+
+1. Compile CSlib from within cslib/src with one of the following:
+ % make lib_parallel # build parallel library with ZMQ socket support
+ % make lib_serial # build serial library with ZMQ support
+ % make lib_parallel zmq=no # build parallel lib with no ZMQ support
+ % make lib_serial zmq=no # build serial lib with no ZMQ support
+
+2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to
+ cslib/src/libmessage.a
+
+3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq
+ to lib/message/Makefile.lammps, depending on whether you
+ build the library with ZMQ support or not.
+ If your ZMQ library is not in a place your shell path finds,
+ you can set the INCLUDE and PATH variables in Makefile.lammps
+ to point to the dirs where the ZMQ include and library files are.
+
+-----------------
+
+When these steps are complete you can build LAMMPS
+with the MESSAGAE package installed:
+
+% cd lammps/src
+% make yes-message
+% make mpi (or whatever target you wish)
+
+Note that if you download and unpack a new LAMMPS tarball, you will
+need to re-build the CSlib in this dir.
diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE
new file mode 100644
index 0000000000..7a36e21daf
--- /dev/null
+++ b/lib/message/cslib/LICENSE
@@ -0,0 +1,32 @@
+Program: CSlib client/server coupling library
+
+Copyright 2018 National Technology & Engineering Solutions of Sandia,
+LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
+U.S. Government retains certain rights in this software. This
+software is distributed under the modified Berkeley Software
+Distribution (BSD) License.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+* Neither the name of Sandia Corporation nor the names of contributors
+ to this software may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/lib/message/cslib/README b/lib/message/cslib/README
new file mode 100644
index 0000000000..37f4a97d54
--- /dev/null
+++ b/lib/message/cslib/README
@@ -0,0 +1,23 @@
+This is the the Client/Server messaging library (CSlib).
+
+Only the source directory and license file are included here as part
+of the LAMMPS distribution. The full CSlib distribution, including
+documentation and test codes, can be found at the website:
+http://cslib.sandia.gov (as of Aug 2018).
+
+The contact author is
+
+Steve Plimpton
+Sandia National Laboratories
+sjplimp@sandia.gov
+http://www.sandia.gov/~sjplimp
+
+The CSlib is distributed as open-source code under the modified
+Berkeley Software Distribution (BSD) License. See the accompanying
+LICENSE file.
+
+This directory contains the following:
+
+README this file
+LICENSE GNU LGPL license
+src source files for library
diff --git a/lib/message/cslib/src/Makefile b/lib/message/cslib/src/Makefile
new file mode 100644
index 0000000000..83cf902220
--- /dev/null
+++ b/lib/message/cslib/src/Makefile
@@ -0,0 +1,107 @@
+# Makefile for CSlib = client/server messaging library
+# type "make help" for options
+
+SHELL = /bin/sh
+
+# ----------------------------------------
+# should only need to change this section
+# compiler/linker settings
+# ----------------------------------------
+
+CC = g++
+CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI)
+SHFLAGS = -fPIC
+ARCHIVE = ar
+ARCHFLAGS = -rc
+SHLIBFLAGS = -shared
+
+# files
+
+LIB = libcsmpi.a
+SHLIB = libcsmpi.so
+SRC = $(wildcard *.cpp)
+INC = $(wildcard *.h)
+OBJ = $(SRC:.cpp=.o)
+
+# build with ZMQ support or not
+
+zmq = yes
+ZMQ = $(shell echo $(zmq) | tr a-z A-Z)
+
+ifeq ($(ZMQ),YES)
+ ZMQLIB = -lzmq
+else
+ CCFLAGS += -I./STUBS_ZMQ
+endif
+
+# build with MPI support or not
+
+mpi = yes
+MPI = $(shell echo $(mpi) | tr a-z A-Z)
+
+ifeq ($(MPI),YES)
+ CC = mpicxx
+else
+ CCFLAGS += -I./STUBS_MPI
+ LIB = libcsnompi.a
+ SHLIB = libcsnompi.so
+endif
+
+# targets
+
+shlib: shlib_parallel shlib_serial
+
+lib: lib_parallel lib_serial
+
+all: shlib lib
+
+help:
+ @echo 'make default = shlib'
+ @echo 'make shlib build 2 shared CSlibs: parallel & serial'
+ @echo 'make lib build 2 static CSlibs: parallel & serial'
+ @echo 'make all build 4 CSlibs: shlib and lib'
+ @echo 'make shlib_parallel build shared parallel CSlib'
+ @echo 'make shlib_serial build shared serial CSlib'
+ @echo 'make lib_parallel build static parallel CSlib'
+ @echo 'make lib_serial build static serial CSlib'
+ @echo 'make ... zmq=no build w/out ZMQ support'
+ @echo 'make clean remove all *.o files'
+ @echo 'make clean-all remove *.o and lib files'
+ @echo 'make tar create a tarball, 2 levels up'
+
+shlib_parallel:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=yes
+
+shlib_serial:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=no
+
+lib_parallel:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=yes
+
+lib_serial:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=no
+
+static: $(OBJ)
+ $(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ)
+
+shared: $(OBJ)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB)
+
+clean:
+ @rm -f *.o *.pyc
+
+clean-all:
+ @rm -f *.o *.pyc lib*.a lib*.so
+
+tar:
+ cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \
+ cslib/doc cslib/src cslib/test
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) $(SHFLAGS) -c $<
diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h
new file mode 100644
index 0000000000..2919e4c3a2
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_MPI/mpi.h
@@ -0,0 +1,96 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// MPI constants and dummy functions
+
+#ifndef MPI_DUMMY_H
+#define MPI_DUMMY_H
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+
+namespace CSLIB_NS {
+
+typedef int MPI_Comm;
+typedef int MPI_Fint;
+typedef int MPI_Datatype;
+typedef int MPI_Status;
+typedef int MPI_Op;
+typedef int MPI_Info;
+
+#define MPI_COMM_WORLD 0
+#define MPI_MAX_PORT_NAME 0
+#define MPI_INFO_NULL 0
+#define MPI_INT 1
+#define MPI_LONG_LONG 2
+#define MPI_FLOAT 3
+#define MPI_DOUBLE 4
+#define MPI_CHAR 5
+#define MPI_SUM 0
+
+static void MPI_Init(int *, char ***) {}
+static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;}
+static void MPI_Comm_rank(MPI_Comm, int *) {}
+static void MPI_Comm_size(MPI_Comm, int *) {}
+
+static void MPI_Open_port(MPI_Info, char *) {}
+static void MPI_Close_port(const char *) {}
+static void MPI_Comm_accept(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+static void MPI_Comm_connect(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+
+static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {}
+static void MPI_Comm_free(MPI_Comm *) {}
+
+static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {}
+static void MPI_Recv(void *, int, MPI_Datatype, int, int,
+ MPI_Comm, MPI_Status *) {}
+
+static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type,
+ MPI_Op op, MPI_Comm)
+{
+ if (type == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype,
+ MPI_Op op,MPI_Comm)
+{
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+
+static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {}
+static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype,
+ void *out, int, MPI_Datatype, MPI_Comm)
+{
+ // assuming incount = 1
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype,
+ void *out, const int *, const int *,
+ MPI_Datatype, MPI_Comm)
+{
+ if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int));
+ else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t));
+ else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float));
+ else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double));
+ else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char));
+}
+
+static void MPI_Abort(MPI_Comm, int) {exit(1);}
+static void MPI_Finalize() {}
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
new file mode 100644
index 0000000000..2f02eb4035
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
@@ -0,0 +1,36 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// ZMQ constants and dummy functions
+
+#ifndef ZMQ_DUMMY_H
+#define ZMQ_DUMMY_H
+
+namespace CSLIB_NS {
+
+#define ZMQ_REQ 0
+#define ZMQ_REP 0
+
+static void *zmq_ctx_new() {return NULL;}
+static void *zmq_connect(void *, char *) {return NULL;}
+static int zmq_bind(void *, char *) {return 0;}
+static void *zmq_socket(void *,int) {return NULL;}
+static void zmq_close(void *) {}
+static void zmq_ctx_destroy(void *) {}
+static void zmq_send(void *, void *, int, int) {}
+static void zmq_recv(void *, void *, int, int) {}
+
+};
+
+#endif
diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp
new file mode 100644
index 0000000000..874333607e
--- /dev/null
+++ b/lib/message/cslib/src/cslib.cpp
@@ -0,0 +1,768 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include "cslib.h"
+#include "msg_file.h"
+#include "msg_zmq.h"
+#include "msg_mpi_one.h"
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+#define MAXTYPE 5 // # of defined field data types
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm)
+{
+ if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm);
+ else myworld = 0;
+
+#ifdef MPI_NO
+ if (pcomm)
+ error_all("constructor(): CSlib invoked with MPI_Comm "
+ "but built w/out MPI support");
+#endif
+#ifdef MPI_YES // NOTE: this could be OK to allow ??
+ // would allow a parallel app to invoke CSlib
+ // in parallel and/or in serial
+ if (!pcomm)
+ error_all("constructor(): CSlib invoked w/out MPI_Comm "
+ "but built with MPI support");
+#endif
+
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+ else error_all("constructor(): Invalid client/server arg");
+
+ if (pcomm == NULL) {
+ me = 0;
+ nprocs = 1;
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr);
+ else if (strcmp(mode,"mpi/one") == 0)
+ error_all("constructor(): No mpi/one mode for serial lib usage");
+ else if (strcmp(mode,"mpi/two") == 0)
+ error_all("constructor(): No mpi/two mode for serial lib usage");
+ else error_all("constructor(): Unknown mode");
+
+ } else if (pcomm) {
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world);
+ else error_all("constructor(): Unknown mode");
+ }
+
+ maxfield = 0;
+ fieldID = fieldtype = fieldlen = fieldoffset = NULL;
+ maxheader = 0;
+ header = NULL;
+ maxbuf = 0;
+ buf = NULL;
+
+ recvcounts = displs = NULL;
+ maxglobal = 0;
+ allids = NULL;
+ maxfieldbytes = 0;
+ fielddata = NULL;
+
+ pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::~CSlib()
+{
+ deallocate_fields();
+ sfree(header);
+ sfree(buf);
+
+ sfree(recvcounts);
+ sfree(displs);
+ sfree(allids);
+ sfree(fielddata);
+
+ delete msg;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send(int msgID_caller, int nfield_caller)
+{
+ if (nfield_caller < 0) error_all("send(): Invalid nfield");
+
+ msgID = msgID_caller;
+ nfield = nfield_caller;
+ allocate_fields();
+
+ fieldcount = 0;
+ nbuf = 0;
+
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int(int id, int value)
+{
+ pack(id,1,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int64(int id, int64_t value)
+{
+ pack(id,2,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_float(int id, float value)
+{
+ pack(id,3,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_double(int id, double value)
+{
+ pack(id,4,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_string(int id, char *value)
+{
+ pack(id,5,strlen(value)+1,value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack(int id, int ftype, int flen, void *data)
+{
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype");
+ if (flen < 0) error_all("pack(): Invalid flen");
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ memcpy(&buf[nbuf],data,nbytes);
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_parallel(int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack_parallel(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype");
+ if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ // NOTE: check for overflow of maxglobal and flen
+
+ int nglobal;
+ MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world);
+ int flen = nper*nglobal;
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ // nlocal datums, each of nper length, from all procs
+ // final data in buf = datums for all natoms, ordered by ids
+
+ if (recvcounts == NULL) {
+ recvcounts = (int *) smalloc(nprocs*sizeof(int));
+ displs = (int *) smalloc(nprocs*sizeof(int));
+ }
+
+ MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ if (ids && nglobal > maxglobal) {
+ sfree(allids);
+ maxglobal = nglobal;
+ // NOTE: maxglobal*sizeof(int) could overflow int
+ allids = (int *) smalloc(maxglobal*sizeof(int));
+ }
+
+ MPI_Allgatherv(ids,nlocal,MPI_INT,allids,
+ recvcounts,displs,MPI_INT,world);
+
+ int nlocalsize = nper*nlocal;
+ MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ if (ftype == 1) {
+ int *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int *) fielddata;
+ } else alldata = (int *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata,
+ recvcounts,displs,MPI_INT,world);
+ if (ids) {
+ int *bufptr = (int *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 2) {
+ int64_t *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int64_t *) fielddata;
+ } else alldata = (int64_t *) &buf[nbuf];
+ // NOTE: may be just MPI_LONG on some machines
+ MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata,
+ recvcounts,displs,MPI_LONG_LONG,world);
+ if (ids) {
+ int64_t *bufptr = (int64_t *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 3) {
+ float *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (float *) fielddata;
+ } else alldata = (float *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata,
+ recvcounts,displs,MPI_FLOAT,world);
+ if (ids) {
+ float *bufptr = (float *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 4) {
+ double *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (double *) fielddata;
+ } else alldata = (double *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata,
+ recvcounts,displs,MPI_DOUBLE,world);
+ if (ids) {
+ double *bufptr = (double *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (ftype == 5) {
+ char *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (char *) fielddata;
+ } else alldata = (char *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata,
+ recvcounts,displs,MPI_CHAR,world);
+ if (ids) {
+ char *bufptr = (char *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ memcpy(&bufptr[j],&alldata[m],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send_message()
+{
+ // setup header message
+
+ int m = 0;
+ header[m++] = msgID;
+ header[m++] = nfield;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ header[m++] = fieldID[ifield];
+ header[m++] = fieldtype[ifield];
+ header[m++] = fieldlen[ifield];
+ }
+
+ msg->send(nheader,header,nbuf,buf);
+ nsend++;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::recv(int &nfield_caller, int *&fieldID_caller,
+ int *&fieldtype_caller, int *&fieldlen_caller)
+{
+ msg->recv(maxheader,header,maxbuf,buf);
+ nrecv++;
+
+ // unpack header message
+
+ int m = 0;
+ msgID = header[m++];
+ nfield = header[m++];
+ allocate_fields();
+
+ int nbytes,nbytesround;
+
+ nbuf = 0;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ fieldID[ifield] = header[m++];
+ fieldtype[ifield] = header[m++];
+ fieldlen[ifield] = header[m++];
+ fieldoffset[ifield] = nbuf;
+ onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround);
+ nbuf += nbytesround;
+ }
+
+ // return message parameters
+
+ nfield_caller = nfield;
+ fieldID_caller = fieldID;
+ fieldtype_caller = fieldtype;
+ fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::unpack_int(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int(): Unknown field ID");
+ if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1");
+
+ int *ptr = (int *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int64_t CSlib::unpack_int64(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int64(): Unknown field ID");
+ if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1");
+
+ int64_t *ptr = (int64_t *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+float CSlib::unpack_float(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_float(): Unknown field ID");
+ if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1");
+
+ float *ptr = (float *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double CSlib::unpack_double(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_double(): Unknown field ID");
+ if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1");
+
+ double *ptr = (double *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+char *CSlib::unpack_string(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_string(): Unknown field ID");
+ if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype");
+
+ char *ptr = (char *) unpack(id);
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::unpack(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+ return &buf[fieldoffset[ifield]];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack(int id, void *data)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+
+ int ftype = fieldtype[ifield];
+ int nbytes = fieldlen[ifield];
+ if (ftype == 1) nbytes *= sizeof(int);
+ else if (ftype == 2) nbytes *= sizeof(int64_t);
+ else if (ftype == 3) nbytes *= sizeof(float);
+ else if (ftype == 4) nbytes *= sizeof(double);
+ memcpy(data,&buf[fieldoffset[ifield]],nbytes);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_parallel(): Unknown field ID");
+ if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ int upto;
+ if (!ids) {
+ MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world);
+ upto -= nlocal;
+ }
+
+ if (fieldtype[ifield] == 1) {
+ int *local = (int *) data;
+ int *global = (int *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 2) {
+ int64_t *local = (int64_t *) data;
+ int64_t *global = (int64_t *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 3) {
+ float *local = (float *) data;
+ float *global = (float *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 4) {
+ double *local = (double *) data;
+ double *global = (double *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (fieldtype[ifield] == 5) {
+ char *local = (char *) data;
+ char *global = (char *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ memcpy(&local[m],&global[j],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::extract(int flag)
+{
+ if (flag == 1) return nsend;
+ if (flag == 2) return nrecv;
+ error_all("extract(): Invalid flag");
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround)
+{
+ int64_t bigbytes,bigbytesround;
+ int64_t biglen = flen;
+
+ if (ftype == 1) bigbytes = biglen * sizeof(int);
+ else if (ftype == 2) bigbytes = biglen * sizeof(int64_t);
+ else if (ftype == 3) bigbytes = biglen * sizeof(float);
+ else if (ftype == 4) bigbytes = biglen * sizeof(double);
+ else if (ftype == 5) bigbytes = biglen * sizeof(char);
+ bigbytesround = roundup(bigbytes,8);
+
+ if (nbuf + bigbytesround > INT_MAX)
+ error_all("pack(): Message size exceeds 32-bit integer limit");
+
+ nbytes = (int) bigbytes;
+ nbytesround = (int) bigbytesround;
+ if (nbuf + nbytesround > maxbuf) {
+ maxbuf = nbuf + nbytesround;
+ buf = (char *) srealloc(buf,maxbuf);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::find_field(int id, int n)
+{
+ int ifield;
+ for (ifield = 0; ifield < n; ifield++)
+ if (id == fieldID[ifield]) return ifield;
+ return -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::allocate_fields()
+{
+ int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int);
+ if (bigbytes > INT_MAX)
+ error_all("send(): Message header size exceeds 32-bit integer limit");
+
+ nheader = 2;
+ nheader += 3 * nfield;
+
+ if (nfield > maxfield) {
+ deallocate_fields();
+ maxfield = nfield;
+ fieldID = new int[maxfield];
+ fieldtype = new int[maxfield];
+ fieldlen = new int[maxfield];
+ fieldoffset = new int[maxfield];
+ }
+
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::deallocate_fields()
+{
+ delete [] fieldID;
+ delete [] fieldtype;
+ delete [] fieldlen;
+ delete [] fieldoffset;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::srealloc(void *ptr, int nbytes)
+{
+ if (nbytes == 0) {
+ sfree(ptr);
+ return NULL;
+ }
+
+ ptr = realloc(ptr,nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ----------------------------------------------------------------------
+ round N up to multiple of nalign and return it
+ NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t
+------------------------------------------------------------------------- */
+
+int64_t CSlib::roundup(int64_t n, int nalign)
+{
+ if (n % nalign == 0) return n;
+ n = (n/nalign + 1) * nalign;
+ return n;
+}
diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h
new file mode 100644
index 0000000000..b4da968026
--- /dev/null
+++ b/lib/message/cslib/src/cslib.h
@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef CSLIB_H
+#define CSLIB_H
+
+#include <stdint.h>
+
+namespace CSLIB_NS {
+
+class CSlib {
+ public:
+ int nsend,nrecv;
+
+ CSlib(int, const char *, const void *, const void *);
+ ~CSlib();
+
+ void send(int, int);
+
+ void pack_int(int, int);
+ void pack_int64(int, int64_t);
+ void pack_float(int, float);
+ void pack_double(int, double);
+ void pack_string(int, char *);
+ void pack(int, int, int, void *);
+ void pack_parallel(int, int, int, int *, int, void *);
+
+ int recv(int &, int *&, int *&, int *&);
+
+ int unpack_int(int);
+ int64_t unpack_int64(int);
+ float unpack_float(int);
+ double unpack_double(int);
+ char *unpack_string(int);
+ void *unpack(int);
+ void unpack(int, void *);
+ void unpack_parallel(int, int, int *, int, void *);
+
+ int extract(int);
+
+ private:
+ uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file
+ // so apps can include this file w/ no MPI on system
+ int me,nprocs;
+ int client,server;
+ int nfield,maxfield;
+ int msgID,fieldcount;
+ int nheader,maxheader;
+ int nbuf,maxbuf;
+ int maxglobal,maxfieldbytes;
+ int *fieldID,*fieldtype,*fieldlen,*fieldoffset;
+ int *header;
+ int *recvcounts,*displs; // nprocs size for Allgathers
+ int *allids; // nglobal size for pack_parallel()
+ char *buf; // maxbuf size for msg with all fields
+ char *fielddata; // maxfieldbytes size for one global field
+ const char *pad;
+
+ class Msg *msg;
+
+ void send_message();
+ void onefield(int, int, int &, int &);
+ int find_field(int, int);
+ void allocate_fields();
+ void deallocate_fields();
+ int64_t roundup(int64_t, int);
+ void *smalloc(int);
+ void *srealloc(void *, int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py
new file mode 100644
index 0000000000..0ba3516255
--- /dev/null
+++ b/lib/message/cslib/src/cslib.py
@@ -0,0 +1,362 @@
+# ------------------------------------------------------------------------
+# CSlib - Client/server library for code coupling
+# http://cslib.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright 2018 National Technology & Engineering Solutions of
+# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+# NTESS, the U.S. Government retains certain rights in this software.
+# This software is distributed under the modified Berkeley Software
+# Distribution (BSD) License.
+#
+# See the README file in the top-level CSlib directory.
+# -------------------------------------------------------------------------
+
+# Python wrapper on CSlib library via ctypes
+
+# ctypes and Numpy data types:
+# 32-bit int = c_int = np.intc = np.int32
+# 64-bit int = c_longlong = np.int64
+# 32-bit floating point = c_float = np.float32
+# 64-bit floating point = c_double = np.float = np.float64
+
+import sys,traceback
+from ctypes import *
+
+# Numpy and mpi4py packages may not exist
+
+try:
+ import numpy as np
+ numpyflag = 1
+except:
+ numpyflag = 0
+
+try:
+ from mpi4py import MPI
+ mpi4pyflag = 1
+except:
+ mpi4pyflag = 0
+
+# wrapper class
+
+class CSlib:
+
+ # instantiate CSlib thru its C-interface
+
+ def __init__(self,csflag,mode,ptr,comm):
+
+ # load libcslib.so
+
+ try:
+ if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL)
+ else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL)
+ except:
+ etype,value,tb = sys.exc_info()
+ traceback.print_exception(etype,value,tb)
+ raise OSError,"Could not load CSlib dynamic library"
+
+ # define ctypes API for each library method
+
+ self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p,
+ POINTER(c_void_p)]
+ self.lib.cslib_open.restype = None
+
+ self.lib.cslib_close.argtypes = [c_void_p]
+ self.lib.cslib_close.restype = None
+
+ self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_send.restype = None
+
+ self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_pack_int.restype = None
+
+ self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong]
+ self.lib.cslib_pack_int64.restype = None
+
+ self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float]
+ self.lib.cslib_pack_float.restype = None
+
+ self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double]
+ self.lib.cslib_pack_double.restype = None
+
+ self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p]
+ self.lib.cslib_pack_string.restype = None
+
+ self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p]
+ self.lib.cslib_pack.restype = None
+
+ self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_pack_parallel.restype = None
+
+ self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int))]
+ self.lib.cslib_recv.restype = c_int
+
+ self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int.restype = c_int
+
+ self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int64.restype = c_longlong
+
+ self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_float.restype = c_float
+
+ self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_double.restype = c_double
+
+ self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_string.restype = c_char_p
+
+ # override return in unpack()
+ self.lib.cslib_unpack.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack.restype = c_void_p
+
+ self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p]
+ self.lib.cslib_unpack_data.restype = None
+
+ # override last arg in unpack_parallel()
+ self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_unpack_parallel.restype = None
+
+ self.lib.cslib_extract.argtypes = [c_void_p,c_int]
+ self.lib.cslib_extract.restype = c_int
+
+ # create an instance of CSlib with or w/out MPI communicator
+
+ self.cs = c_void_p()
+
+ if not comm:
+ self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs))
+ elif not mpi4pyflag:
+ print "Cannot pass MPI communicator to CSlib w/out mpi4py package"
+ sys.exit()
+ else:
+ address = MPI._addressof(comm)
+ comm_ptr = c_void_p(address)
+ if mode == "mpi/one":
+ address = MPI._addressof(ptr)
+ ptrcopy = c_void_p(address)
+ else: ptrcopy = ptr
+ self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs))
+
+ # destroy instance of CSlib
+
+ def __del__(self):
+ if self.cs: self.lib.cslib_close(self.cs)
+
+ def close(self):
+ self.lib.cslib_close(self.cs)
+ self.lib = None
+
+ # send a message
+
+ def send(self,msgID,nfield):
+ self.nfield = nfield
+ self.lib.cslib_send(self.cs,msgID,nfield)
+
+ # pack one field of message
+
+ def pack_int(self,id,value):
+ self.lib.cslib_pack_int(self.cs,id,value)
+
+ def pack_int64(self,id,value):
+ self.lib.cslib_pack_int64(self.cs,id,value)
+
+ def pack_float(self,id,value):
+ self.lib.cslib_pack_float(self.cs,id,value)
+
+ def pack_double(self,id,value):
+ self.lib.cslib_pack_double(self.cs,id,value)
+
+ def pack_string(self,id,value):
+ self.lib.cslib_pack_string(self.cs,id,value)
+
+ def pack(self,id,ftype,flen,data):
+ cdata = self.data_convert(ftype,flen,data)
+ self.lib.cslib_pack(self.cs,id,ftype,flen,cdata)
+
+ def pack_parallel(self,id,ftype,nlocal,ids,nper,data):
+ cids = self.data_convert(1,nlocal,ids)
+ cdata = self.data_convert(ftype,nper*nlocal,data)
+ self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata)
+
+ # convert input data to a ctypes vector to pass to CSlib
+
+ def data_convert(self,ftype,flen,data):
+
+ # tflag = type of data
+ # tflag = 1 if data is list or tuple
+ # tflag = 2 if data is Numpy array
+ # tflag = 3 if data is ctypes vector
+ # same usage of tflag as in unpack function
+
+ txttype = str(type(data))
+ if "numpy" in txttype: tflag = 2
+ elif "c_" in txttype: tflag = 3
+ else: tflag = 1
+
+ # create ctypes vector out of data to pass to lib
+ # cdata = ctypes vector to return
+ # NOTE: error check on ftype and tflag everywhere, also flen
+
+ if ftype == 1:
+ if tflag == 1: cdata = (flen * c_int)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int))
+ elif tflag == 3: cdata = data
+ elif ftype == 2:
+ if tflag == 1: cdata = (flen * c_longlong)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong))
+ elif tflag == 3: cdata = data
+ elif ftype == 3:
+ if tflag == 1: cdata = (flen * c_float)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float))
+ elif tflag == 3: cdata = data
+ elif ftype == 4:
+ if tflag == 1: cdata = (flen * c_double)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double))
+ elif tflag == 3: cdata = data
+
+ return cdata
+
+ # receive a message
+
+ def recv(self):
+ self.lib.cslib_recv.restype = c_int
+ nfield = c_int()
+ fieldID = POINTER(c_int)()
+ fieldtype = POINTER(c_int)()
+ fieldlen = POINTER(c_int)()
+ msgID = self.lib.cslib_recv(self.cs,byref(nfield),
+ byref(fieldID),byref(fieldtype),byref(fieldlen))
+
+ # copy returned C args to native Python int and lists
+ # store them in class so unpack() methods can access the info
+
+ self.nfield = nfield = nfield.value
+ self.fieldID = fieldID[:nfield]
+ self.fieldtype = fieldtype[:nfield]
+ self.fieldlen = fieldlen[:nfield]
+
+ return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen
+
+ # unpack one field of message
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+
+ def unpack_int(self,id):
+ return self.lib.cslib_unpack_int(self.cs,id)
+
+ def unpack_int64(self,id):
+ return self.lib.cslib_unpack_int64(self.cs,id)
+
+ def unpack_float(self,id):
+ return self.lib.cslib_unpack_float(self.cs,id)
+
+ def unpack_double(self,id):
+ return self.lib.cslib_unpack_double(self.cs,id)
+
+ def unpack_string(self,id):
+ return self.lib.cslib_unpack_string(self.cs,id)
+
+ def unpack(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # reset data type of return so can morph by tflag
+ # cannot do this for the generic c_void_p returned by CSlib
+
+ if self.fieldtype[index] == 1:
+ self.lib.cslib_unpack.restype = POINTER(c_int)
+ elif self.fieldtype[index] == 2:
+ self.lib.cslib_unpack.restype = POINTER(c_longlong)
+ elif self.fieldtype[index] == 3:
+ self.lib.cslib_unpack.restype = POINTER(c_float)
+ elif self.fieldtype[index] == 4:
+ self.lib.cslib_unpack.restype = POINTER(c_double)
+ #elif self.fieldtype[index] == 5:
+ # self.lib.cslib_unpack.restype = POINTER(c_char)
+
+ cdata = self.lib.cslib_unpack(self.cs,id)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+ # tflag = 2,3 should NOT perform a data copy
+
+ if tflag == 1:
+ data = cdata[:self.fieldlen[index]]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # handle data array like pack() or unpack_parallel() ??
+
+ def unpack_data(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # unpack one field of message in parallel
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+ # NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg?
+ # as opposed to creating this cdata
+ # does that make any performance difference ?
+ # e.g. should we allow CSlib to populate an existing Numpy array's memory
+
+ def unpack_parallel(self,id,nlocal,ids,nper,tflag=3):
+ cids = self.data_convert(1,nlocal,ids)
+
+ # allocate memory for the returned data
+ # pass cdata ptr to the memory to CSlib unpack_parallel()
+ # this resets data type of last unpack_parallel() arg
+
+ index = self.fieldID.index(id)
+ if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)()
+ elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)()
+ elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)()
+ elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)()
+ #elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)()
+
+ self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+
+ if tflag == 1:
+ data = cdata[:nper*nlocal]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ # NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int
+ # not sure why, reported as bug between ctypes and Numpy here:
+ # https://stackoverflow.com/questions/4964101/pep-3118-
+ # warning-when-using-ctypes-array-as-numpy-array
+ # but why not same warning when just using unpack() ??
+ # in Python these lines give same warning:
+ # >>> import ctypes,numpy
+ # >>> a = (10 * ctypes.c_longlong)()
+ # >>> b = numpy.ctypeslib.as_array(a)
+ data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # extract a library value
+
+ def extract(self,flag):
+ return self.lib.cslib_extract(self.cs,flag)
diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp
new file mode 100644
index 0000000000..c2d69eaf0d
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.cpp
@@ -0,0 +1,239 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// C style library interface to CSlib class
+
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cslib_wrap.h"
+#include "cslib.h"
+
+using namespace CSLIB_NS;
+
+// ----------------------------------------------------------------------
+
+void cslib_open(int csflag, const char *mode, const void *ptr,
+ const void *pcomm, void **csptr)
+{
+ CSlib *cs = new CSlib(csflag,mode,ptr,pcomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran(int csflag, const char *mode, const char *str,
+ const void *pcomm, void **csptr)
+{
+ MPI_Comm ccomm;
+ void *pccomm = NULL;
+
+ if (pcomm) {
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+ }
+
+ CSlib *cs = new CSlib(csflag,mode,str,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran_mpi_one(int csflag, const char *mode,
+ const void *pboth, const void *pcomm,
+ void **csptr)
+{
+ MPI_Comm ccomm,cboth;
+ void *pccomm,*pcboth;
+
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+
+ MPI_Fint *fboth = (MPI_Fint *) pboth;
+ cboth = MPI_Comm_f2c(*fboth);
+ pcboth = &cboth;
+
+ CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_close(void *ptr)
+{
+ CSlib *cs = (CSlib *) ptr;
+ delete cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_send(void *ptr, int msgID, int nfield)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->send(msgID,nfield);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int(void *ptr, int id, int value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int64(void *ptr, int id, int64_t value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int64(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_float(void *ptr, int id, float value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_float(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_double(void *ptr, int id, double value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_double(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_string(void *ptr, int id, char *value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_string(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack(void *ptr, int id, int ftype, int flen, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack(id,ftype,flen,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_parallel(void *ptr, int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_parallel(id,ftype,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_recv(void *ptr, int *nfield_caller,
+ int **fieldID_caller, int **fieldtype_caller,
+ int **fieldlen_caller)
+{
+ CSlib *cs = (CSlib *) ptr;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ *nfield_caller = nfield;
+ *fieldID_caller = fieldID;
+ *fieldtype_caller = fieldtype;
+ *fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_unpack_int(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int(id);
+}
+// ----------------------------------------------------------------------
+
+int64_t cslib_unpack_int64(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int64(id);
+}
+
+// ----------------------------------------------------------------------
+
+float cslib_unpack_float(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_float(id);
+}
+
+// ----------------------------------------------------------------------
+
+double cslib_unpack_double(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_double(id);
+}
+
+// ----------------------------------------------------------------------
+
+char *cslib_unpack_string(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_string(id);
+}
+
+// ----------------------------------------------------------------------
+
+void *cslib_unpack(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack(id);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_data(void *ptr, int id, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack(id,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids,
+ int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack_parallel(id,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_extract(void *ptr, int flag)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->extract(flag);
+}
diff --git a/lib/message/cslib/src/cslib_wrap.f90 b/lib/message/cslib/src/cslib_wrap.f90
new file mode 100644
index 0000000000..cd2e058b78
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.f90
@@ -0,0 +1,147 @@
+! ISO_C_binding wrapper on CSlib C interface
+
+module cslib_wrap
+
+interface
+ subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*),str(*)
+ type(c_ptr), value :: pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran
+
+ subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*)
+ type(c_ptr), value :: pboth,pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran_mpi_one
+
+ subroutine cslib_close(ptr) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ end subroutine cslib_close
+
+ subroutine cslib_send(ptr,msgID,nfield) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: msgID,nfield
+ end subroutine cslib_send
+
+ subroutine cslib_pack_int(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int), value :: value
+ end subroutine cslib_pack_int
+
+ subroutine cslib_pack_int64(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int64_t), value :: value
+ end subroutine cslib_pack_int64
+
+ subroutine cslib_pack_float(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_float), value :: value
+ end subroutine cslib_pack_float
+
+ subroutine cslib_pack_double(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_double), value :: value
+ end subroutine cslib_pack_double
+
+ subroutine cslib_pack_string(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ character(c_char) :: value(*)
+ end subroutine cslib_pack_string
+
+ subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,flen
+ type(c_ptr), value :: data
+ end subroutine cslib_pack
+
+ subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_pack_parallel
+
+ function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_recv
+ type(c_ptr), value :: ptr
+ integer(c_int) :: nfield
+ type(c_ptr) :: fieldID,fieldtype,fieldlen
+ end function cslib_recv
+
+ function cslib_unpack_int(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_unpack_int
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int
+
+ function cslib_unpack_int64(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int64_t) :: cslib_unpack_int64
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int64
+
+ function cslib_unpack_float(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_float) :: cslib_unpack_float
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_float
+
+ function cslib_unpack_double(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_double) :: cslib_unpack_double
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_double
+
+ function cslib_unpack_string(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack_string
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_string
+
+ function cslib_unpack(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack
+
+ subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_unpack_parallel
+
+ function cslib_extract(ptr,flag) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_extract
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: flag
+ end function cslib_extract
+end interface
+
+end module cslib_wrap
diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h
new file mode 100644
index 0000000000..bf7df029c3
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.h
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+/* C style library interface to CSlib class
+ ifdefs allow this file to be included in a C program
+*/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void cslib_open(int, const char *, const void *, const void *, void **);
+void cslib_open_fortran(int, const char *, const char *, const void *, void **);
+void cslib_open_fortran_mpi_one(int, const char *, const void *,
+ const void *, void **);
+void cslib_close(void *);
+
+void cslib_send(void *, int, int);
+
+void cslib_pack_int(void *, int, int);
+void cslib_pack_int64(void *, int, int64_t);
+void cslib_pack_float(void *, int, float);
+void cslib_pack_double(void *, int, double);
+void cslib_pack_string(void *, int, char *);
+void cslib_pack(void *, int, int, int, void *);
+void cslib_pack_parallel(void *, int, int, int, int *, int, void *);
+
+int cslib_recv(void *, int *, int **, int **, int **);
+
+int cslib_unpack_int(void *, int);
+int64_t cslib_unpack_int64(void *, int);
+float cslib_unpack_float(void *, int);
+double cslib_unpack_double(void *, int);
+char *cslib_unpack_string(void *, int);
+void *cslib_unpack(void *, int);
+void cslib_unpack_data(void *, int, void *);
+void cslib_unpack_parallel(void *, int, int, int *, int, void *);
+
+int cslib_extract(void *, int);
+
+#ifdef __cplusplus
+}
+#endif
diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp
new file mode 100644
index 0000000000..c67e4a5c8c
--- /dev/null
+++ b/lib/message/cslib/src/msg.cpp
@@ -0,0 +1,110 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "msg.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
+{
+ world = cworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr)
+{
+ world = 0;
+ me = 0;
+ nprocs = 1;
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::init(int csflag)
+{
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::allocate(int nheader, int &maxheader, int *&header,
+ int nbuf, int &maxbuf, char *&buf)
+{
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+
+ if (nbuf > maxbuf) {
+ sfree(buf);
+ maxbuf = nbuf;
+ buf = (char *) smalloc(maxbuf*sizeof(char));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *Msg::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = (void *) malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"Failed to allocate %d bytes",nbytes);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h
new file mode 100644
index 0000000000..f75942b027
--- /dev/null
+++ b/lib/message/cslib/src/msg.h
@@ -0,0 +1,52 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_H
+#define MSG_H
+
+#include <mpi.h>
+
+namespace CSLIB_NS {
+
+class Msg {
+ public:
+ int nsend,nrecv;
+ MPI_Comm world;
+
+ Msg(int, const void *, MPI_Comm);
+ Msg(int, const void *);
+ virtual ~Msg() {}
+ virtual void send(int, int *, int, char *) = 0;
+ virtual void recv(int &, int *&, int &, char *&) = 0;
+
+ protected:
+ int me,nprocs;
+ int client,server;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int lengths[2];
+
+ void init(int);
+ void allocate(int, int &, int *&, int, int &, char *&);
+ void *smalloc(int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp
new file mode 100644
index 0000000000..d97e249fad
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <unistd.h>
+
+#include "msg_file.h"
+
+using namespace CSLIB_NS;
+
+#define MAXLINE 256
+#define SLEEP 0.1 // delay in CPU secs to check for message file
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::~MsgFile()
+{
+ delete [] fileroot;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::init(char *filename)
+{
+ int n = strlen(filename) + 1;
+ fileroot = new char[n];
+ strcpy(fileroot,filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::send(int nheader, int *header, int nbuf, char *buf)
+{
+ char filename[MAXLINE];
+
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server");
+
+ fp = fopen(filename,"wb");
+ if (!fp) error_one("send(): Could not open send message file");
+ fwrite(lengths,sizeof(int),2,fp);
+ fwrite(header,sizeof(int),nheader,fp);
+ fwrite(buf,1,nbuf,fp);
+ fclose(fp);
+ }
+
+ // create empty signal file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ fp = fopen(filename,"w");
+ fclose(fp);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ char filename[MAXLINE];
+
+ // wait until signal file exists to open message file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+
+ int delay = (int) (1000000 * SLEEP);
+ while (1) {
+ fp = fopen(filename,"r");
+ if (fp) break;
+ usleep(delay);
+ }
+ fclose(fp);
+
+ if (client) sprintf(filename,"%s.%s",fileroot,"server");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client");
+ fp = fopen(filename,"rb");
+ if (!fp) error_one("recv(): Could not open recv message file");
+ }
+
+ // read and broadcast data
+
+ if (me == 0) fread(lengths,sizeof(int),2,fp);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) fread(header,sizeof(int),nheader,fp);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) fread(buf,1,nbuf,fp);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+
+ // delete both message and signal file
+
+ if (me == 0) {
+ fclose(fp);
+ unlink(filename);
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ unlink(filename);
+ }
+}
diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h
new file mode 100644
index 0000000000..d6bd802607
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_FILE_H
+#define MSG_FILE_H
+
+#include <stdio.h>
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgFile : public Msg {
+ public:
+ MsgFile(int, const void *, MPI_Comm);
+ MsgFile(int, const void *);
+ ~MsgFile();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ char *fileroot;
+ FILE *fp;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp
new file mode 100644
index 0000000000..db11735b27
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.cpp
@@ -0,0 +1,82 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_one.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ // NOTE: ideally would skip this call if mpi/two
+ init(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::init(const void *ptr)
+{
+ MPI_Comm *pbothcomm = (MPI_Comm *) ptr;
+ bothcomm = *pbothcomm;
+
+ if (client) {
+ MPI_Comm_size(world,&nprocs);
+ otherroot = nprocs;
+ } else if (server) {
+ otherroot = 0;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ MPI_Status status;
+
+ if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h
new file mode 100644
index 0000000000..4b4140a3f7
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_ONE_H
+#define MSG_MPI_ONE_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgMPIOne : public Msg {
+ public:
+ MsgMPIOne(int, const void *, MPI_Comm);
+ virtual ~MsgMPIOne() {}
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ protected:
+ MPI_Comm bothcomm;
+ int otherroot;
+
+ void init(const void *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp
new file mode 100644
index 0000000000..e9a9e87eeb
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.cpp
@@ -0,0 +1,81 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) :
+ MsgMPIOne(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::~MsgMPITwo()
+{
+ // free the inter comm that spans both client and server
+
+ MPI_Comm_free(&bothcomm);
+ MPI_Close_port(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPITwo::init(char *filename)
+{
+ if (client) {
+ if (me == 0) {
+ FILE *fp = NULL;
+ while (!fp) {
+ fp = fopen(filename,"r");
+ if (!fp) sleep(1);
+ }
+ fgets(port,MPI_MAX_PORT_NAME,fp);
+ //printf("Client port: %s\n",port);
+ fclose(fp);
+ }
+
+ MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world);
+ MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("CLIENT comm connect\n");
+ if (me == 0) unlink(filename);
+
+ } else if (server) {
+ MPI_Open_port(MPI_INFO_NULL,port);
+
+ if (me == 0) {
+ //printf("Server name: %s\n",port);
+ FILE *fp = fopen(filename,"w");
+ fprintf(fp,"%s",port);
+ fclose(fp);
+ }
+
+ MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("SERVER comm accept\n");
+ }
+
+ otherroot = 0;
+}
diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h
new file mode 100644
index 0000000000..7b31db5a63
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.h
@@ -0,0 +1,35 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_TWO_H
+#define MSG_MPI_TWO_H
+
+#include "msg_mpi_one.h"
+
+namespace CSLIB_NS {
+
+class MsgMPITwo : public MsgMPIOne {
+ public:
+ MsgMPITwo(int, const void *, MPI_Comm);
+ ~MsgMPITwo();
+
+ private:
+ char port[MPI_MAX_PORT_NAME];
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp
new file mode 100644
index 0000000000..c2d408f3a5
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.cpp
@@ -0,0 +1,140 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <zmq.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+
+#include "msg_zmq.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::~MsgZMQ()
+{
+ if (me == 0) {
+ zmq_close(socket);
+ zmq_ctx_destroy(context);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgZMQ::init(char *port)
+{
+#ifdef ZMQ_NO
+ error_all("constructor(): Library not built with ZMQ support");
+#endif
+
+ if (me == 0) {
+ int n = strlen(port) + 8;
+ char *socket_name = new char[n];
+ strcpy(socket_name,"tcp://");
+ strcat(socket_name,port);
+
+ if (client) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REQ);
+ zmq_connect(socket,socket_name);
+ } else if (server) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REP);
+ int rc = zmq_bind(socket,socket_name);
+ if (rc) error_one("constructor(): Server could not make socket connection");
+ }
+
+ delete [] socket_name;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ send below has a following ZMQ recv, except last one
+ if client calls send(), it will next call recv()
+ if server calls send(), it will next call recv() from its wait loop
+ in either case, recv() issues a ZMQ recv to match last ZMQ send here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ zmq_send(socket,lengths,2*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) {
+ zmq_send(socket,header,nheader*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) zmq_send(socket,buf,nbuf,0);
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ recv below has a following ZMQ send, except last one
+ if client calls recv(), it will next call send() to ping server again,
+ if server calls recv(), it will next call send() to respond to client
+ in either case, send() issues a ZMQ send to match last ZMQ recv here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ if (me == 0) {
+ zmq_recv(socket,lengths,2*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) {
+ zmq_recv(socket,header,nheader*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) zmq_recv(socket,buf,nbuf,0);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h
new file mode 100644
index 0000000000..c0621a26ff
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_ZMQ_H
+#define MSG_ZMQ_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgZMQ : public Msg {
+ public:
+ MsgZMQ(int, const void *, MPI_Comm);
+ MsgZMQ(int, const void *);
+ ~MsgZMQ();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ void *context,*socket;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/src/MESSAGE/Install.sh b/src/MESSAGE/Install.sh
new file mode 100644
index 0000000000..853dbddcdd
--- /dev/null
+++ b/src/MESSAGE/Install.sh
@@ -0,0 +1,67 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# arg1 = file, arg2 = file it depends on
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+action () {
+ if (test $mode = 0) then
+ rm -f ../$1
+ elif (! cmp -s $1 ../$1) then
+ if (test -z "$2" || test -e ../$2) then
+ cp $1 ..
+ if (test $mode = 2) then
+ echo " updating src/$1"
+ fi
+ fi
+ elif (test -n "$2") then
+ if (test ! -e ../$2) then
+ rm -f ../$1
+ fi
+ fi
+}
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+ test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ # multiline form needed for BSD sed on Macs
+ sed -i -e '4 i \
+include ..\/..\/lib\/message\/Makefile.lammps
+' ../Makefile.package.settings
+ fi
+
+elif (test $1 = 0) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ fi
+
+fi
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
new file mode 100644
index 0000000000..aca5cd41f9
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -0,0 +1,325 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstdio>
+#include <cstring>
+#include "fix_client_md.h"
+#include "update.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+using namespace FixConst;
+
+enum{OTHER,REAL,METAL};
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ if (lmp->clientserver != 1)
+ error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
+ if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");
+
+ if (sizeof(tagint) != 4)
+ error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
+
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else units = OTHER;
+
+ scalar_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ virial_flag = 1;
+ thermo_virial = 1;
+
+ inv_nprocs = 1.0 / comm->nprocs;
+ if (domain->dimension == 2)
+ box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0;
+
+ maxatom = 0;
+ xpbc = NULL;
+
+ // unit conversion factors for REAL
+ // otherwise not needed
+ // message received in METAL units, convert to local REAL units
+
+ fconvert = econvert = pconvert = 1.0;
+ if (units == REAL) {
+ fconvert = econvert = 23.06035; // eV -> Kcal/mole
+ pconvert = 0.986923; // bars -> atmospheres
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::~FixClientMD()
+{
+ memory->destroy(xpbc);
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // all-done message to server
+
+ cs->send(-1,0);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // clean-up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixClientMD::setmask()
+{
+ int mask = 0;
+ mask |= POST_FORCE;
+ mask |= MIN_POST_FORCE;
+ mask |= THERMO_ENERGY;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::init()
+{
+ if (3*atom->natoms > INT_MAX)
+ error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::setup(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // SETUP send at beginning of each run
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+ // optional fields: others in enum above
+
+ int nfields = 8;
+ if (units == OTHER) nfields++;
+ if (atom->q_flag) nfields++;
+
+ cs->send(SETUP,nfields);
+
+ cs->pack_int(DIM,domain->dimension);
+ cs->pack(PERIODICITY,1,3,domain->periodicity);
+
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
+
+ cs->pack_int(NATOMS,atom->natoms);
+ cs->pack_int(NTYPES,atom->ntypes);
+
+ cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (units == OTHER) cs->pack_string(UNITS,update->unit_style);
+
+ if (atom->q_flag)
+ cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
+
+ // receive initial forces, energy, virial
+
+ receive_fev(vflag);
+
+ if (server_error) {
+ char str[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_setup(int vflag)
+{
+ setup(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::post_force(int vflag)
+{
+ int i,j,m;
+
+ // energy and virial setup
+
+ if (vflag) v_setup(vflag);
+ else evflag = 0;
+
+ // STEP send every step
+ // required fields: COORDS
+ // optional fields: ORIGIN, BOX
+
+ // send coords
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfields = 1;
+ if (domain->box_change) nfields += 2;
+
+ cs->send(STEP,nfields);
+
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (domain->box_change) {
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
+ }
+
+ // receive forces, energy, virial
+
+ receive_fev(vflag);
+
+ if (server_error) {
+ char str[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_post_force(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ potential energy from server
+------------------------------------------------------------------------- */
+
+double FixClientMD::compute_scalar()
+{
+ return eng;
+}
+
+/* ----------------------------------------------------------------------
+ pack local coords into xpbc, enforcing PBC
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_coords()
+{
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+
+ if (nlocal > maxatom) {
+ memory->destroy(xpbc);
+ maxatom = atom->nmax;
+ memory->create(xpbc,3*maxatom,"message:xpbc");
+ }
+
+ memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
+
+ int j = 0;
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack box info into box = 3 edge vectors of simulation box
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_box()
+{
+ double *boxlo = domain->boxlo;
+ double *boxhi = domain->boxhi;
+
+ box[0][0] = boxhi[0] - boxlo[0];
+ box[0][1] = 0.0;
+ box[0][2] = 0.0;
+ box[1][0] = domain->xy;
+ box[1][1] = boxhi[1] - boxlo[1];
+ box[1][2] = 0.0;
+ box[2][0] = domain->xz;
+ box[2][1] = domain->yz;
+ box[2][2] = boxhi[2] - boxlo[2];
+}
+
+/* ----------------------------------------------------------------------
+ receive message from server
+ required fields: FORCES, ENERGY, PRESSURE
+ optional field: ERROR
+------------------------------------------------------------------------- */
+
+void FixClientMD::receive_fev(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ double *forces = (double *) cs->unpack(FORCES);
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ bigint natoms = atom->natoms;
+ int m;
+
+ int j = 0;
+ for (tagint id = 1; id <= natoms; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ f[m][0] += fconvert * forces[j++];
+ f[m][1] += fconvert * forces[j++];
+ f[m][2] += fconvert * forces[j++];
+ }
+ }
+
+ eng = econvert * cs->unpack_double(ENERGY);
+
+ if (vflag) {
+ double *v = (double *) cs->unpack(PRESSURE);
+
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = inv_nprocs * pconvert * volume / nktv2p;
+
+ for (int i = 0; i < 6; i++)
+ virial[i] = factor * v[i];
+ }
+
+ // error return
+
+ server_error = 0;
+ if (nfield == 4) server_error = cs->unpack_int(ERROR);
+}
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
new file mode 100644
index 0000000000..1c874c7278
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.h
@@ -0,0 +1,65 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(client/md,FixClientMD)
+
+#else
+
+#ifndef LMP_FIX_CLIENT_MD_H
+#define LMP_FIX_CLIENT_MD_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixClientMD : public Fix {
+ public:
+ FixClientMD(class LAMMPS *, int, char **);
+ ~FixClientMD();
+ int setmask();
+ void init();
+ void setup(int);
+ void min_setup(int);
+ void post_force(int);
+ void min_post_force(int);
+ double compute_scalar();
+
+ private:
+ int maxatom,units,server_error;
+ double eng;
+ double inv_nprocs;
+ double fconvert,econvert,pconvert;
+ double box[3][3];
+ double *xpbc;
+
+ void pack_coords();
+ void pack_box();
+ void receive_fev(int);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
new file mode 100644
index 0000000000..329ce1fbd9
--- /dev/null
+++ b/src/MESSAGE/message.cpp
@@ -0,0 +1,90 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include "message.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+// customize by adding a new server protocol enum
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Message::command(int narg, char **arg)
+{
+ if (narg < 3) error->all(FLERR,"Illegal message command");
+
+ int clientserver;
+ if (strcmp(arg[0],"client") == 0) clientserver = 1;
+ else if (strcmp(arg[0],"server") == 0) clientserver = 2;
+ else error->all(FLERR,"Illegal message command");
+ lmp->clientserver = clientserver;
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[1],"md") == 0) protocol = MD;
+ else if (strcmp(arg[1],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ // instantiate CSlib with chosen communication mode
+
+ if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 ||
+ strcmp(arg[2],"mpi/two") == 0) {
+ if (narg != 4) error->all(FLERR,"Illegal message command");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world);
+
+ } else if (strcmp(arg[2],"mpi/one") == 0) {
+ if (narg != 3) error->all(FLERR,"Illegal message command");
+ if (!lmp->cscomm)
+ error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world);
+
+ } else error->all(FLERR,"Illegal message command");
+
+ // perform initial handshake between client and server
+ // other code being coupled to must perform similar operation
+ // client sends protocol with msgID = 0
+ // server matches it and replies
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ if (clientserver == 1) {
+ cs->send(0,1);
+ cs->pack_string(1,arg[1]);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+
+ } else {
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+ char *pstr = cs->unpack_string(1);
+ if (strcmp(pstr,arg[1]) != 0)
+ error->one(FLERR,"Mismatch in client/server protocol");
+
+ cs->send(0,0);
+ }
+}
diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h
new file mode 100644
index 0000000000..c384a5a7b7
--- /dev/null
+++ b/src/MESSAGE/message.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(message,Message)
+
+#else
+
+#ifndef LMP_MESSAGE_H
+#define LMP_MESSAGE_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Message : protected Pointers {
+ public:
+ Message(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
new file mode 100644
index 0000000000..f587fb76df
--- /dev/null
+++ b/src/MESSAGE/server.cpp
@@ -0,0 +1,50 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include "server.h"
+#include "error.h"
+
+// customize by adding a new server protocol include and enum
+
+#include "server_md.h"
+#include "server_mc.h"
+
+using namespace LAMMPS_NS;
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Server::command(int narg, char **arg)
+{
+ if (narg != 1) error->all(FLERR,"Illegal server command");
+
+ if (lmp->clientserver != 2)
+ error->all(FLERR,"Message command not used to setup LAMMPS as a server");
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[0],"md") == 0) protocol = MD;
+ else if (strcmp(arg[0],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ if (protocol == MD) {
+ ServerMD *server = new ServerMD(lmp);
+ server->loop();
+ } else if (protocol == MC) {
+ ServerMC *server = new ServerMC(lmp);
+ server->loop();
+ }
+}
diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h
new file mode 100644
index 0000000000..579f6ab6f1
--- /dev/null
+++ b/src/MESSAGE/server.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(server,Server)
+
+#else
+
+#ifndef LMP_SERVER_H
+#define LMP_SERVER_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Server : protected Pointers {
+ public:
+ Server(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp
new file mode 100644
index 0000000000..8a7344e86b
--- /dev/null
+++ b/src/MESSAGE/server_mc.cpp
@@ -0,0 +1,148 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "server_mc.h"
+#include "atom.h"
+#include "update.h"
+#include "integrate.h"
+#include "input.h"
+#include "output.h"
+#include "thermo.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+/* ---------------------------------------------------------------------- */
+
+ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMC::loop()
+{
+ int i,j,m;
+ double xold[3],xnew[3];
+ tagint atomid;
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // require atom map
+
+ if (!atom->map_style) error->all(FLERR,"Server mode requires atom map");
+
+ // initialize LAMMPS for dynamics
+
+ input->one("run 0");
+
+ //update->whichflag = 1;
+ //lmp->init();
+
+ // loop on messages
+ // receive a message, process it, send return message if necessary
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ if (msgID == NATOMS) {
+
+ cs->send(msgID,1);
+ cs->pack_int(1,atom->natoms);
+
+ } else if (msgID == EINIT) {
+
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,2);
+ cs->pack_double(1,dval);
+ double *coords = NULL;
+ if (atom->nlocal) coords = &atom->x[0][0];
+ cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords);
+
+ } else if (msgID == DISPLACE) {
+
+ atomid = cs->unpack_int(1);
+ double *xnew = (double *) cs->unpack(2);
+ double **x = atom->x;
+
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ xold[0] = x[m][0];
+ xold[1] = x[m][1];
+ xold[2] = x[m][2];
+ x[m][0] = xnew[0];
+ x[m][1] = xnew[1];
+ x[m][2] = xnew[2];
+ }
+
+ input->one("run 0");
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,1);
+ cs->pack_double(1,dval);
+
+ } else if (msgID == ACCEPT) {
+
+ int accept = cs->unpack_int(1);
+ double **x = atom->x;
+
+ if (!accept) {
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ x[m][0] = xold[0];
+ x[m][1] = xold[1];
+ x[m][2] = xold[2];
+ }
+ }
+
+ cs->send(msgID,0);
+
+ } else if (msgID == RUN) {
+
+ int nsteps = cs->unpack_int(1);
+
+ //input->one("run 100");
+
+ update->nsteps = nsteps;
+ update->firststep = update->ntimestep;
+ update->laststep = update->ntimestep + nsteps;
+
+ update->integrate->setup(1);
+ update->integrate->run(nsteps);
+
+ cs->send(msgID,0);
+
+ } else error->all(FLERR,"Server received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h
new file mode 100644
index 0000000000..d0fb489429
--- /dev/null
+++ b/src/MESSAGE/server_mc.h
@@ -0,0 +1,29 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MC_H
+#define LMP_SERVER_MC_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMC : protected Pointers {
+ public:
+ ServerMC(class LAMMPS *);
+ void loop();
+};
+
+}
+
+#endif
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
new file mode 100644
index 0000000000..aa771b7d46
--- /dev/null
+++ b/src/MESSAGE/server_md.cpp
@@ -0,0 +1,389 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cstring>
+#include "server_md.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "update.h"
+#include "integrate.h"
+#include "kspace.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "comm.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{OTHER,REAL,METAL};
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
+{
+ if (domain->box_exist == 0)
+ error->all(FLERR,"Server command before simulation box is defined");
+
+ if (!atom->map_style) error->all(FLERR,"Server md requires atom map");
+ if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs");
+ if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
+
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else units = OTHER;
+
+ // unit conversion factors for REAL
+ // otherwise not needed
+ // local computation in REAL units, send message in METAL units
+
+ fconvert = econvert = pconvert = 1.0;
+ if (units == REAL) {
+ fconvert = econvert = 1.0 / 23.06035; // Kcal/mole -> eV
+ pconvert = 1.0 / 0.986923; // atmospheres -> bars
+ }
+
+ fcopy = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::~ServerMD()
+{
+ memory->destroy(fcopy);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMD::loop()
+{
+ int i,j,m;
+
+ // cs = instance of CSlib
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // counters
+
+ int forcecalls = 0;
+ int neighcalls = 0;
+
+ // loop on messages
+ // receive a message, process it, send return message
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ // SETUP receive at beginning of each run
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ // NATOMS, NTYPES, TYPES, COORDS
+ // optional fields: others in enum above
+
+ if (msgID == SETUP) {
+
+ int dim = 0;
+ int *periodicity = NULL;
+ int natoms = -1;
+ int ntypes = -1;
+ double *origin = NULL;
+ double *box = NULL;
+ int *types = NULL;
+ double *coords = NULL;
+ char *unit_style = NULL;
+ double *charge = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == DIM) {
+ dim = cs->unpack_int(DIM);
+ if (dim != domain->dimension)
+ error->all(FLERR,"Server md dimension mis-match with client");
+ } else if (fieldID[ifield] == PERIODICITY) {
+ periodicity = (int *) cs->unpack(PERIODICITY);
+ if (periodicity[0] != domain->periodicity[0] ||
+ periodicity[1] != domain->periodicity[1] ||
+ periodicity[2] != domain->periodicity[2])
+ error->all(FLERR,"Server md periodicity mis-match with client");
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
+ } else if (fieldID[ifield] == NATOMS) {
+ natoms = cs->unpack_int(NATOMS);
+ if (3*natoms > INT_MAX)
+ error->all(FLERR,"Server md max atoms is 1/3 of 2^31");
+ } else if (fieldID[ifield] == NTYPES) {
+ ntypes = cs->unpack_int(NTYPES);
+ if (ntypes != atom->ntypes)
+ error->all(FLERR,"Server md ntypes mis-match with client");
+ } else if (fieldID[ifield] == TYPES) {
+ types = (int *) cs->unpack(TYPES);
+ } else if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+
+ } else if (fieldID[ifield] == UNITS) {
+ unit_style = (char *) cs->unpack(UNITS);
+ } else if (fieldID[ifield] == CHARGE) {
+ charge = (double *) cs->unpack(CHARGE);
+ } else error->all(FLERR,"Server md setup field unknown");
+ }
+
+ if (dim == 0 || !periodicity || !origin || !box ||
+ natoms < 0 || ntypes < 0 || !types || !coords)
+ error->all(FLERR,"Required server md setup field not received");
+
+ if (unit_style && strcmp(unit_style,update->unit_style) != 0)
+ error->all(FLERR,"Server md does not match client units");
+
+ if (charge && atom->q_flag == 0)
+ error->all(FLERR,"Server md does not define atom attribute q");
+
+ // reset box, global and local
+ // reset proc decomposition
+
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
+
+ box_change(origin,box);
+
+ domain->set_initial_box();
+ domain->set_global_box();
+ comm->set_proc_grid();
+ domain->set_local_box();
+
+ // clear all atoms
+
+ atom->nlocal = 0;
+ atom->nghost = 0;
+
+ // add atoms that are in my sub-box
+
+ int nlocal = 0;
+ for (int i = 0; i < natoms; i++) {
+ if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue;
+ atom->avec->create_atom(types[i],&coords[3*i]);
+ atom->tag[nlocal] = i+1;
+ if (charge) atom->q[nlocal] = charge[i];
+ nlocal++;
+ }
+
+ int ntotal;
+ MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
+ if (ntotal != natoms)
+ error->all(FLERR,"Server md atom count does not match client");
+
+ atom->map_init();
+ atom->map_set();
+ atom->natoms = natoms;
+
+ // allocate fcopy if needed
+
+ if (units == REAL) {
+ memory->destroy(fcopy);
+ memory->create(fcopy,atom->nlocal,3,"server/md:fcopy");
+ }
+
+ // perform system setup() for dynamics
+ // also OK for minimization, since client runs minimizer
+ // return forces, energy, virial to client
+
+ update->whichflag = 1;
+ lmp->init();
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ forcecalls++;
+
+ send_fev(msgID);
+
+ // STEP receive at each timestep of run or minimization
+ // required fields: COORDS
+ // optional fields: ORIGIN, BOX
+
+ } else if (msgID == STEP) {
+
+ double *coords = NULL;
+ double *origin = NULL;
+ double *box = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
+ } else error->all(FLERR,"Server md step field unknown");
+ }
+
+ if (!coords)
+ error->all(FLERR,"Required server md step field not received");
+
+ // change box size/shape, only if origin and box received
+ // reset global/local box like FixDeform at end_of_step()
+
+ if (origin && box) {
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
+ box_change(origin,box);
+ domain->set_global_box();
+ domain->set_local_box();
+ }
+
+ // assign received coords to owned atoms
+ // closest_image() insures xyz matches current server PBC
+
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+ int nall = atom->natoms;
+
+ j = 0;
+ for (tagint id = 1; id <= nall; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ domain->closest_image(x[m],&coords[j],x[m]);
+ j += 3;
+ }
+ }
+
+ // if no need to reneighbor:
+ // ghost comm
+ // setup_minimal(0) which just computes forces
+ // else:
+ // setup_minimal(1) for pbc, reset_box, reneigh, forces
+
+ int nflag = neighbor->decide();
+ if (nflag == 0) {
+ comm->forward_comm();
+ update->integrate->setup_minimal(0);
+ } else {
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ }
+
+ forcecalls++;
+
+ send_fev(msgID);
+
+ } else error->all(FLERR,"Server MD received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // stats
+
+ if (comm->me == 0) {
+ if (screen) {
+ fprintf(screen,"Server MD calls = %d\n",forcecalls);
+ fprintf(screen,"Server MD reneighborings = %d\n",neighcalls);
+ }
+ if (logfile) {
+ fprintf(logfile,"Server MD calls = %d\n",forcecalls);
+ fprintf(logfile,"Server MD reneighborings %d\n",neighcalls);
+ }
+ }
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ box change due to received message
+------------------------------------------------------------------------- */
+
+void ServerMD::box_change(double *origin, double *box)
+{
+ domain->boxlo[0] = origin[0];
+ domain->boxlo[1] = origin[1];
+ domain->boxlo[2] = origin[2];
+
+ domain->boxhi[0] = origin[0] + box[0];
+ domain->boxhi[1] = origin[1] + box[4];
+ domain->boxhi[2] = origin[2] + box[8];
+
+ domain->xy = box[3];
+ domain->xz = box[6];
+ domain->yz = box[7];
+}
+
+/* ----------------------------------------------------------------------
+ return message with forces, energy, pressure tensor
+ pressure tensor should be just pair and KSpace contributions
+ required fields: FORCES, ENERGY, PRESSURE
+ optional field: ERROR (not ever sending)
+------------------------------------------------------------------------- */
+
+void ServerMD::send_fev(int msgID)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ cs->send(msgID,3);
+
+ double *forces = NULL;
+ if (atom->nlocal) {
+ if (units != REAL) forces = &atom->f[0][0];
+ else {
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ fcopy[i][0] = fconvert*f[i][0];
+ fcopy[i][1] = fconvert*f[i][1];
+ fcopy[i][2] = fconvert*f[i][2];
+ }
+ forces = &fcopy[0][0];
+ }
+ }
+ cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces);
+
+ double eng = force->pair->eng_vdwl + force->pair->eng_coul;
+ double engall;
+ MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
+ engall *= econvert;
+ cs->pack_double(ENERGY,engall);
+
+ double v[6],vall[6];
+ for (int i = 0; i < 6; i++)
+ v[i] = force->pair->virial[i];
+ MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
+
+ if (force->kspace)
+ for (int i = 0; i < 6; i++)
+ vall[i] += force->kspace->virial[i];
+
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = pconvert / volume * nktv2p;
+ for (int i = 0; i < 6; i++) vall[i] *= factor;
+
+ cs->pack(PRESSURE,4,6,vall);
+}
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
new file mode 100644
index 0000000000..289d70bdd8
--- /dev/null
+++ b/src/MESSAGE/server_md.h
@@ -0,0 +1,38 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MD_H
+#define LMP_SERVER_MD_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMD : protected Pointers {
+ public:
+ ServerMD(class LAMMPS *);
+ ~ServerMD();
+ void loop();
+
+ private:
+ int units;
+ double fconvert,econvert,pconvert;
+ double **fcopy;
+
+ void box_change(double *, double *);
+ void send_fev(int);
+};
+
+}
+
+#endif
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe..b9cabfd67b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -53,7 +53,7 @@ endif
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
- granular kim kokkos kspace latte manybody mc meam misc \
+ granular kim kokkos kspace latte manybody mc meam message misc \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap spin srd voronoi
@@ -65,14 +65,14 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
-PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
+PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-qmmm user-quip user-smd user-vtk
PACKSYS = compress mpiio python user-lb
-PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
+PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
user-h5md user-molfile user-netcdf user-qmmm user-quip \
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 328c1bd27b..4181fd5479 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -30,7 +30,6 @@ using namespace LAMMPS_NS;
PairMorseSmoothLinear::PairMorseSmoothLinear(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
-
}
/* ---------------------------------------------------------------------- */
@@ -117,7 +116,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag)
if (eflag) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
+ offset[itype][jtype];
evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
evdwl *= factor_lj;
}
@@ -203,6 +202,14 @@ void PairMorseSmoothLinear::coeff(int narg, char **arg)
alpha[i][j] = alpha_one;
r0[i][j] = r0_one;
cut[i][j] = cut_one;
+
+ morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
+
+ double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
+
+ offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
+ der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
+
setflag[i][j] = 1;
count++;
}
@@ -222,17 +229,13 @@ double PairMorseSmoothLinear::init_one(int i, int j)
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
- double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
-
- offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
- der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
-
d0[j][i] = d0[i][j];
alpha[j][i] = alpha[i][j];
r0[j][i] = r0[i][j];
morse1[j][i] = morse1[i][j];
der_at_cutoff[j][i] = der_at_cutoff[i][j];
offset[j][i] = offset[i][j];
+ cut[j][i] = cut[i][j];
return cut[i][j];
}
diff --git a/src/atom.cpp b/src/atom.cpp
index eb2f357890..95f5406d95 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1533,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
}
/* ----------------------------------------------------------------------
- set all masses as read in from restart file
+ set all masses
+ called from reading of restart file, also from ServerMD
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)
diff --git a/src/domain.cpp b/src/domain.cpp
index 1eb848fe06..8238ab7eea 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1176,12 +1176,12 @@ int Domain::closest_image(int i, int j)
if J is not a valid index like -1, just return it
------------------------------------------------------------------------- */
-int Domain::closest_image(double *pos, int j)
+int Domain::closest_image(const double * const pos, int j)
{
if (j < 0) return j;
- int *sametag = atom->sametag;
- double **x = atom->x;
+ const int * const sametag = atom->sametag;
+ const double * const * const x = atom->x;
int closest = j;
double delx = pos[0] - x[j][0];
@@ -1208,13 +1208,10 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
- not currently used (Jan 2017):
- used to be called by pair TIP4P styles but no longer,
- due to use of other closest_image() method
+ called by ServerMD class and LammpsInterface in lib/atc.
------------------------------------------------------------------------- */
-void Domain::closest_image(const double * const xi, const double * const xj,
- double * const xjimage)
+void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];
diff --git a/src/domain.h b/src/domain.h
index 5581f9a45f..9ebdd6ae94 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -115,9 +115,8 @@ class Domain : protected Pointers {
void minimum_image(double *);
void minimum_image_once(double *);
int closest_image(int, int);
- int closest_image(double *, int);
- void closest_image(const double * const, const double * const,
- double * const);
+ int closest_image(const double * const, int);
+ void closest_image(const double * const, const double * const, double * const);
void remap(double *, imageint &);
void remap(double *);
void remap_near(double *, double *);
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index ea448bd178..dd11dfd0c7 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -412,7 +412,7 @@ void FixTMD::readfile(char *file)
m++;
}
- MPI_Bcast(&eof,sizeof(char *)/sizeof(char),MPI_CHAR,0,world);
+ MPI_Bcast(&eof,sizeof(char *),MPI_CHAR,0,world);
MPI_Bcast(&nlines,1,MPI_INT,0,world);
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
diff --git a/src/lammps.cpp b/src/lammps.cpp
index b73b62537f..21335065f4 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -47,8 +47,8 @@
#include "accelerator_omp.h"
#include "timer.h"
#include "python.h"
-#include "memory.h"
#include "version.h"
+#include "memory.h"
#include "error.h"
#include "lmpinstalledpkgs.h"
@@ -73,12 +73,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
output = NULL;
python = NULL;
+ clientserver = 0;
+ cslib = NULL;
+ cscomm = 0;
+
screen = NULL;
logfile = NULL;
infile = NULL;
initclock = MPI_Wtime();
+ // check if -mpi is first arg
+ // if so, then 2 apps were launched with one mpirun command
+ // this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
+ // e.g. for client/server coupling with another code
+ // in the future LAMMPS might leverage this in other ways
+ // universe communicator needs to shrink to be just LAMMPS
+ // syntax: -mpi color
+ // color = integer for this app, different than other app(s)
+ // do the following:
+ // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
+ // NOTE: this assumes other app(s) does same thing, else will hang!
+ // re-create universe with subcomm
+ // store full multi-app comm in cscomm
+ // cscomm is used by CSLIB package to exchange messages w/ other app
+
+ int iarg = 1;
+ if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0)) {
+ int me,nprocs;
+ MPI_Comm_rank(communicator,&me);
+ MPI_Comm_size(communicator,&nprocs);
+ int color = atoi(arg[iarg+1]);
+ MPI_Comm subcomm;
+ MPI_Comm_split(communicator,color,me,&subcomm);
+ cscomm = communicator;
+ communicator = subcomm;
+ delete universe;
+ universe = new Universe(this,communicator);
+ }
+
// parse input switches
int inflag = 0;
@@ -107,59 +141,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int *pfirst = NULL;
int *plast = NULL;
- int iarg = 1;
+ iarg = 1;
while (iarg < narg) {
- if (strcmp(arg[iarg],"-partition") == 0 ||
- strcmp(arg[iarg],"-p") == 0) {
- universe->existflag = 1;
+
+ if (strcmp(arg[iarg],"-echo") == 0 ||
+ strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- iarg++;
- while (iarg < narg && arg[iarg][0] != '-') {
- universe->add_world(arg[iarg]);
- iarg++;
- }
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-help") == 0 ||
+ strcmp(arg[iarg],"-h") == 0) {
+ if (iarg+1 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ helpflag = 1;
+ citeflag = 0;
+ iarg += 1;
+
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-screen") == 0 ||
- strcmp(arg[iarg],"-sc") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- screenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-log") == 0 ||
- strcmp(arg[iarg],"-l") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- logflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-var") == 0 ||
- strcmp(arg[iarg],"-v") == 0) {
- if (iarg+3 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 3;
- while (iarg < narg && arg[iarg][0] != '-') iarg++;
- } else if (strcmp(arg[iarg],"-echo") == 0 ||
- strcmp(arg[iarg],"-e") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 2;
- } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
- strcmp(arg[iarg],"-ps") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partscreenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-plog") == 0 ||
- strcmp(arg[iarg],"-pl") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partlogflag = iarg + 1;
- iarg += 2;
+
} else if (strcmp(arg[iarg],"-kokkos") == 0 ||
strcmp(arg[iarg],"-k") == 0) {
if (iarg+2 > narg)
@@ -172,6 +177,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
kkfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
kklast = iarg;
+
+ } else if (strcmp(arg[iarg],"-log") == 0 ||
+ strcmp(arg[iarg],"-l") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ logflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-nocite") == 0 ||
+ strcmp(arg[iarg],"-nc") == 0) {
+ citeflag = 0;
+ iarg++;
+
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@@ -188,31 +213,32 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
else break;
}
plast[npack++] = iarg;
- } else if (strcmp(arg[iarg],"-suffix") == 0 ||
- strcmp(arg[iarg],"-sf") == 0) {
+
+ } else if (strcmp(arg[iarg],"-partition") == 0 ||
+ strcmp(arg[iarg],"-p") == 0) {
+ universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- delete [] suffix;
- delete [] suffix2;
- suffix2 = NULL;
- suffix_enable = 1;
- // hybrid option to set fall-back for suffix2
- if (strcmp(arg[iarg+1],"hybrid") == 0) {
- if (iarg+4 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- int n = strlen(arg[iarg+2]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+2]);
- n = strlen(arg[iarg+3]) + 1;
- suffix2 = new char[n];
- strcpy(suffix2,arg[iarg+3]);
- iarg += 4;
- } else {
- int n = strlen(arg[iarg+1]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+1]);
- iarg += 2;
+ iarg++;
+ while (iarg < narg && arg[iarg][0] != '-') {
+ universe->add_world(arg[iarg]);
+ iarg++;
}
+
+ } else if (strcmp(arg[iarg],"-plog") == 0 ||
+ strcmp(arg[iarg],"-pl") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partlogflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
+ strcmp(arg[iarg],"-ps") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partscreenflag = iarg + 1;
+ iarg += 2;
+
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
if (iarg+3 > narg)
@@ -221,6 +247,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
+
} else if (strcmp(arg[iarg],"-restart") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
@@ -241,22 +268,47 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
wdfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wdlast = iarg;
- } else if (strcmp(arg[iarg],"-nocite") == 0 ||
- strcmp(arg[iarg],"-nc") == 0) {
- citeflag = 0;
- iarg++;
- } else if (strcmp(arg[iarg],"-help") == 0 ||
- strcmp(arg[iarg],"-h") == 0) {
- if (iarg+1 > narg)
+
+ } else if (strcmp(arg[iarg],"-screen") == 0 ||
+ strcmp(arg[iarg],"-sc") == 0) {
+ if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- helpflag = 1;
- citeflag = 0;
- iarg += 1;
- } else {
- char msg[2048];
- sprintf( msg, "Invalid command-line argument \"%s\"\n", arg[iarg] );
- error->universe_all(FLERR,msg);
- }
+ screenflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-suffix") == 0 ||
+ strcmp(arg[iarg],"-sf") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ delete [] suffix;
+ delete [] suffix2;
+ suffix2 = NULL;
+ suffix_enable = 1;
+ // hybrid option to set fall-back for suffix2
+ if (strcmp(arg[iarg+1],"hybrid") == 0) {
+ if (iarg+4 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ int n = strlen(arg[iarg+2]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+2]);
+ n = strlen(arg[iarg+3]) + 1;
+ suffix2 = new char[n];
+ strcpy(suffix2,arg[iarg+3]);
+ iarg += 4;
+ } else {
+ int n = strlen(arg[iarg+1]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+1]);
+ iarg += 2;
+ }
+
+ } else if (strcmp(arg[iarg],"-var") == 0 ||
+ strcmp(arg[iarg],"-v") == 0) {
+ if (iarg+3 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 3;
+ while (iarg < narg && arg[iarg][0] != '-') iarg++;
+
}
// if no partition command-line switch, universe is one world with all procs
@@ -599,6 +651,14 @@ LAMMPS::~LAMMPS()
delete [] suffix;
delete [] suffix2;
+ // free the MPI comm created by -mpi command-line arg processed in constructor
+ // it was passed to universe as if original universe world
+ // may have been split later by partitions, universe will free the splits
+ // free a copy of uorig here, so check in universe destructor will still work
+
+ MPI_Comm copy = universe->uorig;
+ if (cscomm) MPI_Comm_free(©);
+
delete input;
delete universe;
delete error;
@@ -818,6 +878,7 @@ void LAMMPS::help()
"-in filename : read input from file, not stdin (-i)\n"
"-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n"
"-log none/filename : where to send log output (-l)\n"
+ "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n"
"-nocite : disable writing log.cite file (-nc)\n"
"-package style ... : invoke package command (-pk)\n"
"-partition size1 size2 ... : assign partition sizes (-p)\n"
diff --git a/src/lammps.h b/src/lammps.h
index b2c8673471..5ccef3026e 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -51,6 +51,10 @@ class LAMMPS {
int num_package; // number of cmdline package commands
int cite_enable; // 1 if generating log.cite, 0 if disabled
+ int clientserver; // 0 = neither, 1 = client, 2 = server
+ void *cslib; // client/server messaging via CSlib
+ MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode
+
class KokkosLMP *kokkos; // KOKKOS accelerator class
class AtomKokkos *atomKK; // KOKKOS version of Atom class
class MemoryKokkos *memoryKK; // KOKKOS version of Memory class
diff --git a/src/library.cpp b/src/library.cpp
index 245ae7ba84..a46689da09 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1515,7 +1515,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
- "invalid total atoms " BIGINT_FORMAT " %lld",lmp->atom->natoms,natoms_prev+n);
+ "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT,
+ lmp->atom->natoms,natoms_prev+n);
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,str);
}
diff --git a/src/version.h b/src/version.h
index 2192b25d91..fbeeabff8d 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "22 Aug 2018"
+#define LAMMPS_VERSION "31 Aug 2018"
--
GitLab
From c192236a7e50a4a83e0fdca78fffa9174f1ee790 Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Wed, 5 Sep 2018 11:28:06 -0400
Subject: [PATCH 229/332] Commit before switching to old master.
---
src/lammps.cpp | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 21335065f4..fcdfecf30a 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -309,6 +309,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
iarg += 3;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
+ } else error->universe_all(FLERR,"Invalid command-line argument");
}
// if no partition command-line switch, universe is one world with all procs
--
GitLab
From 1c8feed69fa0d364c752ac768af263263c297db2 Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Wed, 5 Sep 2018 11:38:04 -0400
Subject: [PATCH 230/332] Removed gpu makefile from wrong branch.
---
lib/gpu/Makefile.linux | 52 ------------------------------------------
1 file changed, 52 deletions(-)
delete mode 100644 lib/gpu/Makefile.linux
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
deleted file mode 100644
index b0218c8d39..0000000000
--- a/lib/gpu/Makefile.linux
+++ /dev/null
@@ -1,52 +0,0 @@
-# /* ----------------------------------------------------------------------
-# Generic Linux Makefile for CUDA
-# - Change CUDA_ARCH for your GPU
-# ------------------------------------------------------------------------- */
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.standard
-
-ifeq ($(CUDA_HOME),)
-CUDA_HOME = /opt/cuda
-endif
-
-NVCC = nvcc
-
-# older CUDA
-#CUDA_ARCH = -arch=sm_21
-# newer CUDA
-#CUDA_ARCH = -arch=sm_13
-# older CUDA
-#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
-CUDA_ARCH = -arch=sm_61
-
-# this setting should match LAMMPS Makefile
-# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
-
-LMP_INC = -DLAMMPS_SMALLBIG
-
-# precision for GPU calculations
-# -D_SINGLE_SINGLE # Single precision for all calculations
-# -D_DOUBLE_DOUBLE # Double precision for all calculations
-# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
-
-CUDA_PRECISION = -D_SINGLE_DOUBLE
-
-CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDA_LIB = -L$(CUDA_HOME)/lib64
-CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC
-
-CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
-CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
-
-BIN_DIR = ./
-OBJ_DIR = ./
-LIB_DIR = ./
-AR = ar
-BSH = /bin/sh
-
-CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
-
-include Nvidia.makefile
-
--
GitLab
From 9b38a5b359f1622d68d9946119ee1053882c1a4b Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Wed, 5 Sep 2018 11:39:41 -0400
Subject: [PATCH 231/332] Replaced gpu Makefile with the one from upstream so
as not to delete it.
---
lib/gpu/Makefile.linux | 52 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)
create mode 100644 lib/gpu/Makefile.linux
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
new file mode 100644
index 0000000000..9580bfd4ae
--- /dev/null
+++ b/lib/gpu/Makefile.linux
@@ -0,0 +1,52 @@
+# /* ----------------------------------------------------------------------
+# Generic Linux Makefile for CUDA
+# - Change CUDA_ARCH for your GPU
+# ------------------------------------------------------------------------- */
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.standard
+
+ifeq ($(CUDA_HOME),)
+CUDA_HOME = /usr/local/cuda
+endif
+
+NVCC = nvcc
+
+# older CUDA
+#CUDA_ARCH = -arch=sm_21
+# newer CUDA
+#CUDA_ARCH = -arch=sm_13
+# older CUDA
+#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
+CUDA_ARCH = -arch=sm_35
+
+# this setting should match LAMMPS Makefile
+# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
+
+LMP_INC = -DLAMMPS_SMALLBIG
+
+# precision for GPU calculations
+# -D_SINGLE_SINGLE # Single precision for all calculations
+# -D_DOUBLE_DOUBLE # Double precision for all calculations
+# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
+
+CUDA_PRECISION = -D_SINGLE_DOUBLE
+
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
+CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC
+
+CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
+CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
+
+BIN_DIR = ./
+OBJ_DIR = ./
+LIB_DIR = ./
+AR = ar
+BSH = /bin/sh
+
+CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
+
+include Nvidia.makefile
+
--
GitLab
From 5003354fba49486aba084ca9af97cea5649e7414 Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Wed, 5 Sep 2018 11:42:48 -0400
Subject: [PATCH 232/332] Replaced a tab with whitespace.
---
src/USER-MISC/pair_morse_smooth_linear.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 4181fd5479..a88e7a1a27 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -116,7 +116,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag)
if (eflag) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
+ offset[itype][jtype];
evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
evdwl *= factor_lj;
}
--
GitLab
From 510e09f4ef002cf633a1060497fef4e92c735904 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 5 Sep 2018 13:39:18 -0400
Subject: [PATCH 233/332] patch 5Sep18
---
doc/src/Manual.txt | 4 ++--
src/version.h | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index e442aa1808..5af157d8ea 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="31 Aug 2018 version">
+<META NAME="docnumber" CONTENT="5 Sep 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-31 Aug 2018 version :c,h2
+5 Sep 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/src/version.h b/src/version.h
index fbeeabff8d..0b8c1e8736 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "31 Aug 2018"
+#define LAMMPS_VERSION "5 Sep 2018"
--
GitLab
From ad498811b1f254e946edc6812f64e827d44e63d1 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 5 Sep 2018 16:04:35 -0400
Subject: [PATCH 234/332] cmake: add missing fix_omp.h and fix_omp.cpp to
compilation
---
cmake/CMakeLists.txt | 3 ++-
cmake/Modules/StyleHeaderUtils.cmake | 4 ++++
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 3634138747..62a2fbdef4 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -777,6 +777,7 @@ if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
@@ -785,7 +786,7 @@ if(PKG_USER-OMP)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-
+ RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake
index 2b00a81c8d..d621e4c9c0 100644
--- a/cmake/Modules/StyleHeaderUtils.cmake
+++ b/cmake/Modules/StyleHeaderUtils.cmake
@@ -85,6 +85,10 @@ function(RegisterNPairStyle path)
AddStyleHeader(${path} NPAIR)
endfunction(RegisterNPairStyle)
+function(RegisterFixStyle path)
+ AddStyleHeader(${path} FIX)
+endfunction(RegisterFixStyle)
+
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
--
GitLab
From ba1c5d3191da1effbcd8af6ab0df56b886578527 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 5 Sep 2018 21:39:09 -0400
Subject: [PATCH 235/332] Avoid buffer overflow during errors with long
filenames
---
src/error.cpp | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/error.cpp b/src/error.cpp
index 3feaf1d1ac..913239ac49 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -75,7 +75,7 @@ void Error::universe_all(const char *file, int line, const char *str)
update->whichflag = 0;
char msg[100];
- sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);
+ snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line);
throw LAMMPSException(msg);
#else
MPI_Finalize();
@@ -100,7 +100,7 @@ void Error::universe_one(const char *file, int line, const char *str)
update->whichflag = 0;
char msg[100];
- sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);
+ snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line);
throw LAMMPSAbortException(msg, universe->uworld);
#else
MPI_Abort(universe->uworld,1);
@@ -151,7 +151,7 @@ void Error::all(const char *file, int line, const char *str)
update->whichflag = 0;
char msg[100];
- sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line);
+ snprintf(msg, 100, "ERROR: %s (%s:%d)\n", str, truncpath(file), line);
if (universe->nworlds > 1) {
throw LAMMPSAbortException(msg, universe->uworld);
@@ -201,7 +201,7 @@ void Error::one(const char *file, int line, const char *str)
update->whichflag = 0;
char msg[100];
- sprintf(msg, "ERROR on proc %d: %s (%s:%d)\n", me, str, file, line);
+ snprintf(msg, 100, "ERROR on proc %d: %s (%s:%d)\n", me, str, truncpath(file), line);
throw LAMMPSAbortException(msg, world);
#else
MPI_Abort(world,1);
--
GitLab
From ca04e8f31c62224dc8b01d19d229d21bf0cbe89a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 02:57:53 -0400
Subject: [PATCH 236/332] use snprintf() in a bunch of cases to avoid
overflowing fixed size buffers with unchecked strings
---
src/fix_ave_chunk.cpp | 2 +-
src/fix_ave_correlate.cpp | 2 +-
src/fix_ave_histo.cpp | 2 +-
src/fix_ave_time.cpp | 2 +-
src/fix_enforce2d.cpp | 2 +-
src/fix_print.cpp | 2 +-
src/fix_property_atom.cpp | 8 ++++----
src/fix_tmd.cpp | 6 +++---
src/force.cpp | 4 ++--
src/input.cpp | 14 +++++++-------
src/lammps.cpp | 16 ++++++++--------
src/memory.cpp | 3 ++-
src/modify.cpp | 9 +++++----
src/molecule.cpp | 2 +-
src/neighbor.cpp | 2 +-
src/pair_coul_streitz.cpp | 2 +-
16 files changed, 40 insertions(+), 38 deletions(-)
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 1aead70644..11ba4a41a5 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -225,7 +225,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/chunk file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix ave/chunk file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 198caf1514..5c95f20ec2 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -149,7 +149,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index ce32167b74..a5bf8db557 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -937,7 +937,7 @@ void FixAveHisto::options(int iarg, int narg, char **arg)
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix ave/histo file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 53354ee066..50654b6561 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -1042,7 +1042,7 @@ void FixAveTime::options(int iarg, int narg, char **arg)
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix ave/time file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index ef7eb3a0ef..986ded5d16 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -78,7 +78,7 @@ void FixEnforce2D::init()
flist[nfixlist++] = modify->fix[i];
else {
char msg[256];
- sprintf(msg,"Fix enforce2d must be defined after fix %s",modify->fix[i]->style);
+ snprintf(msg,256,"Fix enforce2d must be defined after fix %s",modify->fix[i]->style);
error->all(FLERR,msg);
}
}
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index 16218e0088..969fcf8140 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -60,7 +60,7 @@ FixPrint::FixPrint(LAMMPS *lmp, int narg, char **arg) :
else fp = fopen(arg[iarg+1],"a");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix print file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix print file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 5b12b6def2..c89419f850 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -224,7 +224,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
if (nwords != nvalue+1) {
char str[128];
- sprintf(str,"Incorrect %s format in data file",keyword);
+ snprintf(str,128,"Incorrect %s format in data file",keyword);
error->all(FLERR,str);
}
@@ -242,7 +242,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == NULL) {
char str[128];
- sprintf(str,"Too few lines in %s section of data file",keyword);
+ snprintf(str,128,"Too few lines in %s section of data file",keyword);
error->one(FLERR,str);
}
int format_ok = 1;
@@ -252,14 +252,14 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
}
if (!format_ok) {
char str[128];
- sprintf(str,"Incorrect %s format in data file",keyword);
+ snprintf(str,128,"Incorrect %s format in data file",keyword);
error->all(FLERR,str);
}
itag = ATOTAGINT(values[0]) + id_offset;
if (itag <= 0 || itag > map_tag_max) {
char str[128];
- sprintf(str,"Invalid atom ID in %s section of data file",keyword);
+ snprintf(str,128,"Invalid atom ID in %s section of data file",keyword);
error->one(FLERR,str);
}
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index dd11dfd0c7..4cbb244bc0 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -75,7 +75,7 @@ nfileevery(0), fp(NULL), xf(NULL), xold(NULL)
fp = fopen(arg[6],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix tmd file %s",arg[6]);
+ snprintf(str,128,"Cannot open fix tmd file %s",arg[6]);
error->one(FLERR,str);
}
fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back",
@@ -523,7 +523,7 @@ void FixTMD::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
- sprintf(gunzip,"gzip -c -d %s",file);
+ snprintf(gunzip,128,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
@@ -538,7 +538,7 @@ void FixTMD::open(char *file)
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/force.cpp b/src/force.cpp
index 8ee301982d..91fccd7197 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -182,8 +182,8 @@ void Force::init()
if (pair_restart) {
if (!pair) {
char msg[128];
- sprintf(msg,"Must re-specify non-restarted pair style (%s) "
- "after read_restart", pair_restart);
+ snprintf(msg,128,"Must re-specify non-restarted pair style (%s) "
+ "after read_restart", pair_restart);
error->all(FLERR,msg);
}
}
diff --git a/src/input.cpp b/src/input.cpp
index f41c8458ea..2834e36913 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -267,7 +267,7 @@ void Input::file(const char *filename)
infile = fopen(filename,"r");
if (infile == NULL) {
char str[128];
- sprintf(str,"Cannot open input script %s",filename);
+ snprintf(str,128,"Cannot open input script %s",filename);
error->one(FLERR,str);
}
infiles[0] = infile;
@@ -526,7 +526,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
*fmtflag='\0';
}
- sprintf(immediate,fmtstr,variable->compute_equal(var));
+ snprintf(immediate,256,fmtstr,variable->compute_equal(var));
value = immediate;
// single character variable name, e.g. $a
@@ -541,7 +541,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
if (value == NULL) {
char str[128];
- sprintf(str,"Substitution for illegal variable %s",var);
+ snprintf(str,128,"Substitution for illegal variable %s",var);
error->one(FLERR,str);
}
// check if storage in str2 needs to be expanded
@@ -1047,7 +1047,7 @@ void Input::include()
infile = fopen(arg[0],"r");
if (infile == NULL) {
char str[128];
- sprintf(str,"Cannot open input script %s",arg[0]);
+ snprintf(str,128,"Cannot open input script %s",arg[0]);
error->one(FLERR,str);
}
infiles[nfile++] = infile;
@@ -1072,7 +1072,7 @@ void Input::jump()
infile = fopen(arg[0],"r");
if (infile == NULL) {
char str[128];
- sprintf(str,"Cannot open input script %s",arg[0]);
+ snprintf(str,128,"Cannot open input script %s",arg[0]);
error->one(FLERR,str);
}
infiles[nfile-1] = infile;
@@ -1117,7 +1117,7 @@ void Input::log()
if (logfile == NULL) {
char str[128];
- sprintf(str,"Cannot open logfile %s",arg[0]);
+ snprintf(str,128,"Cannot open logfile %s",arg[0]);
error->one(FLERR,str);
}
}
@@ -1196,7 +1196,7 @@ void Input::print()
else fp = fopen(arg[iarg+1],"a");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open print file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open print file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/lammps.cpp b/src/lammps.cpp
index fcdfecf30a..04d8daa478 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -385,7 +385,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
else infile = fopen(arg[inflag],"r");
if (infile == NULL) {
char str[128];
- sprintf(str,"Cannot open input script %s",arg[inflag]);
+ snprintf(str,128,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
}
}
@@ -416,7 +416,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
screen = NULL;
else {
char str[128];
- sprintf(str,"%s.%d",arg[screenflag],universe->iworld);
+ snprintf(str,128,"%s.%d",arg[screenflag],universe->iworld);
screen = fopen(str,"w");
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
}
@@ -424,7 +424,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
screen = NULL;
else {
char str[128];
- sprintf(str,"%s.%d",arg[partscreenflag],universe->iworld);
+ snprintf(str,128,"%s.%d",arg[partscreenflag],universe->iworld);
screen = fopen(str,"w");
if (screen == NULL) error->one(FLERR,"Cannot open screen file");
} else screen = NULL;
@@ -440,7 +440,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
logfile = NULL;
else {
char str[128];
- sprintf(str,"%s.%d",arg[logflag],universe->iworld);
+ snprintf(str,128,"%s.%d",arg[logflag],universe->iworld);
logfile = fopen(str,"w");
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
}
@@ -448,7 +448,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
logfile = NULL;
else {
char str[128];
- sprintf(str,"%s.%d",arg[partlogflag],universe->iworld);
+ snprintf(str,128,"%s.%d",arg[partlogflag],universe->iworld);
logfile = fopen(str,"w");
if (logfile == NULL) error->one(FLERR,"Cannot open logfile");
} else logfile = NULL;
@@ -457,7 +457,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
infile = fopen(arg[inflag],"r");
if (infile == NULL) {
char str[128];
- sprintf(str,"Cannot open input script %s",arg[inflag]);
+ snprintf(str,128,"Cannot open input script %s",arg[inflag]);
error->one(FLERR,str);
}
} else infile = NULL;
@@ -579,10 +579,10 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (restartflag) {
char cmd[128];
- sprintf(cmd,"read_restart %s\n",rfile);
+ snprintf(cmd,128,"read_restart %s\n",rfile);
if (restartremapflag) strcat(cmd," remap\n");
input->one(cmd);
- sprintf(cmd,"write_data %s",dfile);
+ snprintf(cmd,128,"write_data %s",dfile);
for (iarg = wdfirst; iarg < wdlast; iarg++)
sprintf(&cmd[strlen(cmd)]," %s",arg[iarg]);
strcat(cmd," noinit\n");
diff --git a/src/memory.cpp b/src/memory.cpp
index 429cf75c00..7a23a23079 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -121,6 +121,7 @@ void Memory::sfree(void *ptr)
void Memory::fail(const char *name)
{
char str[128];
- sprintf(str,"Cannot create/grow a vector/array of pointers for %s",name);
+ snprintf(str,128,
+ "Cannot create/grow a vector/array of pointers for %s",name);
error->one(FLERR,str);
}
diff --git a/src/modify.cpp b/src/modify.cpp
index c5a680a3bd..8a0d1afa2c 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -239,7 +239,8 @@ void Modify::init()
for (i = 0; i < nfix; i++)
if (!fix[i]->dynamic_group_allow && group->dynamic[fix[i]->igroup]) {
char str[128];
- sprintf(str,"Fix %s does not allow use of dynamic group",fix[i]->id);
+ snprintf(str,128,
+ "Fix %s does not allow use of dynamic group",fix[i]->id);
error->all(FLERR,str);
}
@@ -247,7 +248,7 @@ void Modify::init()
if (!compute[i]->dynamic_group_allow &&
group->dynamic[compute[i]->igroup]) {
char str[128];
- sprintf(str,"Compute %s does not allow use of dynamic group",fix[i]->id);
+ snprintf(str,128,"Compute %s does not allow use of dynamic group",fix[i]->id);
error->all(FLERR,str);
}
@@ -889,7 +890,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (fix[ifix] == NULL) {
char str[128];
- sprintf(str,"Unknown fix style %s",arg[2]);
+ snprintf(str,128,"Unknown fix style %s",arg[2]);
error->all(FLERR,str);
}
@@ -1191,7 +1192,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
if (compute[ncompute] == NULL) {
char str[128];
- sprintf(str,"Unknown compute style %s",arg[2]);
+ snprintf(str,128,"Unknown compute style %s",arg[2]);
error->all(FLERR,str);
}
diff --git a/src/molecule.cpp b/src/molecule.cpp
index dfbe3e1e08..454459084a 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -1632,7 +1632,7 @@ void Molecule::open(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open molecule file %s",file);
+ snprintf(str,128,"Cannot open molecule file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 759f84e29f..bc22fffc48 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1408,7 +1408,7 @@ void Neighbor::init_topology()
void Neighbor::print_pairwise_info()
{
int i,m;
- char str[128];
+ char str[256];
NeighRequest *rq;
FILE *out;
diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp
index 1d725f4ca8..920770ed7f 100644
--- a/src/pair_coul_streitz.cpp
+++ b/src/pair_coul_streitz.cpp
@@ -258,7 +258,7 @@ void PairCoulStreitz::read_file(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open coul/streitz potential file %s",file);
+ snprintf(str,128,"Cannot open coul/streitz potential file %s",file);
error->one(FLERR,str);
}
}
--
GitLab
From fbc1c1cfdd2194c78e0f77393bbc060e32a74a63 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 09:57:10 -0400
Subject: [PATCH 237/332] replace fixed buffer sprintf() with straight
fprintf()
---
src/neighbor.cpp | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index bc22fffc48..84494bfbc5 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1408,7 +1408,6 @@ void Neighbor::init_topology()
void Neighbor::print_pairwise_info()
{
int i,m;
- char str[256];
NeighRequest *rq;
FILE *out;
@@ -1457,18 +1456,17 @@ void Neighbor::print_pairwise_info()
rq = requests[i];
if (rq->pair) {
char *pname = force->pair_match_ptr((Pair *) rq->requestor);
- sprintf(str," (%d) pair %s",i+1,pname);
+ fprintf(out," (%d) pair %s",i+1,pname);
} else if (rq->fix) {
- sprintf(str," (%d) fix %s",i+1,((Fix *) rq->requestor)->style);
+ fprintf(out," (%d) fix %s",i+1,((Fix *) rq->requestor)->style);
} else if (rq->compute) {
- sprintf(str," (%d) compute %s",i+1,
+ fprintf(out," (%d) compute %s",i+1,
((Compute *) rq->requestor)->style);
} else if (rq->command) {
- sprintf(str," (%d) command %s",i+1,rq->command_style);
+ fprintf(out," (%d) command %s",i+1,rq->command_style);
} else if (rq->neigh) {
- sprintf(str," (%d) neighbor class addition",i+1);
+ fprintf(out," (%d) neighbor class addition",i+1);
}
- fprintf(out,"%s",str);
if (rq->occasional) fprintf(out,", occasional");
else fprintf(out,", perpetual");
--
GitLab
From 4d52cb9245b74d7d4690637738efffb1045ce1e5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 09:57:43 -0400
Subject: [PATCH 238/332] more buffer overflow avoiding through using
snprintf()
---
src/pair_table.cpp | 2 +-
src/read_data.cpp | 6 +++---
src/read_restart.cpp | 6 +++---
src/reader.cpp | 4 ++--
src/universe.cpp | 4 ++--
src/variable.cpp | 20 ++++++++++----------
src/write_coeff.cpp | 4 ++--
src/write_data.cpp | 2 +-
src/write_restart.cpp | 4 ++--
9 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 5c43761cab..0d692caccb 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -362,7 +362,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 5faa8f9646..26c406c1d6 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -706,7 +706,7 @@ void ReadData::command(int narg, char **arg)
} else {
char str[128];
- sprintf(str,"Unknown identifier in data file: %s",keyword);
+ snprintf(str,128,"Unknown identifier in data file: %s",keyword);
error->all(FLERR,str);
}
@@ -1919,7 +1919,7 @@ void ReadData::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
- sprintf(gunzip,"gzip -c -d %s",file);
+ snprintf(gunzip,128,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
@@ -1934,7 +1934,7 @@ void ReadData::open(char *file)
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 7d8e6ca395..9be035e1a1 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -138,7 +138,7 @@ void ReadRestart::command(int narg, char **arg)
fp = fopen(hfile,"rb");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open restart file %s",hfile);
+ snprintf(str,128,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
if (multiproc) delete [] hfile;
@@ -297,7 +297,7 @@ void ReadRestart::command(int narg, char **arg)
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open restart file %s",procfile);
+ snprintf(str,128,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
@@ -369,7 +369,7 @@ void ReadRestart::command(int narg, char **arg)
fp = fopen(procfile,"rb");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open restart file %s",procfile);
+ snprintf(str,128,"Cannot open restart file %s",procfile);
error->one(FLERR,str);
}
delete [] procfile;
diff --git a/src/reader.cpp b/src/reader.cpp
index f6e8bd39eb..22a21812e6 100644
--- a/src/reader.cpp
+++ b/src/reader.cpp
@@ -41,7 +41,7 @@ void Reader::open_file(const char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[1024];
- sprintf(gunzip,"gzip -c -d %s",file);
+ snprintf(gunzip,1024,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
@@ -56,7 +56,7 @@ void Reader::open_file(const char *file)
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/universe.cpp b/src/universe.cpp
index 45b4318ec9..410d12dcb3 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -204,7 +204,7 @@ void Universe::add_world(char *str)
if (!valid) {
char msg[128];
- sprintf(msg,"Invalid partition string '%s'",str);
+ snprintf(msg,128,"Invalid partition string '%s'",str);
error->universe_all(FLERR,msg);
}
} else nper = nprocs;
@@ -269,7 +269,7 @@ char *date2num(const char *version)
year = atoi(version);
}
- char *ver = new char[10];
+ char *ver = new char[64];
sprintf(ver,"%04d%02d%02d", year % 10000, month, day % 100);
return ver;
diff --git a/src/variable.cpp b/src/variable.cpp
index 3c54eac1ef..1595456f33 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -528,7 +528,7 @@ void Variable::set(int narg, char **arg)
for (int i = 0; i < n-1; i++)
if (!isalnum(names[nvar][i]) && names[nvar][i] != '_') {
char errmsg[128];
- sprintf(errmsg,"Variable name '%s' must have only alphanumeric "
+ snprintf(errmsg,128,"Variable name '%s' must have only alphanumeric "
"characters or underscore",names[nvar]);
error->all(FLERR,errmsg);
}
@@ -586,7 +586,7 @@ int Variable::next(int narg, char **arg)
ivar = find(arg[iarg]);
if (ivar < 0) {
char errmsg[128];
- sprintf(errmsg,"Invalid variable '%s' in next command",arg[iarg]);
+ snprintf(errmsg,128,"Invalid variable '%s' in next command",arg[iarg]);
error->all(FLERR,errmsg);
}
if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue;
@@ -886,7 +886,7 @@ char *Variable::retrieve(char *name)
int ifunc = python->variable_match(data[ivar][0],name,0);
if (ifunc < 0) {
char errmsg[128];
- sprintf(errmsg,"Python variable '%s' does not match Python function",name);
+ snprintf(errmsg,128,"Python variable '%s' does not match Python function",name);
error->all(FLERR,errmsg);
}
python->invoke_function(ifunc,data[ivar][1]);
@@ -1597,7 +1597,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
int ifix = modify->find_fix(word+2);
if (ifix < 0) {
char msg[128];
- sprintf(msg,"Invalid fix ID '%s' in variable formula",word+2);
+ snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2);
print_var_error(FLERR,msg,ivar);
}
Fix *fix = modify->fix[ifix];
@@ -2032,8 +2032,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
argstack,nargstack,ivar));
else {
char msg[128];
- sprintf(msg,"Invalid math/group/special function '%s()'"
- "in variable formula", word);
+ snprintf(msg,128,"Invalid math/group/special function '%s()'"
+ "in variable formula", word);
print_var_error(FLERR,msg,ivar);
}
delete [] contents;
@@ -2092,7 +2092,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
int flag = output->thermo->evaluate_keyword(word,&value1);
if (flag) {
char msg[128];
- sprintf(msg,"Invalid thermo keyword '%s' in variable formula",word);
+ snprintf(msg,128,"Invalid thermo keyword '%s' in variable formula",word);
print_var_error(FLERR,msg,ivar);
}
if (tree) {
@@ -4013,7 +4013,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
int icompute = modify->find_compute(&args[0][2]);
if (icompute < 0) {
char msg[128];
- sprintf(msg,"Invalid compute ID '%s' in variable formula",word+2);
+ snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2);
print_var_error(FLERR,msg,ivar);
}
compute = modify->compute[icompute];
@@ -4656,7 +4656,7 @@ void Variable::print_var_error(const char *srcfile, int lineno,
if ((ivar >= 0) && (ivar < nvar)) {
char msg[128];
- sprintf(msg,"Variable %s: %s",names[ivar],errmsg);
+ snprintf(msg,128,"Variable %s: %s",names[ivar],errmsg);
error->all(srcfile,lineno,msg);
} else error->all(srcfile,lineno,errmsg);
}
@@ -4944,7 +4944,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file variable file %s",file);
+ snprintf(str,128,"Cannot open file variable file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index 5f82a480fd..99172c09f0 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -51,7 +51,7 @@ void WriteCoeff::command(int narg, char **arg)
char str[256], coeff[256];
FILE *one = fopen(file,"wb+");
if (one == NULL) {
- sprintf(str,"Cannot open coeff file %s",file);
+ snprintf(str,256,"Cannot open coeff file %s",file);
error->one(FLERR,str);
}
@@ -86,7 +86,7 @@ void WriteCoeff::command(int narg, char **arg)
FILE *two = fopen(file+4,"w");
if (two == NULL) {
- sprintf(str,"Cannot open coeff file %s",file+4);
+ snprintf(str,256,"Cannot open coeff file %s",file+4);
error->one(FLERR,str);
}
fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n",
diff --git a/src/write_data.cpp b/src/write_data.cpp
index 96bf081157..f18e30de52 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -183,7 +183,7 @@ void WriteData::write(char *file)
fp = fopen(file,"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open data file %s",file);
+ snprintf(str,128,"Cannot open data file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 1bfbb382a8..edb6dfa7e8 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -269,7 +269,7 @@ void WriteRestart::write(char *file)
fp = fopen(hfile,"wb");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open restart file %s",hfile);
+ snprintf(str,128,"Cannot open restart file %s",hfile);
error->one(FLERR,str);
}
if (multiproc) delete [] hfile;
@@ -334,7 +334,7 @@ void WriteRestart::write(char *file)
fp = fopen(multiname,"wb");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open restart file %s",multiname);
+ snprintf(str,128,"Cannot open restart file %s",multiname);
error->one(FLERR,str);
}
write_int(PROCSPERFILE,nclusterprocs);
--
GitLab
From 9c27548a5c4dd6e7126c0fb76b3a366a9f0bef6a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 10:45:48 -0400
Subject: [PATCH 239/332] more replacing of sprintf() with snprintf()
---
src/GPU/pair_eam_alloy_gpu.cpp | 2 +-
src/GPU/pair_eam_fs_gpu.cpp | 2 +-
src/GRANULAR/fix_wall_gran_region.cpp | 8 +-
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +-
src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +-
src/KOKKOS/pair_exp6_rx_kokkos.cpp | 2 +-
src/MANYBODY/fix_qeq_comb.cpp | 2 +-
src/MANYBODY/pair_adp.cpp | 2 +-
src/MANYBODY/pair_airebo.cpp | 4 +-
src/MANYBODY/pair_bop.cpp | 4 +-
src/MANYBODY/pair_comb.cpp | 2 +-
src/MANYBODY/pair_comb3.cpp | 8 +-
src/MANYBODY/pair_eam.cpp | 2 +-
src/MANYBODY/pair_eam_alloy.cpp | 2 +-
src/MANYBODY/pair_eam_cd.cpp | 2 +-
src/MANYBODY/pair_eam_fs.cpp | 2 +-
src/MANYBODY/pair_eim.cpp | 2 +-
src/MANYBODY/pair_gw.cpp | 2 +-
src/MANYBODY/pair_gw_zbl.cpp | 2 +-
src/MANYBODY/pair_lcbop.cpp | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +-
src/MANYBODY/pair_polymorphic.cpp | 2 +-
src/MANYBODY/pair_sw.cpp | 2 +-
src/MANYBODY/pair_tersoff.cpp | 2 +-
src/MANYBODY/pair_tersoff_mod.cpp | 2 +-
src/MANYBODY/pair_tersoff_mod_c.cpp | 2 +-
src/MANYBODY/pair_tersoff_zbl.cpp | 2 +-
src/MANYBODY/pair_vashishta.cpp | 2 +-
src/MEAM/pair_meam.cpp | 8 +-
src/MISC/fix_ttm.cpp | 4 +-
src/MOLECULE/angle_table.cpp | 2 +-
src/MOLECULE/bond_table.cpp | 2 +-
src/MOLECULE/fix_cmap.cpp | 4 +-
src/POEMS/fix_poems.cpp | 4 +-
src/QEQ/fix_qeq.cpp | 2 +-
src/REAX/fix_reax_bonds.cpp | 11 +-
src/REPLICA/neb.cpp | 4 +-
src/REPLICA/tad.cpp | 5 +-
src/RIGID/fix_rigid.cpp | 8 +-
src/RIGID/fix_rigid_small.cpp | 8 +-
src/SNAP/pair_snap.cpp | 4 +-
src/USER-BOCS/fix_bocs.cpp | 39 +++----
src/USER-DIFFRACTION/fix_saed_vtk.cpp | 10 +-
src/USER-DPD/fix_eos_table.cpp | 2 +-
src/USER-DPD/fix_eos_table_rx.cpp | 4 +-
src/USER-DPD/fix_rx.cpp | 4 +-
src/USER-DPD/pair_exp6_rx.cpp | 4 +-
src/USER-DPD/pair_multi_lucy.cpp | 2 +-
src/USER-DPD/pair_multi_lucy_rx.cpp | 2 +-
src/USER-INTEL/pair_eam_alloy_intel.cpp | 2 +-
src/USER-INTEL/pair_eam_fs_intel.cpp | 2 +-
src/USER-MEAMC/pair_meamc.cpp | 8 +-
src/USER-MISC/fix_ave_correlate_long.cpp | 2 +-
src/USER-MISC/fix_bond_react.cpp | 2 +-
src/USER-MISC/fix_gle.cpp | 4 +-
src/USER-MISC/fix_ttm_mod.cpp | 6 +-
src/USER-MISC/pair_agni.cpp | 2 +-
src/USER-MISC/pair_edip.cpp | 2 +-
src/USER-MISC/pair_edip_multi.cpp | 2 +-
src/USER-MISC/pair_extep.cpp | 2 +-
src/USER-MISC/pair_ilp_graphene_hbn.cpp | 2 +-
src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 2 +-
src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 2 +-
src/USER-MISC/pair_meam_spline.cpp | 2 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 106 +++++++++---------
src/USER-MISC/pair_tersoff_table.cpp | 2 +-
src/USER-MOLFILE/reader_molfile.cpp | 4 +-
67 files changed, 171 insertions(+), 188 deletions(-)
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 3a8e440bdc..11af562f15 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -364,7 +364,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
fptr = fopen(filename,"r");
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index 51681d563b..ef8dd09e23 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -364,7 +364,7 @@ void PairEAMFSGPU::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index 4a6be5f3c9..8633587ad5 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -113,16 +113,16 @@ void FixWallGranRegion::init()
strcmp(region_style,region->style) != 0 ||
nregion != region->nregion) {
char str[256];
- sprintf(str,"Region properties for region %s changed between runs, "
- "resetting its motion",idregion);
+ snprintf(str,256,"Region properties for region %s changed between runs, "
+ "resetting its motion",idregion);
error->warning(FLERR,str);
region->reset_vel();
}
if (motion_resetflag){
char str[256];
- sprintf(str,"Region properties for region %s are inconsistent "
- "with restart file, resetting its motion",idregion);
+ snprintf(str,256,"Region properties for region %s are inconsistent "
+ "with restart file, resetting its motion",idregion);
error->warning(FLERR,str);
region->reset_vel();
}
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index fc19da1c8a..49e1313c26 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -992,7 +992,7 @@ void PairEAMAlloyKokkos<DeviceType>::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 8f5571bf29..ee0a799826 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -992,7 +992,7 @@ void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
index 810173d219..f38feea5f4 100644
--- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
@@ -1725,7 +1725,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open exp6/rx potential file %s",file);
+ snprintf(str,128,"Cannot open exp6/rx potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index e46da9bfe7..7146ee9d65 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -67,7 +67,7 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 831f1d0efa..7b48522e84 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -551,7 +551,7 @@ void PairADP::read_file(char *filename)
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open ADP potential file %s",filename);
+ snprintf(str,128,"Cannot open ADP potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index ac3ed36a83..067eb1634f 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -3373,9 +3373,9 @@ void PairAIREBO::read_file(char *filename)
if (fp == NULL) {
char str[128];
if (morseflag)
- sprintf(str,"Cannot open AIREBO-M potential file %s",filename);
+ snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename);
else
- sprintf(str,"Cannot open AIREBO potential file %s",filename);
+ snprintf(str,128,"Cannot open AIREBO potential file %s",filename);
error->one(FLERR,str);
}
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 87a23dff99..ca0f229068 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -4976,7 +4976,7 @@ void PairBOP::read_table(char *filename)
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open BOP potential file %s",filename);
+ snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
fgets(s,MAXLINE,fp); // skip first comment line
@@ -5079,7 +5079,7 @@ void PairBOP::read_table(char *filename)
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open BOP potential file %s",filename);
+ snprintf(str,128,"Cannot open BOP potential file %s",filename);
error->one(FLERR,str);
}
fgets(s,MAXLINE,fp); // skip first comment line
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index e7b0d27b6e..85ea4812bf 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -597,7 +597,7 @@ void PairComb::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open COMB potential file %s",file);
+ snprintf(str,128,"Cannot open COMB potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 72360be5f0..106b83eeba 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -320,11 +320,7 @@ void PairComb3::read_lib()
if (comm->me == 0) {
FILE *fp = force->open_potential("lib.comb3");
- if (fp == NULL) {
- char str[128];
- sprintf(str,"Cannot open COMB3 lib.comb3 file");
- error->one(FLERR,str);
- }
+ if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file");
// read and store at the same time
fgets(s,MAXLIB,fp);
@@ -607,7 +603,7 @@ void PairComb3::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open COMB3 potential file %s",file);
+ snprintf(str,128,"Cannot open COMB3 potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 87bcebb111..f4b4901075 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -460,7 +460,7 @@ void PairEAM::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index eed38f79e9..c004030240 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -127,7 +127,7 @@ void PairEAMAlloy::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
index 5b8b241b45..8db1b6dd9a 100644
--- a/src/MANYBODY/pair_eam_cd.cpp
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -504,7 +504,7 @@ void PairEAMCD::read_h_coeff(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s", filename);
+ snprintf(str,128,"Cannot open EAM potential file %s", filename);
error->one(FLERR,str);
}
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index 2b5d530d3a..bbda84fdf1 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -127,7 +127,7 @@ void PairEAMFS::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index 6703e159e6..b0fa1b1eef 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -461,7 +461,7 @@ void PairEIM::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EIM potential file %s",filename);
+ snprintf(str,128,"Cannot open EIM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index 0aff4970bb..f2d3b67eb0 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -381,7 +381,7 @@ void PairGW::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open GW potential file %s",file);
+ snprintf(str,128,"Cannot open GW potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp
index 81d4866e84..f3dd1bc04b 100644
--- a/src/MANYBODY/pair_gw_zbl.cpp
+++ b/src/MANYBODY/pair_gw_zbl.cpp
@@ -77,7 +77,7 @@ void PairGWZBL::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open GW potential file %s",file);
+ snprintf(str,128,"Cannot open GW potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 57373c4f85..88477e48f3 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -978,7 +978,7 @@ void PairLCBOP::read_file(char *filename)
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open LCBOP potential file %s",filename);
+ snprintf(str,128,"Cannot open LCBOP potential file %s",filename);
error->one(FLERR,str);
}
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index 01718d14cd..ce449e4890 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -299,7 +299,7 @@ void PairNb3bHarmonic::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open nb3b/harmonic potential file %s",file);
+ snprintf(str,128,"Cannot open nb3b/harmonic potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index ce9af66d30..41c5892d4e 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -573,7 +573,7 @@ void PairPolymorphic::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open polymorphic potential file %s",file);
+ snprintf(str,128,"Cannot open polymorphic potential file %s",file);
error->one(FLERR,str);
}
// move past comments to first data line
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index da470d568a..91e11b3d26 100644
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -363,7 +363,7 @@ void PairSW::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Stillinger-Weber potential file %s",file);
+ snprintf(str,128,"Cannot open Stillinger-Weber potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 45068e5c2e..54101aef9e 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -404,7 +404,7 @@ void PairTersoff::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp
index 73297fb534..e8fdecfe01 100644
--- a/src/MANYBODY/pair_tersoff_mod.cpp
+++ b/src/MANYBODY/pair_tersoff_mod.cpp
@@ -60,7 +60,7 @@ void PairTersoffMOD::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp
index 0d0016664a..4a5904c106 100644
--- a/src/MANYBODY/pair_tersoff_mod_c.cpp
+++ b/src/MANYBODY/pair_tersoff_mod_c.cpp
@@ -55,7 +55,7 @@ void PairTersoffMODC::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp
index 1692c88a50..353e3d2264 100644
--- a/src/MANYBODY/pair_tersoff_zbl.cpp
+++ b/src/MANYBODY/pair_tersoff_zbl.cpp
@@ -77,7 +77,7 @@ void PairTersoffZBL::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 54b184ea39..b4c3086ca8 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -369,7 +369,7 @@ void PairVashishta::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Vashishta potential file %s",file);
+ snprintf(str,128,"Cannot open Vashishta potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index 5aa13ab02e..b8f5291338 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -464,7 +464,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
fp = force->open_potential(globalfile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open MEAM potential file %s",globalfile);
+ snprintf(str,128,"Cannot open MEAM potential file %s",globalfile);
error->one(FLERR,str);
}
}
@@ -645,7 +645,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
fp = force->open_potential(userfile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open MEAM potential file %s",userfile);
+ snprintf(str,128,"Cannot open MEAM potential file %s",userfile);
error->one(FLERR,str);
}
}
@@ -694,8 +694,8 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
if (strcmp(params[0],keywords[which]) == 0) break;
if (which == nkeywords) {
char str[128];
- sprintf(str,"Keyword %s in MEAM parameter file not recognized",
- params[0]);
+ snprintf(str,128,"Keyword %s in MEAM parameter file not recognized",
+ params[0]);
error->all(FLERR,str);
}
nindex = nparams - 2;
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index c8f33c73b7..4e15581377 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -71,7 +71,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
fpr = fopen(arg[13],"r");
if (fpr == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",arg[13]);
+ snprintf(str,128,"Cannot open file %s",arg[13]);
error->one(FLERR,str);
}
@@ -84,7 +84,7 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
fp = fopen(arg[15],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ttm file %s",arg[15]);
+ snprintf(str,128,"Cannot open fix ttm file %s",arg[15]);
error->one(FLERR,str);
}
}
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index 235e9b4d5b..2867865497 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -369,7 +369,7 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index a5c579042b..392904149d 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -298,7 +298,7 @@ void BondTable::read_table(Table *tb, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index b527eef020..a889a8d0db 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -644,7 +644,7 @@ void FixCMAP::read_grid_map(char *cmapfile)
fp = force->open_potential(cmapfile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix cmap file %s",cmapfile);
+ snprintf(str,128,"Cannot open fix cmap file %s",cmapfile);
error->one(FLERR,str);
}
}
@@ -1076,7 +1076,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf,
if (nwords != 7) {
char str[128];
- sprintf(str,"Incorrect %s format in data file",keyword);
+ snprintf(str,128,"Incorrect %s format in data file",keyword);
error->all(FLERR,str);
}
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index 2c2fefb250..f345d52aab 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -369,7 +369,7 @@ void FixPOEMS::init()
if (pflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
- sprintf(str,"Fix %s alters forces after fix poems",modify->fix[i]->id);
+ snprintf(str,128,"Fix %s alters forces after fix poems",modify->fix[i]->id);
error->warning(FLERR,str);
}
}
@@ -961,7 +961,7 @@ void FixPOEMS::readfile(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix poems file %s",file);
+ snprintf(str,128,"Cannot open fix poems file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 0fe041209f..49e0a6d423 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -715,7 +715,7 @@ void FixQEq::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix qeq parameter file %s",file);
+ snprintf(str,128,"Cannot open fix qeq parameter file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index 84e4a66e6c..5273cd1faa 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -53,7 +53,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
if (suffix && strcmp(suffix,".gz") == 0) {
#ifdef LAMMPS_GZIP
char gzip[128];
- sprintf(gzip,"gzip -6 > %s",arg[4]);
+ snprintf(gzip128,,"gzip -6 > %s",arg[4]);
#ifdef _WIN32
fp = _popen(gzip,"wb");
#else
@@ -66,7 +66,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]);
+ snprintf(str,128,"Cannot open fix reax/bonds file %s",arg[4]);
error->one(FLERR,str);
}
}
@@ -222,11 +222,8 @@ void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
numbonds = nint(buf[j+2]);
fprintf(fp," %d %d %d",nint(buf[j]),nint(buf[j+1]),numbonds);
j += 3;
- if (numbonds > nsbmax_most) {
- char str[128];
- sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
- error->one(FLERR,str);
- }
+ if (numbonds > nsbmax_most)
+ error->one(FLERR,"Fix reax/bonds numbonds > nsbmax_most");
// print connection table
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index c9aedf7401..9a4de9ca0b 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -549,7 +549,7 @@ void NEB::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
- sprintf(gunzip,"gzip -c -d %s",file);
+ snprintf(gunz128,ip,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
@@ -564,7 +564,7 @@ void NEB::open(char *file)
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 46073952fc..da42ba6fae 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -712,10 +712,7 @@ void TAD::perform_neb(int ievent)
args[0] = (char *) "neb";
args[1] = (char *) "all";
args[2] = (char *) "neb";
- char str[128];
- args[3] = str;
- double kspring = 1.0;
- sprintf(args[3],"%f",kspring);
+ args[3] = (char *) "1.0";
modify->add_fix(narg2,args);
fix_neb = (Fix *) modify->fix[modify->nfix-1];
delete [] args;
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index c15a909ada..39c49ca1c4 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -730,7 +730,7 @@ void FixRigid::init()
if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
- sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+ snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
error->warning(FLERR,str);
}
}
@@ -2271,7 +2271,7 @@ void FixRigid::readfile(int which, double *vec,
fp = fopen(infile,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix rigid infile %s",infile);
+ snprintf(str,128,"Cannot open fix rigid infile %s",infile);
error->one(FLERR,str);
}
@@ -2380,11 +2380,11 @@ void FixRigid::write_restart_file(char *file)
if (me) return;
char outfile[128];
- sprintf(outfile,"%s.rigid",file);
+ snprintf(outfile,128,"%s.rigid",file);
FILE *fp = fopen(outfile,"w");
if (fp == NULL) {
char str[192];
- sprintf(str,"Cannot open fix rigid restart file %s",outfile);
+ snprintf(str,192,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index d5d3d36083..44e1870e0a 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -569,7 +569,7 @@ void FixRigidSmall::init()
if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
- sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+ snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
error->warning(FLERR,str);
}
}
@@ -2482,7 +2482,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
fp = fopen(infile,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix rigid/small infile %s",infile);
+ snprintf(str,128,"Cannot open fix rigid/small infile %s",infile);
error->one(FLERR,str);
}
@@ -2597,11 +2597,11 @@ void FixRigidSmall::write_restart_file(char *file)
if (me == 0) {
char outfile[128];
- sprintf(outfile,"%s.rigid",file);
+ snprintf(outfile,128,"%s.rigid",file);
fp = fopen(outfile,"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix rigid restart file %s",outfile);
+ snprintf(str,128,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index eaefb0325d..9f4c6bf5e2 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -1591,7 +1591,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
fpcoeff = force->open_potential(coefffilename);
if (fpcoeff == NULL) {
char str[128];
- sprintf(str,"Cannot open SNAP coefficient file %s",coefffilename);
+ snprintf(str,128,"Cannot open SNAP coefficient file %s",coefffilename);
error->one(FLERR,str);
}
}
@@ -1757,7 +1757,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
fpparam = force->open_potential(paramfilename);
if (fpparam == NULL) {
char str[128];
- sprintf(str,"Cannot open SNAP parameter file %s",paramfilename);
+ snprintf(str,128,"Cannot open SNAP parameter file %s",paramfilename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 03fc94ae58..bf11b1d6ba 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -207,12 +207,11 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
p_basis_type = 2;
spline_length = read_F_table( arg[iarg+1], p_basis_type );
iarg += 2;
- } else
- {
- char * errmsg = (char *) calloc(150,sizeof(char));
- sprintf(errmsg,"CG basis type %s is not recognized\nSupported "
- "basis types: analytic linear_spline cubic_spline",arg[iarg]);
- error->all(FLERR,errmsg);
+ } else {
+ char errmsg[256];
+ snprintf(errmsg,256,"CG basis type %s is not recognized\nSupported "
+ "basis types: analytic linear_spline cubic_spline",arg[iarg]);
+ error->all(FLERR,errmsg);
} // END NJD MRD
} else if (strcmp(arg[iarg],"tchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
@@ -243,9 +242,9 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else {
- char * errmsg = (char *) calloc(80,sizeof(char));
- sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s"
- ,arg[iarg]);
+ char errmsg[128];
+ snprintf(errmsg,128,"Illegal fix bocs command: unrecognized keyword %s"
+ ,arg[iarg]);
error->all(FLERR,errmsg);
}
}
@@ -641,20 +640,16 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
{
data[i] = (double *) calloc(n_entries,sizeof(double));
}
- }
- else
- {
- char * errmsg = (char *) calloc(50,sizeof(char));
- sprintf(errmsg,"Unable to open file: %s\n",filename);
+ } else {
+ char errmsg[128];
+ snprintf(errmsg,128,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
n_entries = 0;
fpi = fopen(filename,"r");
- if (fpi)
- {
- while( fgets(line,199,fpi))
- {
+ if (fpi) {
+ while( fgets(line,199,fpi)) {
++n_entries;
test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
if (test_sscanf == 2)
@@ -668,11 +663,9 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
"line %d of file %s\n\tline: %s",n_entries,filename,line);
}
}
- }
- else
- {
- char * errmsg = (char *) calloc(50,sizeof(char));
- sprintf(errmsg,"Unable to open file: %s\n",filename);
+ } else {
+ char errmsg[128];
+ snprintf(errmsg,128,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
fclose(fpi);
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index ad9c76ac6b..882c13bc3e 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -424,12 +424,12 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
fclose(fp);
char nName [128];
- sprintf(nName,"%s.%d.vtk",filename,nOutput);
+ snprintf(nName,128,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix saed/vtk file %s",nName);
+ snprintf(str,128,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
@@ -550,13 +550,13 @@ void FixSAEDVTK::options(int narg, char **arg)
filename = new char[n];
strcpy(filename,arg[iarg+1]);
- char nName [128];
- sprintf(nName,"%s.%d.vtk",filename,nOutput);
+ char nName [128];
+ snprintf(nName,128,"%s.%d.vtk",filename,nOutput);
fp = fopen(nName,"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix saed/vtk file %s",nName);
+ snprintf(str,128,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
}
}
diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp
index e57a3788bf..7d701f5fb8 100644
--- a/src/USER-DPD/fix_eos_table.cpp
+++ b/src/USER-DPD/fix_eos_table.cpp
@@ -200,7 +200,7 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 181c7dccfa..779cee0e8b 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -309,7 +309,7 @@ void FixEOStableRX::read_file(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open eos table/rx potential file %s",file);
+ snprintf(str,128,"Cannot open eos table/rx potential file %s",file);
error->one(FLERR,str);
}
}
@@ -419,7 +419,7 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
FILE *fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 1a9c43704d..97668471c8 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -272,7 +272,7 @@ void FixRX::post_constructor()
fp = force->open_potential(kineticsFile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open rx file %s",kineticsFile);
+ snprintf(str,128,"Cannot open rx file %s",kineticsFile);
error->one(FLERR,str);
}
}
@@ -859,7 +859,7 @@ void FixRX::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open rx file %s",file);
+ snprintf(str,128,"Cannot open rx file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 057c8fa119..0251f019c5 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -730,7 +730,7 @@ void PairExp6rx::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open exp6/rx potential file %s",file);
+ snprintf(str,128,"Cannot open exp6/rx potential file %s",file);
error->one(FLERR,str);
}
}
@@ -841,7 +841,7 @@ void PairExp6rx::read_file2(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open polynomial file %s",file);
+ snprintf(str,128,"Cannot open polynomial file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index f911d8299e..19a4a02f0b 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -350,7 +350,7 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
FILE *fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 13c838fe01..f3ad86eb2f 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -495,7 +495,7 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,128,"Cannot open file %s",file);
error->one(FLERR,str);
}
diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp
index 192b39b2e8..da8a180fff 100644
--- a/src/USER-INTEL/pair_eam_alloy_intel.cpp
+++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp
@@ -126,7 +126,7 @@ void PairEAMAlloyIntel::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp
index 61bb6e0b4d..043f77db3e 100644
--- a/src/USER-INTEL/pair_eam_fs_intel.cpp
+++ b/src/USER-INTEL/pair_eam_fs_intel.cpp
@@ -126,7 +126,7 @@ void PairEAMFSIntel::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index eca1040c9c..ff2a1180b5 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -328,7 +328,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
fp = force->open_potential(globalfile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open MEAM potential file %s",globalfile);
+ snprintf(str,128,"Cannot open MEAM potential file %s",globalfile);
error->one(FLERR,str);
}
}
@@ -509,7 +509,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
fp = force->open_potential(userfile);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open MEAM potential file %s",userfile);
+ snprintf(str,128,"Cannot open MEAM potential file %s",userfile);
error->one(FLERR,str);
}
}
@@ -558,8 +558,8 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
if (strcmp(params[0],keywords[which]) == 0) break;
if (which == nkeywords) {
char str[128];
- sprintf(str,"Keyword %s in MEAM parameter file not recognized",
- params[0]);
+ snprintf(str,128,"Keyword %s in MEAM parameter file not recognized",
+ params[0]);
error->all(FLERR,str);
}
nindex = nparams - 2;
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index 0ce6121bf9..5c9f478a65 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -165,7 +165,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]);
+ snprintf(str,128,"Cannot open fix ave/correlate/long file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index ceac93178d..ae4534f825 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -2529,7 +2529,7 @@ void FixBondReact::open(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open superimpose file %s",file);
+ snprintf(str,128,"Cannot open superimpose file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 0b08fab4ca..01da7f87cf 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -232,7 +232,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
fgle = force->open_potential(fname);
if (fgle == NULL) {
char str[128];
- sprintf(str,"Cannot open A-matrix file %s",fname);
+ snprintf(str,128,"Cannot open A-matrix file %s",fname);
error->one(FLERR,str);
}
if (screen) fprintf(screen,"Reading A-matrix from %s\n", fname);
@@ -302,7 +302,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
fgle = force->open_potential(fname);
if (fgle == NULL) {
char str[128];
- sprintf(str,"Cannot open C-matrix file %s",fname);
+ snprintf(str,128,"Cannot open C-matrix file %s",fname);
error->one(FLERR,str);
}
if (screen)
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index 65f8e90ec3..a423b510e5 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -86,7 +86,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
FILE *fpr_2 = force->open_potential(arg[4]);
if (fpr_2 == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",arg[4]);
+ snprintf(str,128,"Cannot open file %s",arg[4]);
error->all(FLERR,str);
}
@@ -99,7 +99,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
FILE *fpr = force->open_potential(arg[8]);
if (fpr == NULL) {
char str[128];
- sprintf(str,"Cannot open file %s",arg[8]);
+ snprintf(str,128,"Cannot open file %s",arg[8]);
error->all(FLERR,str);
}
@@ -111,7 +111,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
fp = fopen(arg[10],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ttm/mod file %s",arg[10]);
+ snprintf(str,128,"Cannot open fix ttm/mod file %s",arg[10]);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 998582f619..0277969d15 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -363,7 +363,7 @@ void PairAGNI::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open AGNI potential file %s",file);
+ snprintf(str,128,"Cannot open AGNI potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 4716e271d7..491268567f 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -877,7 +877,7 @@ void PairEDIP::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open EDIP potential file %s",file);
+ snprintf(str,128,"Cannot open EDIP potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index fc76aadb0b..f56650d2f6 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -644,7 +644,7 @@ void PairEDIPMulti::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open EDIP potential file %s",file);
+ snprintf(str,128,"Cannot open EDIP potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index 49c562471f..1e7d17f040 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -591,7 +591,7 @@ void PairExTeP::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open ExTeP potential file %s",file);
+ snprintf(str,128,"Cannot open ExTeP potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 7e11cdff4f..6b92595472 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -880,7 +880,7 @@ void PairILPGrapheneHBN::read_file(char *filename)
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open ILP potential file %s",filename);
+ snprintf(str,128,"Cannot open ILP potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index bc3bfaeba9..18870ef69a 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -885,7 +885,7 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open KC potential file %s",filename);
+ snprintf(str,128,"Cannot open KC potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
index fb7d5ae40e..b39b9fdb72 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -315,7 +315,7 @@ void PairKolmogorovCrespiZ::read_file(char *filename)
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open KC potential file %s",filename);
+ snprintf(str,128,"Cannot open KC potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index e6ea6c2ae4..0300e2c7a2 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -439,7 +439,7 @@ void PairMEAMSpline::read_file(const char* filename)
FILE *fp = force->open_potential(filename);
if(fp == NULL) {
char str[1024];
- sprintf(str,"Cannot open spline MEAM potential file %s", filename);
+ snprintf(str,128,"Cannot open spline MEAM potential file %s", filename);
error->one(FLERR,str);
}
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index 891913ccfc..20dade5e5f 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -462,64 +462,64 @@ void PairMEAMSWSpline::coeff(int narg, char **arg)
void PairMEAMSWSpline::read_file(const char* filename)
{
- if(comm->me == 0) {
- FILE *fp = force->open_potential(filename);
- if(fp == NULL) {
- char str[1024];
- sprintf(str,"Cannot open spline MEAM potential file %s", filename);
- error->one(FLERR,str);
- }
+ if(comm->me == 0) {
+ FILE *fp = force->open_potential(filename);
+ if(fp == NULL) {
+ char str[1024];
+ snprintf(str,128,"Cannot open spline MEAM potential file %s", filename);
+ error->one(FLERR,str);
+ }
- // Skip first line of file.
- char line[MAXLINE];
- fgets(line, MAXLINE, fp);
+ // Skip first line of file.
+ char line[MAXLINE];
+ fgets(line, MAXLINE, fp);
- // Parse spline functions.
- phi.parse(fp, error);
- F.parse(fp, error);
- G.parse(fp, error);
- rho.parse(fp, error);
- U.parse(fp, error);
- f.parse(fp, error);
- g.parse(fp, error);
+ // Parse spline functions.
+ phi.parse(fp, error);
+ F.parse(fp, error);
+ G.parse(fp, error);
+ rho.parse(fp, error);
+ U.parse(fp, error);
+ f.parse(fp, error);
+ g.parse(fp, error);
- fclose(fp);
- }
+ fclose(fp);
+ }
- // Transfer spline functions from master processor to all other processors.
- phi.communicate(world, comm->me);
- rho.communicate(world, comm->me);
- f.communicate(world, comm->me);
- U.communicate(world, comm->me);
- g.communicate(world, comm->me);
- F.communicate(world, comm->me);
- G.communicate(world, comm->me);
-
- // Calculate 'zero-point energy' of single atom in vacuum.
- zero_atom_energy = U.eval(0.0);
-
- // Determine maximum cutoff radius of all relevant spline functions.
- cutoff = 0.0;
- if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
- if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
- if(f.cutoff() > cutoff) cutoff = f.cutoff();
- if(F.cutoff() > cutoff) cutoff = F.cutoff();
-
- // Set LAMMPS pair interaction flags.
- for(int i = 1; i <= atom->ntypes; i++) {
- for(int j = 1; j <= atom->ntypes; j++) {
- setflag[i][j] = 1;
- cutsq[i][j] = cutoff;
- }
- }
+ // Transfer spline functions from master processor to all other processors.
+ phi.communicate(world, comm->me);
+ rho.communicate(world, comm->me);
+ f.communicate(world, comm->me);
+ U.communicate(world, comm->me);
+ g.communicate(world, comm->me);
+ F.communicate(world, comm->me);
+ G.communicate(world, comm->me);
+
+ // Calculate 'zero-point energy' of single atom in vacuum.
+ zero_atom_energy = U.eval(0.0);
+
+ // Determine maximum cutoff radius of all relevant spline functions.
+ cutoff = 0.0;
+ if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
+ if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
+ if(f.cutoff() > cutoff) cutoff = f.cutoff();
+ if(F.cutoff() > cutoff) cutoff = F.cutoff();
+
+ // Set LAMMPS pair interaction flags.
+ for(int i = 1; i <= atom->ntypes; i++) {
+ for(int j = 1; j <= atom->ntypes; j++) {
+ setflag[i][j] = 1;
+ cutsq[i][j] = cutoff;
+ }
+ }
- // phi.writeGnuplot("phi.gp", "Phi(r)");
- // rho.writeGnuplot("rho.gp", "Rho(r)");
- // f.writeGnuplot("f.gp", "f(r)");
- // U.writeGnuplot("U.gp", "U(rho)");
- // g.writeGnuplot("g.gp", "g(x)");
- // F.writeGnuplot("F.gp", "F(r)");
- // G.writeGnuplot("G.gp", "G(x)");
+ // phi.writeGnuplot("phi.gp", "Phi(r)");
+ // rho.writeGnuplot("rho.gp", "Rho(r)");
+ // f.writeGnuplot("f.gp", "f(r)");
+ // U.writeGnuplot("U.gp", "U(rho)");
+ // g.writeGnuplot("g.gp", "g(x)");
+ // F.writeGnuplot("F.gp", "F(r)");
+ // G.writeGnuplot("G.gp", "G(x)");
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index d7e28a1e40..d1044cc336 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -845,7 +845,7 @@ void PairTersoffTable::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index 6348009d8f..8e49f56d5c 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -113,12 +113,12 @@ void ReaderMolfile::open_file(const char *file)
rv = mf->open(file,&natoms);
if (rv != MFI::E_NONE) {
- sprintf(str,"Cannot open file %s",file);
+ snprintf(str,1024,"Cannot open file %s",file);
error->one(FLERR,str);
}
if (natoms < 1) {
- sprintf(str,"No atoms in file %s",file);
+ snprintf(str,1024,"No atoms in file %s",file);
error->one(FLERR,str);
}
--
GitLab
From db510af5822fb39a9cdd76d72b73cd180682b48f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 11:32:44 -0400
Subject: [PATCH 240/332] more fixes for potential buffer overflows by using
snprintf() instead of sprintf()
---
src/USER-OMP/pair_eam_alloy_omp.cpp | 2 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 2 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 4 +-
src/USER-REAXC/fix_reaxc_species.cpp | 6 +-
src/USER-REAXC/pair_reaxc.cpp | 2 +-
src/USER-SMD/fix_smd_integrate_tlsph.cpp | 2 +-
src/USER-SMD/fix_smd_integrate_ulsph.cpp | 2 +-
.../fix_smd_move_triangulated_surface.cpp | 2 +-
src/USER-SMD/fix_smd_wall_surface.cpp | 487 +++++++++---------
10 files changed, 249 insertions(+), 262 deletions(-)
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp
index bbb3b03b02..78b4735863 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp
+++ b/src/USER-OMP/pair_eam_alloy_omp.cpp
@@ -126,7 +126,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp
index a678c887a0..17fecf9b4f 100644
--- a/src/USER-OMP/pair_eam_fs_omp.cpp
+++ b/src/USER-OMP/pair_eam_fs_omp.cpp
@@ -126,7 +126,7 @@ void PairEAMFSOMP::read_file(char *filename)
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
- sprintf(str,"Cannot open EAM potential file %s",filename);
+ snprintf(str,128,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
index ce3e6fea75..096a42b1a8 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
@@ -97,7 +97,7 @@ void PairTersoffZBLOMP::read_file(char *file)
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open Tersoff potential file %s",file);
+ snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index fb40b2042e..9dc347826f 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -62,7 +62,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
if (suffix && strcmp(suffix,".gz") == 0) {
#ifdef LAMMPS_GZIP
char gzip[128];
- sprintf(gzip,"gzip -6 > %s",arg[4]);
+ snprintf(gzip,128,"gzip -6 > %s",arg[4]);
#ifdef _WIN32
fp = _popen(gzip,"wb");
#else
@@ -75,7 +75,7 @@ FixReaxCBonds::FixReaxCBonds(LAMMPS *lmp, int narg, char **arg) :
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix reax/c/bonds file %s",arg[4]);
+ snprintf(str,128,"Cannot open fix reax/c/bonds file %s",arg[4]);
error->one(FLERR,str);
}
}
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 8ec7f4174f..46426d484a 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -98,9 +98,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
}
if (me == 0 && rene_flag) {
- char str[128];
- sprintf(str,"Resetting reneighboring criteria for fix reax/c/species");
- error->warning(FLERR,str);
+ error->warning(FLERR,"Resetting reneighboring criteria for fix reax/c/species");
}
tmparg = NULL;
@@ -127,7 +125,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix reax/c/species file %s",arg[6]);
+ snprintf(str,128,"Cannot open fix reax/c/species file %s",arg[6]);
error->one(FLERR,str);
}
}
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 378d20952c..85bd8471b4 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -301,7 +301,7 @@ void PairReaxC::coeff( int nargs, char **args )
Read_Force_Field(fp, &(system->reax_param), control);
else {
char str[128];
- sprintf(str,"Cannot open ReaxFF potential file %s",file);
+ snprintf(str,128,"Cannot open ReaxFF potential file %s",file);
error->all(FLERR,str);
}
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index 1eae45161f..f931ae94ff 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -86,7 +86,7 @@ FixSMDIntegrateTlsph::FixSMDIntegrateTlsph(LAMMPS *lmp, int narg, char **arg) :
}
} else {
char msg[128];
- sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
+ snprintf(msg,128, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
error->all(FLERR, msg);
}
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 685d6af5a8..6c4705eb96 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -119,7 +119,7 @@ FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) :
}
} else {
char msg[128];
- sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
+ snprintf(msg,128, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
error->all(FLERR, msg);
}
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index b0944f1186..fe8695b23e 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -200,7 +200,7 @@ FixSMDMoveTriSurf::FixSMDMoveTriSurf(LAMMPS *lmp, int narg, char **arg) :
} else {
char msg[128];
- sprintf(msg, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]);
+ snprintf(msg,128, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]);
error->all(FLERR, msg);
}
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 4dd415f53e..a37ba67a80 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -223,62 +223,59 @@ int FixSMDWallSurface::count_words(const char *line) {
void FixSMDWallSurface::read_triangles(int pass) {
- double coord[3];
-
- int nlocal_previous = atom->nlocal;
- int ilocal = nlocal_previous;
- int m;
- int me;
-
- bigint natoms_previous = atom->natoms;
- Vector3d *vert;
- vert = new Vector3d[3];
- Vector3d normal, center;
-
- FILE *fp = fopen(filename, "r");
- if (fp == NULL) {
- char str[128];
- sprintf(str, "Cannot open file %s", filename);
- error->one(FLERR, str);
- }
-
- MPI_Comm_rank(world, &me);
- if (me == 0) {
- if (screen) {
- if (pass == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- fprintf(screen, " scanning triangle pairs ...\n");
- } else {
- fprintf(screen, " reading triangle pairs ...\n");
- }
- }
- if (logfile) {
- if (pass == 0) {
- fprintf(logfile, " scanning triangle pairs ...\n");
- } else {
- fprintf(logfile, " reading triangle pairs ...\n");
- }
- }
- }
-
- char str[128];
- char line[256];
- char *retpointer;
- char **values;
- int nwords;
-
- // read STL solid name
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading number of triangle pairs");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords < 1) {
- sprintf(str, "first line of file is incorrect");
- error->one(FLERR, str);
- }
+ double coord[3];
+
+ int nlocal_previous = atom->nlocal;
+ int ilocal = nlocal_previous;
+ int m;
+ int me;
+
+ bigint natoms_previous = atom->natoms;
+ Vector3d *vert;
+ vert = new Vector3d[3];
+ Vector3d normal, center;
+
+ FILE *fp = fopen(filename, "r");
+ if (fp == NULL) {
+ char str[128];
+ snprintf(str,128, "Cannot open file %s", filename);
+ error->one(FLERR, str);
+ }
+
+ MPI_Comm_rank(world, &me);
+ if (me == 0) {
+ if (screen) {
+ if (pass == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ fprintf(screen, " scanning triangle pairs ...\n");
+ } else {
+ fprintf(screen, " reading triangle pairs ...\n");
+ }
+ }
+ if (logfile) {
+ if (pass == 0) {
+ fprintf(logfile, " scanning triangle pairs ...\n");
+ } else {
+ fprintf(logfile, " reading triangle pairs ...\n");
+ }
+ }
+ }
+
+ char line[256];
+ char *retpointer;
+ char **values;
+ int nwords;
+
+ // read STL solid name
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ error->one(FLERR,"error reading number of triangle pairs");
+ }
+
+ nwords = count_words(line);
+ if (nwords < 1) {
+ error->one(FLERR,"first line of file is incorrect");
+ }
// values = new char*[nwords];
// values[0] = strtok(line, " \t\n\r\f");
@@ -295,211 +292,203 @@ void FixSMDWallSurface::read_triangles(int pass) {
// cout << "STL file contains solid body with name: " << values[1] << endl;
// }
- // iterate over STL facets util end of body is reached
-
- while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line
-
- // evaluate facet line
- nwords = count_words(line);
- if (nwords != 5) {
- //sprintf(str, "found end solid line");
- //error->message(FLERR, str);
- break;
- } else {
- // should be facet line
- }
-
- values = new char*[nwords];
- values[0] = strtok(line, " \t\n\r\f");
- if (values[0] == NULL)
- error->all(FLERR, "Incorrect atom format in data file");
- for (m = 1; m < nwords; m++) {
- values[m] = strtok(NULL, " \t\n\r\f");
- if (values[m] == NULL)
- error->all(FLERR, "Incorrect atom format in data file");
- }
-
- normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]);
- //cout << "normal is " << normal << endl;
-
- delete[] values;
-
- // read outer loop line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading outer loop");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 2) {
- sprintf(str, "error reading outer loop");
- error->one(FLERR, str);
- }
-
- // read vertex lines
-
- for (int k = 0; k < 3; k++) {
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading vertex line");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 4) {
- sprintf(str, "error reading vertex line");
- error->one(FLERR, str);
- }
-
- values = new char*[nwords];
- values[0] = strtok(line, " \t\n\r\f");
- if (values[0] == NULL)
- error->all(FLERR, "Incorrect vertex line");
- for (m = 1; m < nwords; m++) {
- values[m] = strtok(NULL, " \t\n\r\f");
- if (values[m] == NULL)
- error->all(FLERR, "Incorrect vertex line");
- }
-
- vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]);
- //cout << "vertex is " << vert[k] << endl;
- //printf("%s %s %s\n", values[1], values[2], values[3]);
- delete[] values;
- //exit(1);
-
- }
-
- // read end loop line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading endloop");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 1) {
- sprintf(str, "error reading endloop");
- error->one(FLERR, str);
- }
-
- // read end facet line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading endfacet");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 1) {
- sprintf(str, "error reading endfacet");
- error->one(FLERR, str);
- }
-
- // now we have a normal and three vertices ... proceed with adding triangle
-
- center = (vert[0] + vert[1] + vert[2]) / 3.0;
-
- // cout << "center is " << center << endl;
-
- double r1 = (center - vert[0]).norm();
- double r2 = (center - vert[1]).norm();
- double r3 = (center - vert[2]).norm();
- double r = MAX(r1, r2);
- r = MAX(r, r3);
-
- /*
- * if atom/molecule is in my subbox, create it
- * ... use x0 to hold triangle normal.
- * ... use smd_data_9 to hold the three vertices
- * ... use x to hold triangle center
- * ... radius is the mmaximal distance from triangle center to all vertices
- */
-
- // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]);
- // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]);
- // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]);
- //printf("ilocal = %d\n", ilocal);
- if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2]
- && center(2) < subhi[2]) {
- //printf("******* KERATIN nlocal=%d ***\n", nlocal);
- coord[0] = center(0);
- coord[1] = center(1);
- coord[2] = center(2);
- atom->avec->create_atom(wall_particle_type, coord);
-
- /*
- * need to initialize pointers to atom vec arrays here, because they could have changed
- * due to calling grow() in create_atoms() above;
- */
-
- tagint *mol = atom->molecule;
- int *type = atom->type;
- double *radius = atom->radius;
- double *contact_radius = atom->contact_radius;
- double **smd_data_9 = atom->smd_data_9;
- double **x0 = atom->x0;
-
- radius[ilocal] = r; //ilocal;
- contact_radius[ilocal] = r; //ilocal;
- mol[ilocal] = wall_molecule_id;
- type[ilocal] = wall_particle_type;
- x0[ilocal][0] = normal(0);
- x0[ilocal][1] = normal(1);
- x0[ilocal][2] = normal(2);
- smd_data_9[ilocal][0] = vert[0](0);
- smd_data_9[ilocal][1] = vert[0](1);
- smd_data_9[ilocal][2] = vert[0](2);
- smd_data_9[ilocal][3] = vert[1](0);
- smd_data_9[ilocal][4] = vert[1](1);
- smd_data_9[ilocal][5] = vert[1](2);
- smd_data_9[ilocal][6] = vert[2](0);
- smd_data_9[ilocal][7] = vert[2](1);
- smd_data_9[ilocal][8] = vert[2](2);
-
- ilocal++;
- }
-
- }
+ // iterate over STL facets util end of body is reached
+
+ while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line
+
+ // evaluate facet line
+ nwords = count_words(line);
+ if (nwords != 5) {
+ //sprintf(str, "found end solid line");
+ //error->message(FLERR, str);
+ break;
+ } else {
+ // should be facet line
+ }
+
+ values = new char*[nwords];
+ values[0] = strtok(line, " \t\n\r\f");
+ if (values[0] == NULL)
+ error->all(FLERR, "Incorrect atom format in data file");
+ for (m = 1; m < nwords; m++) {
+ values[m] = strtok(NULL, " \t\n\r\f");
+ if (values[m] == NULL)
+ error->all(FLERR, "Incorrect atom format in data file");
+ }
+
+ normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]);
+ //cout << "normal is " << normal << endl;
+
+ delete[] values;
+
+ // read outer loop line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ error->one(FLERR, "error reading outer loop");
+ }
+
+ nwords = count_words(line);
+ if (nwords != 2) {
+ error->one(FLERR,"error reading outer loop");
+ }
+
+ // read vertex lines
+
+ for (int k = 0; k < 3; k++) {
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ error->one(FLERR,"error reading vertex line");
+ }
+
+ nwords = count_words(line);
+ if (nwords != 4) {
+ error->one(FLERR,"error reading vertex line");
+ }
+
+ values = new char*[nwords];
+ values[0] = strtok(line, " \t\n\r\f");
+ if (values[0] == NULL)
+ error->all(FLERR,"Incorrect vertex line");
+ for (m = 1; m < nwords; m++) {
+ values[m] = strtok(NULL, " \t\n\r\f");
+ if (values[m] == NULL)
+ error->all(FLERR, "Incorrect vertex line");
+ }
+
+ vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]);
+ //cout << "vertex is " << vert[k] << endl;
+ //printf("%s %s %s\n", values[1], values[2], values[3]);
+ delete[] values;
+ //exit(1);
+
+ }
+
+ // read end loop line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ error->one(FLERR, "error reading endloop");
+ }
+
+ nwords = count_words(line);
+ if (nwords != 1) {
+ error->one(FLERR,"error reading endloop");
+ }
+
+ // read end facet line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ error->one(FLERR,"error reading endfacet");
+ }
+
+ nwords = count_words(line);
+ if (nwords != 1) {
+ error->one(FLERR,"error reading endfacet");
+ }
+
+ // now we have a normal and three vertices ... proceed with adding triangle
+
+ center = (vert[0] + vert[1] + vert[2]) / 3.0;
+
+ // cout << "center is " << center << endl;
+
+ double r1 = (center - vert[0]).norm();
+ double r2 = (center - vert[1]).norm();
+ double r3 = (center - vert[2]).norm();
+ double r = MAX(r1, r2);
+ r = MAX(r, r3);
+
+ /*
+ * if atom/molecule is in my subbox, create it
+ * ... use x0 to hold triangle normal.
+ * ... use smd_data_9 to hold the three vertices
+ * ... use x to hold triangle center
+ * ... radius is the mmaximal distance from triangle center to all vertices
+ */
+
+ // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]);
+ // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]);
+ // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]);
+ //printf("ilocal = %d\n", ilocal);
+ if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2]
+ && center(2) < subhi[2]) {
+ //printf("******* KERATIN nlocal=%d ***\n", nlocal);
+ coord[0] = center(0);
+ coord[1] = center(1);
+ coord[2] = center(2);
+ atom->avec->create_atom(wall_particle_type, coord);
+
+ /*
+ * need to initialize pointers to atom vec arrays here, because they could have changed
+ * due to calling grow() in create_atoms() above;
+ */
+
+ tagint *mol = atom->molecule;
+ int *type = atom->type;
+ double *radius = atom->radius;
+ double *contact_radius = atom->contact_radius;
+ double **smd_data_9 = atom->smd_data_9;
+ double **x0 = atom->x0;
+
+ radius[ilocal] = r; //ilocal;
+ contact_radius[ilocal] = r; //ilocal;
+ mol[ilocal] = wall_molecule_id;
+ type[ilocal] = wall_particle_type;
+ x0[ilocal][0] = normal(0);
+ x0[ilocal][1] = normal(1);
+ x0[ilocal][2] = normal(2);
+ smd_data_9[ilocal][0] = vert[0](0);
+ smd_data_9[ilocal][1] = vert[0](1);
+ smd_data_9[ilocal][2] = vert[0](2);
+ smd_data_9[ilocal][3] = vert[1](0);
+ smd_data_9[ilocal][4] = vert[1](1);
+ smd_data_9[ilocal][5] = vert[1](2);
+ smd_data_9[ilocal][6] = vert[2](0);
+ smd_data_9[ilocal][7] = vert[2](1);
+ smd_data_9[ilocal][8] = vert[2](2);
+
+ ilocal++;
+ }
+
+ }
// set new total # of atoms and error check
- bigint nblocal = atom->nlocal;
- MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world);
- if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
- error->all(FLERR, "Too many total atoms");
+ bigint nblocal = atom->nlocal;
+ MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world);
+ if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
+ error->all(FLERR, "Too many total atoms");
// add IDs for newly created atoms
// check that atom IDs are valid
- if (atom->tag_enable)
- atom->tag_extend();
- atom->tag_check();
+ if (atom->tag_enable)
+ atom->tag_extend();
+ atom->tag_check();
// create global mapping of atoms
// zero nghost in case are adding new atoms to existing atoms
- if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
- }
+ if (atom->map_style) {
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
+ }
// print status
- if (comm->me == 0) {
- if (screen) {
- printf("... fix smd/wall_surface finished reading triangulated surface\n");
- fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
- if (logfile) {
- fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n");
- fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
- fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
- }
-
- delete[] vert;
- fclose(fp);
+ if (comm->me == 0) {
+ if (screen) {
+ printf("... fix smd/wall_surface finished reading triangulated surface\n");
+ fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+ if (logfile) {
+ fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n");
+ fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
+ fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+ }
+
+ delete[] vert;
+ fclose(fp);
}
--
GitLab
From 84657f1531c0da11a7ee11b7d3e553b79d15cd1b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 12:00:04 -0400
Subject: [PATCH 241/332] final pass at sprintf() buffer overflow prevention.
also fix typo in previous commit
---
src/REPLICA/neb.cpp | 2 +-
src/USER-SMD/pair_smd_tlsph.cpp | 4 ++--
src/USER-SMD/pair_smd_ulsph.cpp | 4 ++--
src/USER-SMTBQ/pair_smtbq.cpp | 2 +-
src/USER-UEF/dump_cfg_uef.cpp | 4 +---
5 files changed, 7 insertions(+), 9 deletions(-)
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 9a4de9ca0b..3963379356 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -549,7 +549,7 @@ void NEB::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
- snprintf(gunz128,ip,"gzip -c -d %s",file);
+ snprintf(gunzip,128,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 09fe3b1180..ab6b7d2785 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -1684,8 +1684,8 @@ void PairTlsph::coeff(int narg, char **arg) {
} // end energy release rate failure criterion
else {
- sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
- error->all(FLERR, str);
+ snprintf(str,128,"unknown *KEYWORD: %s", arg[ioffset]);
+ error->all(FLERR, str);
}
}
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index ff3720b2ff..50af6e2356 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -1331,8 +1331,8 @@ void PairULSPH::coeff(int narg, char **arg) {
} // end *ARTIFICIAL_STRESS
else {
- sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
- error->all(FLERR, str);
+ snprintf(str,128, "unknown *KEYWORD: %s", arg[ioffset]);
+ error->all(FLERR, str);
}
}
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index a8cce49749..c2690dc864 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -399,7 +399,7 @@ void PairSMTBQ::read_file(char *file)
fp = force->open_potential(file);
if ( fp == NULL ) {
char str[128];
- sprintf(str,"Cannot open SMTBQ potential file %s",file);
+ snprintf(str,128,"Cannot open SMTBQ potential file %s",file);
error->one(FLERR,str);
}
diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp
index 44af823332..58b3ec5a1f 100644
--- a/src/USER-UEF/dump_cfg_uef.cpp
+++ b/src/USER-UEF/dump_cfg_uef.cpp
@@ -90,9 +90,7 @@ void DumpCFGUef::write_header(bigint n)
if (atom->peri_flag) scale = atom->pdscale;
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
- char str[64];
- sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
- fprintf(fp,str,n);
+ fprintf(fp,"Number of particles = " BIGINT_FORMAT "\n",n);
fprintf(fp,"A = %g Angstrom (basic length-scale)\n",scale);
// in box[][] columns are cell edges
// in H0, rows are cell edges
--
GitLab
From b3079f3aec02e74ce14616b6fdf91454e2bd35f2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 12:05:32 -0400
Subject: [PATCH 242/332] rename files and classes for pair style eam/cd/omp to
follow the rename of the non-threaded classes
---
src/Purge.list | 3 +++
...pair_cdeam_omp.cpp => pair_eam_cd_omp.cpp} | 14 ++++++------
.../{pair_cdeam_omp.h => pair_eam_cd_omp.h} | 22 +++++++++----------
3 files changed, 21 insertions(+), 18 deletions(-)
rename src/USER-OMP/{pair_cdeam_omp.cpp => pair_eam_cd_omp.cpp} (97%)
rename src/USER-OMP/{pair_cdeam_omp.h => pair_eam_cd_omp.h} (71%)
diff --git a/src/Purge.list b/src/Purge.list
index cb98636b1c..c70392c935 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -24,6 +24,9 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
+# renamed on 6 September 2018
+pair_cdeam_omp.h
+pair_cdeam_omp.cpp
# renamed on 31 July 2018
pair_cdeam.h
pair_cdeam.cpp
diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_eam_cd_omp.cpp
similarity index 97%
rename from src/USER-OMP/pair_cdeam_omp.cpp
rename to src/USER-OMP/pair_eam_cd_omp.cpp
index c3a9454567..68c01c83d2 100644
--- a/src/USER-OMP/pair_cdeam_omp.cpp
+++ b/src/USER-OMP/pair_eam_cd_omp.cpp
@@ -15,7 +15,7 @@
#include <cmath>
#include <cstring>
-#include "pair_cdeam_omp.h"
+#include "pair_eam_cd_omp.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
@@ -44,8 +44,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) :
- PairEAM(lmp), PairCDEAM(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR)
+PairEAMCDOMP::PairEAMCDOMP(LAMMPS *lmp, int _cdeamVersion) :
+ PairEAM(lmp), PairEAMCD(lmp,_cdeamVersion), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
@@ -53,7 +53,7 @@ PairCDEAMOMP::PairCDEAMOMP(LAMMPS *lmp, int _cdeamVersion) :
/* ---------------------------------------------------------------------- */
-void PairCDEAMOMP::compute(int eflag, int vflag)
+void PairEAMCDOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
@@ -143,7 +143,7 @@ void PairCDEAMOMP::compute(int eflag, int vflag)
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR, int CDEAMVERSION>
-void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
+void PairEAMCDOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -534,10 +534,10 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
/* ---------------------------------------------------------------------- */
-double PairCDEAMOMP::memory_usage()
+double PairEAMCDOMP::memory_usage()
{
double bytes = memory_usage_thr();
- bytes += PairCDEAM::memory_usage();
+ bytes += PairEAMCD::memory_usage();
return bytes;
}
diff --git a/src/USER-OMP/pair_cdeam_omp.h b/src/USER-OMP/pair_eam_cd_omp.h
similarity index 71%
rename from src/USER-OMP/pair_cdeam_omp.h
rename to src/USER-OMP/pair_eam_cd_omp.h
index 2839ab0ed0..d46a5383f5 100644
--- a/src/USER-OMP/pair_cdeam_omp.h
+++ b/src/USER-OMP/pair_eam_cd_omp.h
@@ -17,23 +17,23 @@
#ifdef PAIR_CLASS
-PairStyle(eam/cd/omp,PairCDEAM_OneSiteOMP)
-PairStyle(eam/cd/old/omp,PairCDEAM_TwoSiteOMP)
+PairStyle(eam/cd/omp,PairEAMCD_OneSiteOMP)
+PairStyle(eam/cd/old/omp,PairEAMCD_TwoSiteOMP)
#else
-#ifndef LMP_PAIR_CDEAM_OMP_H
-#define LMP_PAIR_CDEAM_OMP_H
+#ifndef LMP_PAIR_EAM_CD_OMP_H
+#define LMP_PAIR_EAM_CD_OMP_H
-#include "pair_cdeam.h"
+#include "pair_eam_cd.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
-class PairCDEAMOMP : public PairCDEAM, public ThrOMP {
+class PairEAMCDOMP : public PairEAMCD, public ThrOMP {
public:
- PairCDEAMOMP(class LAMMPS *, int);
+ PairEAMCDOMP(class LAMMPS *, int);
virtual void compute(int, int);
virtual double memory_usage();
@@ -44,19 +44,19 @@ class PairCDEAMOMP : public PairCDEAM, public ThrOMP {
};
/// The one-site concentration formulation of CD-EAM.
- class PairCDEAM_OneSiteOMP : public PairCDEAMOMP
+ class PairEAMCD_OneSiteOMP : public PairEAMCDOMP
{
public:
/// Constructor.
- PairCDEAM_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 1) {}
+ PairEAMCD_OneSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 1) {}
};
/// The two-site concentration formulation of CD-EAM.
- class PairCDEAM_TwoSiteOMP : public PairCDEAMOMP
+ class PairEAMCD_TwoSiteOMP : public PairEAMCDOMP
{
public:
/// Constructor.
- PairCDEAM_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAMOMP(lmp, 2) {}
+ PairEAMCD_TwoSiteOMP(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCDOMP(lmp, 2) {}
};
}
--
GitLab
From b915716b6007ff25717640eda7246595352ba22c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 12:27:10 -0400
Subject: [PATCH 243/332] fix inconsistency resulting from error in
auto-replace macro
---
src/USER-MISC/pair_meam_sw_spline.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index 20dade5e5f..e17c13865d 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -466,7 +466,7 @@ void PairMEAMSWSpline::read_file(const char* filename)
FILE *fp = force->open_potential(filename);
if(fp == NULL) {
char str[1024];
- snprintf(str,128,"Cannot open spline MEAM potential file %s", filename);
+ snprintf(str,1024,"Cannot open spline MEAM potential file %s", filename);
error->one(FLERR,str);
}
--
GitLab
From efd582fb21d11dcb32c10a6cc4267b9578ece81d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 13:13:20 -0400
Subject: [PATCH 244/332] update list of code owners for automatic review
requests. started assigning core files
---
.github/CODEOWNERS | 67 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index b91e58a83f..4f561a4c19 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -17,6 +17,7 @@ src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
+src/MESSAGE/* @sjplimp
src/SPIN/* @julient31
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
@@ -32,16 +33,82 @@ src/USER-PHONON/* @lingtikong
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
+src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
src/USER-VTK/* @rbberger
+
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
+src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-MISC/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
+src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+
+# core LAMMPS classes
+src/lammps.* @sjplimp
+src/pointers.h @sjplimp
+src/atom.* @sjplimp
+src/atom_vec.* @sjplimp
+src/angle.* @sjplimp
+src/bond.* @sjplimp
+src/comm*.* @sjplimp
+src/compute.* @sjplimp
+src/dihedral.* @sjplimp
+src/domain.* @sjplimp
+src/dump*.* @sjplimp
+src/error.* @sjplimp
+src/finish.* @sjplimp
+src/fix.* @sjplimp
+src/force.* @sjplimp
+src/group.* @sjplimp
+src/improper.* @sjplimp
+src/kspace.* @sjplimp
+src/lmptyp.h @sjplimp
+src/library.* @sjplimp
+src/main.cpp @sjplimp
+src/memory.* @sjplimp
+src/modify.* @sjplimp
+src/molecule.* @sjplimp
+src/my_page.h @sjplimp
+src/my_pool_chunk.h @sjplimp
+src/npair*.* @sjplimp
+src/ntopo*.* @sjplimp
+src/nstencil*.* @sjplimp
+src/neighbor.* @sjplimp
+src/nbin*.* @sjplimp
+src/neigh_*.* @sjplimp
+src/output.* @sjplimp
+src/pair.* @sjplimp
+src/rcb.* @sjplimp
+src/random_*.* @sjplimp
+src/region*.* @sjplimp
+src/rcb.* @sjplimp
+src/read*.* @sjplimp
+src/rerun.* @sjplimp
+src/run.* @sjplimp
+src/respa.* @sjplimp
+src/set.* @sjplimp
+src/special.* @sjplimp
+src/suffix.h @sjplimp
+src/thermo.* @sjplimp
+src/universe.* @sjplimp
+src/update.* @sjplimp
+src/variable.* @sjplimp
+src/verlet.* @sjplimp
+src/velocity.* @sjplimp
+src/write_data.* @sjplimp
+src/write_restart.* @sjplimp
+
+# overrides for specific files
+src/dump_movie.* @akohlmey
+src/exceptions.h @rbberger
+src/fix_nh.* @athomps
+src/info.* @akohlmey @rbberger
+src/timer.* @akohlmey
# tools
tools/msi2lmp/* @akohlmey
--
GitLab
From d7b00f86f88cb2266de9eaaf3a8ef0729f9ce42a Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 6 Sep 2018 14:18:28 -0600
Subject: [PATCH 245/332] cmake: fix Eigen3 detection
For some reason FindEigen3.cmake defines all cap. variables, i.e.
Eigen3_FOUND -> EIGEN3_FOUND
---
cmake/CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 2e238cdf2b..149f9da817 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -551,7 +551,7 @@ if(PKG_USER-SMD)
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3)
- if(NOT Eigen3_FOUND)
+ if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
--
GitLab
From 8f8aee65d20f9b11ab4e7f70e9412202ae9fdfc5 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@lanl.gov>
Date: Thu, 6 Sep 2018 14:37:08 -0600
Subject: [PATCH 246/332] cmake: fix globbing of emacs files
Done by: sed -i '/GLOB/s@/\*\.@/[^.]*.@g' CMakeLists.txt
---
cmake/CMakeLists.txt | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 2e238cdf2b..45e6870ce8 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT
# To avoid conflicts with the conventional Makefile build system, we build everything here
-file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
+file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
@@ -348,7 +348,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
- file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
+ file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
else()
@@ -603,7 +603,7 @@ endif()
if(PKG_MESSAGE)
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
- file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
if(BUILD_SHARED_LIBS)
@@ -720,8 +720,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
foreach(PKG ${DEFAULT_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
- file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
- file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+ file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+ file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -739,8 +739,8 @@ endforeach()
foreach(PKG ${ACCEL_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
- file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
- file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+ file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+ file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -754,7 +754,7 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
- file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
+ file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
@@ -1039,7 +1039,7 @@ if(PKG_GPU)
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
- file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+ file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
@@ -1052,15 +1052,15 @@ if(PKG_GPU)
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
- file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
+ file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
- file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
- file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
+ file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+ file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
@@ -1109,7 +1109,7 @@ if(PKG_GPU)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
- file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
+ file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
foreach(GPU_KERNEL ${GPU_LIB_CU})
@@ -1236,7 +1236,7 @@ if(BUILD_DOC)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
- file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
+ file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
--
GitLab
From 44fcdc40244a5f146f20c4ec01fab20720c60413 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 21:20:47 -0400
Subject: [PATCH 247/332] update reference examples with versions that do not
vary by MPI rank count
---
examples/USER/misc/mop/data.mop | 2467 +++++++++++++++++
examples/USER/misc/mop/in.compute_stress_mop | 44 +-
.../mop/log.5Sep18.compute_stress_mop.g++.1 | 111 +
.../mop/log.5Sep18.compute_stress_mop.g++.4 | 111 +
examples/USER/misc/mop/moppz.time.reference | 405 ++-
examples/USER/misc/mop/mopz0.time.reference | 5 +-
examples/USER/misc/mop/profile.z.reference | 227 --
7 files changed, 2883 insertions(+), 487 deletions(-)
create mode 100644 examples/USER/misc/mop/data.mop
create mode 100644 examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1
create mode 100644 examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4
delete mode 100644 examples/USER/misc/mop/profile.z.reference
diff --git a/examples/USER/misc/mop/data.mop b/examples/USER/misc/mop/data.mop
new file mode 100644
index 0000000000..7f158d7626
--- /dev/null
+++ b/examples/USER/misc/mop/data.mop
@@ -0,0 +1,2467 @@
+LAMMPS data file via write_data, version 31 Aug 2018, timestep = 0
+
+1224 atoms
+2 atom types
+
+0.0000000000000000e+00 9.5244063118091962e+00 xlo xhi
+0.0000000000000000e+00 9.5244063118091962e+00 ylo yhi
+-2.0e+00 1.6e+01 zlo zhi
+
+Masses
+
+1 1
+2 1
+
+Atoms # atomic
+
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+794 2 7.9370052598409979e-01 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
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+798 2 2.3811015779522990e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
+801 2 3.1748021039363992e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0
+802 2 3.9685026299204984e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
+805 2 4.7622031559045981e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0
+806 2 5.5559036818886973e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
+809 2 6.3496042078727983e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0
+810 2 7.1433047338568993e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
+813 2 7.9370052598409968e+00 0.0000000000000000e+00 -1.5874010519681994e+00 0 0 0
+814 2 8.7307057858250960e+00 7.9370052598409979e-01 -1.5874010519681994e+00 0 0 0
+817 2 0.0000000000000000e+00 1.5874010519681996e+00 -1.5874010519681994e+00 0 0 0
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+821 2 1.5874010519681996e+00 1.5874010519681996e+00 -1.5874010519681994e+00 0 0 0
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+825 2 3.1748021039363992e+00 1.5874010519681996e+00 -1.5874010519681994e+00 0 0 0
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+857 2 6.3496042078727983e+00 3.1748021039363992e+00 -1.5874010519681994e+00 0 0 0
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+861 2 7.9370052598409968e+00 3.1748021039363992e+00 -1.5874010519681994e+00 0 0 0
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+865 2 0.0000000000000000e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0
+866 2 7.9370052598409979e-01 5.5559036818886973e+00 -1.5874010519681994e+00 0 0 0
+869 2 1.5874010519681996e+00 4.7622031559045981e+00 -1.5874010519681994e+00 0 0 0
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+925 2 4.7622031559045981e+00 7.9370052598409968e+00 -1.5874010519681994e+00 0 0 0
+926 2 5.5559036818886973e+00 8.7307057858250960e+00 -1.5874010519681994e+00 0 0 0
+929 2 6.3496042078727983e+00 7.9370052598409968e+00 -1.5874010519681994e+00 0 0 0
+930 2 7.1433047338568993e+00 8.7307057858250960e+00 -1.5874010519681994e+00 0 0 0
+933 2 7.9370052598409968e+00 7.9370052598409968e+00 -1.5874010519681994e+00 0 0 0
+934 2 8.7307057858250960e+00 8.7307057858250960e+00 -1.5874010519681994e+00 0 0 0
+795 2 7.9370052598409979e-01 0.0000000000000000e+00 -7.9370052598409924e-01 0 0 0
+796 2 0.0000000000000000e+00 7.9370052598409979e-01 -7.9370052598409924e-01 0 0 0
+937 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
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+800 2 1.5874010519681996e+00 7.9370052598409979e-01 -7.9370052598409924e-01 0 0 0
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diff --git a/examples/USER/misc/mop/in.compute_stress_mop b/examples/USER/misc/mop/in.compute_stress_mop
index cfa97f5dfe..442596dcf1 100644
--- a/examples/USER/misc/mop/in.compute_stress_mop
+++ b/examples/USER/misc/mop/in.compute_stress_mop
@@ -1,30 +1,20 @@
variable T equal 0.8
variable p_solid equal 0.05
-lattice fcc 1.0
-region box block 0.0 6.0 0.0 6.0 -2.0 12.0
-create_box 2 box
+read_data data.mop
-mass * 1.0
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
-region solid_bottom block INF INF INF INF -1.1 0.1
-region liquid block INF INF INF INF 1.1 8.9
-region solid_up block INF INF INF INF 9.9 11.1
-
-create_atoms 1 region liquid
-delete_atoms porosity liquid 0.26 88765
-group liquid region liquid
-
-create_atoms 2 region solid_bottom
-group solid_bottom region solid_bottom
-create_atoms 2 region solid_up
-group solid_up region solid_up
-group solid union solid_bottom solid_up
+group liquid type 1
+group solid type 2
+region bottom block INF INF INF INF INF 7.0
+group bottom region bottom
+group solid_bottom intersect solid bottom
+group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
@@ -35,28 +25,16 @@ compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
-thermo 10000
+thermo 1000
thermo_modify flush yes temp Tliq
-dump 1 all atom 10000 dump.lammpstrj
-
fix fxbal all balance 1000 1.05 shift z 10 1.05
-velocity liquid create $T 47298 dist gaussian rot yes
-run 50000
-undump 1
-reset_timestep 0
-
-compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
-
-compute liquidStress_ke liquid stress/atom NULL ke
-compute liquidStress_vir liquid stress/atom NULL virial
-fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
compute mopz0 all stress/mop z center kin conf
-fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
-fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
-run 40000
+run 0
diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1 b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1
new file mode 100644
index 0000000000..7b3f24cf38
--- /dev/null
+++ b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.1
@@ -0,0 +1,111 @@
+LAMMPS (5 Sep 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+variable T equal 0.8
+variable p_solid equal 0.05
+
+read_data data.mop
+ orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1224 atoms
+ reading velocities ...
+ 1224 velocities
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+group liquid type 1
+792 atoms in group liquid
+group solid type 2
+432 atoms in group solid
+region bottom block INF INF INF INF INF 7.0
+group bottom region bottom
+630 atoms in group bottom
+group solid_bottom intersect solid bottom
+216 atoms in group solid_bottom
+group solid_up subtract solid solid_bottom
+216 atoms in group solid_up
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+variable faSolid equal 0.05*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix nvtliq liquid nvt temp 0.8 $T 0.5
+fix nvtliq liquid nvt temp 0.8 0.8 0.5
+fix_modify nvtliq temp Tliq
+WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
+
+thermo 1000
+thermo_modify flush yes temp Tliq
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+
+compute mopz0 all stress/mop z center kin conf
+fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
+
+compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 0
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 13
+ 3 neighbor lists, perpetual/occasional/extra = 1 2 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute stress/mop, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (3) compute stress/mop/profile, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.596 | 3.596 | 3.596 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 1224 atoms
+
+167.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 1224 ave 1224 max 1224 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2975 ave 2975 max 2975 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40241 ave 40241 max 40241 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40241
+Ave neighs/atom = 32.8766
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4 b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4
new file mode 100644
index 0000000000..dd1dc0af0f
--- /dev/null
+++ b/examples/USER/misc/mop/log.5Sep18.compute_stress_mop.g++.4
@@ -0,0 +1,111 @@
+LAMMPS (5 Sep 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+ using 1 OpenMP thread(s) per MPI task
+variable T equal 0.8
+variable p_solid equal 0.05
+
+read_data data.mop
+ orthogonal box = (0 0 -2) to (9.52441 9.52441 16)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 1224 atoms
+ reading velocities ...
+ 1224 velocities
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+group liquid type 1
+792 atoms in group liquid
+group solid type 2
+432 atoms in group solid
+region bottom block INF INF INF INF INF 7.0
+group bottom region bottom
+630 atoms in group bottom
+group solid_bottom intersect solid bottom
+216 atoms in group solid_bottom
+group solid_up subtract solid solid_bottom
+216 atoms in group solid_up
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+variable faSolid equal 0.05*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix nvtliq liquid nvt temp 0.8 $T 0.5
+fix nvtliq liquid nvt temp 0.8 0.8 0.5
+fix_modify nvtliq temp Tliq
+WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
+
+thermo 1000
+thermo_modify flush yes temp Tliq
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+
+compute mopz0 all stress/mop z center kin conf
+fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
+
+compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 0
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 13
+ 3 neighbor lists, perpetual/occasional/extra = 1 2 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute stress/mop, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (3) compute stress/mop/profile, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.509 | 3.51 | 3.511 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.82011245 -3.0642111 0 -2.2692246 0.16906107 1632.8577
+Loop time of 4.06504e-05 on 4 procs for 0 steps with 1224 atoms
+
+65.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 4.065e-05 | | |100.00
+
+Nlocal: 306 ave 320 max 295 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost: 1450.25 ave 1485 max 1422 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs: 10060.2 ave 10866 max 9507 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 40241
+Ave neighs/atom = 32.8766
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/USER/misc/mop/moppz.time.reference b/examples/USER/misc/mop/moppz.time.reference
index f8d4b532ea..1550df422d 100644
--- a/examples/USER/misc/mop/moppz.time.reference
+++ b/examples/USER/misc/mop/moppz.time.reference
@@ -1,226 +1,185 @@
# Time-averaged data for fix moppzt
# TimeStep Number-of-rows
# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
-40000 222
-1 -3.1 0 0 0 0 0 0
-2 -3 0 0 0 0 0 0
-3 -2.9 0 0 0 0 0 0
-4 -2.8 0 0 0 0 0 0
-5 -2.7 0 0 0 0 0 0
-6 -2.6 0 0 0 0 0 0
-7 -2.5 0 0 0 0 0 0
-8 -2.4 0 0 0 0 0 0
-9 -2.3 0 0 0 0 0 0
-10 -2.2 0 0 0 0 0 0
-11 -2.1 0 0 0 0 0 0
-12 -2 0 0 0 0 0 0
-13 -1.9 0 0 0 0 0 0
-14 -1.8 0 0 0 0 0 0
-15 -1.7 0 0 0 0 0 0
-16 -1.6 0 0 0 0 0 0
-17 -1.5 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-18 -1.4 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-19 -1.3 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-20 -1.2 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-21 -1.1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-22 -1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-23 -0.9 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-24 -0.8 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
-25 -0.7 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-26 -0.6 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-27 -0.5 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-28 -0.4 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-29 -0.3 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-30 -0.2 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-31 -0.1 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-32 0 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
-33 0.1 0 0 0 -0.00643877 -0.00486842 0.0289193
-34 0.2 0 0 0 -0.00643877 -0.00486842 0.0289193
-35 0.3 0 0 0 -0.00643877 -0.00486842 0.0289193
-36 0.4 0 0 0 -0.00643877 -0.00486842 0.0289193
-37 0.5 0 0 0 -0.00643877 -0.00486842 0.0289193
-38 0.6 -0.00279194 0.0093508 0.013353 -0.00639358 -0.00380391 0.021025
-39 0.7 -0.00373537 0.0122501 0.0840939 -0.00503616 -0.0112127 -0.132562
-40 0.8 0.061158 -0.0280862 0.636594 0.00453591 -0.00214426 -0.557591
-41 0.9 -0.000266217 -0.0385723 0.969803 -0.0100643 0.00387732 -0.972644
-42 1 -0.0667633 -0.0208723 0.846848 0.0121337 -0.000646173 -0.936078
-43 1.1 -0.0479918 0.0444386 0.783228 0.0206387 -0.00229641 -0.640358
-44 1.2 0.0907347 -0.00458127 0.508479 0.0271462 -0.0136805 -0.427689
-45 1.3 0.0346947 -0.015182 0.397443 0.0162624 -0.0165167 -0.323227
-46 1.4 0.0576422 -0.00277706 0.359744 0.0291978 -0.0156949 -0.265795
-47 1.5 0.0596081 -0.00318334 0.238852 0.0157713 -0.0150214 -0.273303
-48 1.6 0.016955 0.0183139 0.459661 0.00421857 -0.0129777 -0.340127
-49 1.7 0.0697698 -0.0115622 0.431809 -0.0258679 0.00300245 -0.510533
-50 1.8 0.100399 -0.0797432 0.71209 -0.0501721 0.00810306 -0.680932
-51 1.9 0.0500614 -0.0191708 0.789407 -0.0486138 0.0173172 -0.750564
-52 2 -0.00914799 -0.0341791 0.626456 -0.0471521 0.000678372 -0.701829
-53 2.1 0.0369963 0.0256396 0.706456 -0.0509059 0.0173155 -0.620292
-54 2.2 -0.0579061 -0.0608427 0.484532 -0.0294166 0.000458726 -0.521648
-55 2.3 0.00709018 -0.0497913 0.439925 -0.0279961 -0.0102977 -0.43579
-56 2.4 -0.00695344 -0.000619047 0.441961 -0.0248115 -0.0244491 -0.417814
-57 2.5 -0.0375477 0.0725146 0.521221 -0.0140031 -0.0302539 -0.426543
-58 2.6 -0.00333415 0.0411399 0.550053 -0.0244236 -0.0246652 -0.444765
-59 2.7 0.0325652 -0.0422058 0.421026 -0.00606598 -0.038332 -0.507456
-60 2.8 -0.0246015 -0.0468897 0.635467 -0.035645 -0.0428363 -0.541653
-61 2.9 -0.00247499 0.00564888 0.643559 -0.0442198 -0.0211607 -0.539113
-62 3 -0.0320027 -0.0392749 0.603448 -0.0273872 -0.0458147 -0.544274
-63 3.1 -0.00250831 0.0294524 0.630966 -0.0228213 -0.00709569 -0.534171
-64 3.2 -0.0115271 0.0256808 0.597281 -0.00722677 0.00276478 -0.493192
-65 3.3 -0.00826942 -0.0763258 0.569383 -0.0294055 0.00152838 -0.470596
-66 3.4 -4.4607e-05 0.00409392 0.454468 0.00536302 0.00576224 -0.443972
-67 3.5 -0.00145279 -0.0180142 0.532694 0.0162497 0.0129368 -0.488614
-68 3.6 -0.0435087 -0.0436055 0.544955 0.0257295 0.0204122 -0.51687
-69 3.7 -0.0154394 0.0136176 0.609813 0.0132893 -0.00555839 -0.551156
-70 3.8 -0.011446 -0.00706375 0.661117 0.0380525 0.0191365 -0.531052
-71 3.9 -0.0804251 -0.0761665 0.563738 0.0489132 0.0190947 -0.509251
-72 4 0.0127481 0.0455454 0.566261 0.038016 0.0126592 -0.515555
-73 4.1 -0.00153026 -0.025983 0.584368 0.0243742 0.00388593 -0.487748
-74 4.2 0.0488435 0.00522856 0.535885 0.0161854 -0.000859699 -0.487082
-75 4.3 -0.118588 0.134127 0.503423 -0.00404382 -0.00428885 -0.494589
-76 4.4 0.0134608 -0.0373908 0.598776 -0.0285097 -0.00468738 -0.48047
-77 4.5 0.0765487 0.055302 0.608029 -0.0450575 -0.0157753 -0.509701
-78 4.6 -0.05585 -0.0462818 0.618931 -0.0170038 -0.0358189 -0.55692
-79 4.7 0.0164839 -0.0352014 0.611466 -0.0237058 -0.0240414 -0.617077
-80 4.8 0.0436038 -0.00458656 0.612365 0.00997088 -0.0562156 -0.613109
-81 4.9 0.0352871 -0.0611231 0.776314 0.0338943 -0.0604021 -0.613378
-82 5 -0.0568251 -0.0247083 0.510044 0.00279028 -0.028082 -0.595866
-83 5.1 -1.10188e-05 -0.0120973 0.53437 0.00398708 -0.02584 -0.573631
-84 5.2 0.00992898 0.0313027 0.59329 0.00561749 0.00711019 -0.522198
-85 5.3 0.00120683 -0.0356538 0.548184 -0.0200955 0.0381984 -0.52012
-86 5.4 0.0762501 -0.00822531 0.541107 -0.0241871 0.0330327 -0.540077
-87 5.5 0.0461718 0.0519605 0.629188 -0.0222764 0.0226954 -0.551385
-88 5.6 -0.0590515 0.0287662 0.549344 -0.0420534 0.031427 -0.540878
-89 5.7 -0.021125 -0.0231434 0.508528 -0.0342499 0.0495904 -0.52078
-90 5.8 0.00366259 0.0218644 0.572742 -0.0417272 0.0150681 -0.502333
-91 5.9 -0.0198693 -0.0259311 0.564659 -0.0309091 0.0326989 -0.512076
-92 6 0.00390271 -0.00109073 0.543964 -0.00911548 -0.00232516 -0.51614
-93 6.1 0.0628801 -0.0660743 0.587361 0.00381158 0.0024442 -0.515185
-94 6.2 0.00152013 0.0147332 0.572594 0.0229772 0.0059129 -0.507687
-95 6.3 0.026454 0.0873166 0.571276 0.0178474 0.00279111 -0.513827
-96 6.4 0.0951526 -0.0589118 0.598299 0.00448651 0.0259024 -0.53599
-97 6.5 0.0619766 0.0863723 0.669836 -0.00873277 -0.00553461 -0.523788
-98 6.6 -0.0634325 0.0307315 0.69454 -0.0196477 0.0147324 -0.502773
-99 6.7 0.012962 0.00747902 0.51076 -0.0151695 0.0156039 -0.52839
-100 6.8 -0.039811 -0.00360989 0.6489 0.0120414 0.00259849 -0.491579
-101 6.9 -0.0327932 0.0484302 0.616791 -0.0091501 0.0040499 -0.499037
-102 7 0.0490981 0.105001 0.502159 0.0042417 0.00326159 -0.506754
-103 7.1 -0.0581682 0.0395551 0.590876 -0.00115276 0.025084 -0.510536
-104 7.2 -0.0278943 -0.0337449 0.607452 -0.0238974 0.0310696 -0.495835
-105 7.3 -0.0493484 -0.0370496 0.660977 0.0111283 0.0129981 -0.491408
-106 7.4 -0.0206342 -0.0567824 0.5974 0.0172099 -0.00710845 -0.51165
-107 7.5 -0.00940992 0.0303369 0.49934 0.0124837 -0.03568 -0.524051
-108 7.6 -0.0366305 0.0394555 0.459697 -0.00731655 -0.0233235 -0.52555
-109 7.7 -0.0110182 0.0639483 0.563437 -0.00857366 -0.00211197 -0.542335
-110 7.8 0.010323 0.0810661 0.550813 0.00585594 0.0131706 -0.540418
-111 7.9 -0.048191 0.0123444 0.551013 -0.0166757 0.00475367 -0.538792
-112 8 -0.0214946 0.0509729 0.576751 0.0195793 0.0328914 -0.532263
-113 8.1 0.0456292 0.0094789 0.558949 0.00867662 0.0158926 -0.524578
-114 8.2 -0.0512688 -0.091908 0.641645 0.00301901 0.00974779 -0.534635
-115 8.3 -0.00783193 -0.0632416 0.552394 0.00796143 0.0380808 -0.524053
-116 8.4 0.01777 -0.0376654 0.511021 0.0161297 0.0278027 -0.542342
-117 8.5 -0.0327248 -0.0899092 0.578655 0.0137482 0.0472277 -0.524035
-118 8.6 -0.0636407 -0.0252334 0.590898 -0.00601759 0.049413 -0.533022
-119 8.7 -0.0572488 0.0633104 0.744174 0.00670858 0.0337276 -0.548476
-120 8.8 -0.100349 0.0190862 0.738246 0.0194621 0.0386781 -0.547124
-121 8.9 0.0284238 -0.0710504 0.616557 -0.00223469 0.0256231 -0.545488
-122 9 0.0455527 0.0379271 0.549399 0.0219986 7.02084e-05 -0.554089
-123 9.1 -0.00572797 -0.0537564 0.619963 0.0151132 0.00535174 -0.541016
-124 9.2 0.0209666 0.0411495 0.526906 0.00505244 -0.0117546 -0.543559
-125 9.3 0.0350478 0.0441003 0.520438 -0.0102555 -0.0105673 -0.536683
-126 9.4 0.0546092 -0.0171837 0.598682 0.00942578 -0.0283571 -0.520765
-127 9.5 0.0180568 0.00850647 0.720246 0.0282267 -0.0412171 -0.533637
-128 9.6 0.0106648 0.0437645 0.575689 0.0151481 -0.0346536 -0.558032
-129 9.7 -0.155141 -0.00267266 0.637799 0.00208151 -0.0132553 -0.567237
-130 9.8 -0.00666603 -0.103109 0.55371 -0.00920682 0.0140328 -0.515539
-131 9.9 0.0146007 0.0526576 0.484032 -0.0113123 -0.0112639 -0.503197
-132 10 0.0146807 0.0352591 0.573481 0.015403 -0.0258601 -0.471611
-133 10.1 0.00213124 -0.036368 0.623151 0.00161826 -0.0216583 -0.471559
-134 10.2 -1.19073e-05 -0.0619808 0.588624 -0.0259091 0.00687593 -0.462229
-135 10.3 0.0570578 0.0539259 0.656283 -0.0441705 0.000600941 -0.490565
-136 10.4 -0.00888513 0.0460147 0.630823 -0.0474928 0.00205316 -0.502978
-137 10.5 0.0573266 0.0238284 0.547514 -0.0310441 0.00283003 -0.511855
-138 10.6 0.121504 0.0275327 0.615782 -0.030126 -0.0249915 -0.502326
-139 10.7 -0.0156129 -0.0437632 0.630716 0.00504067 -0.0180025 -0.545656
-140 10.8 -0.0218563 -0.0432434 0.605473 0.0104081 -0.041452 -0.579481
-141 10.9 -0.020486 0.0829505 0.610883 0.0122548 -0.0306657 -0.542298
-142 11 0.0195236 0.0729355 0.664827 0.0428504 -0.0338841 -0.517077
-143 11.1 0.0139034 0.0474138 0.664459 0.0249658 -0.0397278 -0.50611
-144 11.2 0.0179999 0.0121222 0.559603 0.0412521 -0.0516893 -0.454643
-145 11.3 0.0268913 -0.0259516 0.494548 0.0514919 -0.0324735 -0.432382
-146 11.4 0.0700355 0.00851857 0.474027 0.0146607 -0.0194147 -0.460328
-147 11.5 0.0274298 -0.0148551 0.667014 0.0264921 -0.0415723 -0.515389
-148 11.6 0.0463183 0.0187287 0.515272 -0.00909174 -0.0310966 -0.558989
-149 11.7 -0.0235634 -0.0412073 0.7427 -0.0125128 -0.0333824 -0.61481
-150 11.8 0.0321678 -0.0192894 0.644069 -0.0285241 -0.0157538 -0.581231
-151 11.9 -0.00435038 -0.0267837 0.544583 -0.0261629 -0.00830545 -0.547874
-152 12 -0.0336443 0.0295318 0.549275 -0.0400734 -0.00236707 -0.486501
-153 12.1 0.00727018 0.00541209 0.492761 -0.0257499 -0.00129429 -0.419029
-154 12.2 0.0283158 -0.0109625 0.530612 -0.00905248 0.000440108 -0.356769
-155 12.3 -0.0733773 0.0287381 0.36636 0.000887014 -0.0072063 -0.350062
-156 12.4 -0.0117385 -0.00497835 0.472524 0.010125 -0.00605897 -0.402028
-157 12.5 0.0748365 -0.0280141 0.641205 -0.00788459 -0.00190551 -0.514353
-158 12.6 -0.031287 -0.0304264 0.781403 -0.0189155 -0.02107 -0.651886
-159 12.7 -0.0453856 0.100627 0.761746 -0.0140253 -0.0328365 -0.713566
-160 12.8 -0.024117 -0.0238699 0.732155 -0.0397416 -0.0143651 -0.632622
-161 12.9 0.0464686 -0.00881426 0.518078 -0.01575 0.0039229 -0.477048
-162 13 0.0662285 -0.053418 0.494651 -0.0215236 -0.00156911 -0.31744
-163 13.1 -0.00957157 -0.0114031 0.198665 -0.0144126 -0.00116237 -0.165427
-164 13.2 0.0148721 -0.0146141 0.144808 -0.013809 0.00154277 -0.0432649
-165 13.3 0.0130082 -0.0195798 0.0662957 -0.0178279 0.00125713 0.0215737
-166 13.4 0.000829942 -0.00381453 0.00218714 -0.0108116 0.0018927 0.0425618
-167 13.5 -0.00384864 -0.005638 0.00637594 -0.00704578 0.00378489 0.0161925
-168 13.6 0 0 0 -0.00602844 0.00291108 -0.0553474
-169 13.7 0 0 0 -0.00530979 -0.00289004 -0.14481
-170 13.8 0 0 0 -0.00906266 -0.00176311 -0.200465
-171 13.9 0 0 0 0.00289955 0.000223381 -0.252608
-172 14 0 0 0 0.00277034 -0.00194448 -0.279276
-173 14.1 0 0 0 0.000240431 -0.000785394 -0.292009
-174 14.2 0 0 0 4.27688e-05 8.277e-05 -0.289271
-175 14.3 0 0 0 -3.58165e-05 5.05721e-05 -0.265846
-176 14.4 0 0 0 -2.28735e-05 3.83404e-05 -0.211496
-177 14.5 0 0 0 -1.50266e-05 1.53466e-05 -0.143001
-178 14.6 0 0 0 -1.89125e-05 2.17035e-05 -0.0975257
-179 14.7 0 0 0 -3.9367e-06 1.12808e-05 -0.0528117
-180 14.8 0 0 0 -8.97431e-06 -2.01724e-06 -0.0235133
-181 14.9 0 0 0 -8.31871e-06 -7.90657e-07 -0.00959154
-182 15 0 0 0 -4.39578e-06 1.15242e-06 -0.00663168
-183 15.1 0 0 0 -4.81121e-06 1.14868e-06 -0.00374977
-184 15.2 0 0 0 -4.6114e-06 -1.95408e-06 -0.0028924
-185 15.3 0 0 0 -4.24836e-06 -5.84343e-06 -0.00186821
-186 15.4 0 0 0 1.63908e-07 -5.33026e-06 -0.00123763
-187 15.5 0 0 0 -4.38526e-06 -4.50778e-06 -0.000652976
-188 15.6 0 0 0 -4.21332e-07 -2.92016e-07 -0.000215754
-189 15.7 0 0 0 3.72451e-08 -1.02432e-08 -5.34533e-05
-190 15.8 0 0 0 5.31804e-08 -3.83997e-07 -3.16961e-05
-191 15.9 0 0 0 0 0 0
-192 16 0 0 0 0 0 0
-193 16.1 0 0 0 0 0 0
-194 16.2 0 0 0 0 0 0
-195 16.3 0 0 0 0 0 0
-196 16.4 0 0 0 0 0 0
-197 16.5 0 0 0 0 0 0
-198 16.6 0 0 0 0 0 0
-199 16.7 0 0 0 0 0 0
-200 16.8 0 0 0 0 0 0
-201 16.9 0 0 0 0 0 0
-202 17 0 0 0 0 0 0
-203 17.1 0 0 0 0 0 0
-204 17.2 0 0 0 0 0 0
-205 17.3 0 0 0 0 0 0
-206 17.4 0 0 0 0 0 0
-207 17.5 0 0 0 0 0 0
-208 17.6 0 0 0 0 0 0
-209 17.7 0 0 0 0 0 0
-210 17.8 0 0 0 0 0 0
-211 17.9 0 0 0 0 0 0
-212 18 0 0 0 0 0 0
-213 18.1 0 0 0 0 0 0
-214 18.2 0 0 0 0 0 0
-215 18.3 0 0 0 0 0 0
-216 18.4 0 0 0 0 0 0
-217 18.5 0 0 0 0 0 0
-218 18.6 0 0 0 0 0 0
-219 18.7 0 0 0 0 0 0
-220 18.8 0 0 0 0 0 0
-221 18.9 0 0 0 0 0 0
-222 19 0 0 0 0 0 0
+0 181
+1 -2 0 0 0 0 0 0
+2 -1.9 0 0 0 0 0 0
+3 -1.8 0 0 0 0 0 0
+4 -1.7 0 0 0 0 0 0
+5 -1.6 0 0 0 0 0 0
+6 -1.5 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+7 -1.4 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+8 -1.3 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+9 -1.2 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+10 -1.1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+11 -1 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+12 -0.9 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+13 -0.8 0 0 0 -9.81273e-05 0.000228605 -0.00421138
+14 -0.7 0 0 0 -0.000370675 -0.00240125 -0.26848
+15 -0.6 0 0 0 -0.000370675 -0.00240125 -0.26848
+16 -0.5 0 0 0 -0.000370675 -0.00240125 -0.26848
+17 -0.4 0 0 0 -0.000370675 -0.00240125 -0.26848
+18 -0.3 0 0 0 -0.000370675 -0.00240125 -0.26848
+19 -0.2 0 0 0 -0.000370675 -0.00240125 -0.26848
+20 -0.1 0 0 0 -0.000370675 -0.00240125 -0.26848
+21 0 0 0 0 -0.000370675 -0.00240125 -0.26848
+22 0.1 0 0 0 0.190761 -0.491728 0.287704
+23 0.2 0 0 0 0.190761 -0.491728 0.287704
+24 0.3 0 0 0 0.190761 -0.491728 0.287704
+25 0.4 0 0 0 0.190761 -0.491728 0.287704
+26 0.5 0 0 0 0.190761 -0.491728 0.287704
+27 0.6 0 0 0 0.190761 -0.491728 0.287704
+28 0.7 0 0 0 0.190761 -0.491728 0.287704
+29 0.8 0 0 0 -0.181602 -0.198457 -0.0964774
+30 0.9 0 0 0 -0.15138 0.183353 0.206848
+31 1 0 0 0 0.174362 1.27701 0.600545
+32 1.1 0 0 0 0.160987 0.563442 0.494994
+33 1.2 0 0 0 0.218876 0.59796 0.398527
+34 1.3 0 0 0 0.187614 0.558909 0.372353
+35 1.4 0 0 0 0.118586 0.410013 0.331945
+36 1.5 0 0 0 -0.0514208 0.40381 0.128097
+37 1.6 3.08628 0.241189 5.90817 -0.198262 0.324128 -0.0449302
+38 1.7 0 0 0 -0.104542 0.256677 -0.332854
+39 1.8 0.222123 2.43524 1.10089 -0.324638 -0.168682 -1.06238
+40 1.9 0 0 0 -0.175732 -0.186846 -0.163062
+41 2 0 0 0 -0.137995 0.0920401 -0.260106
+42 2.1 -0.179621 -2.59775 1.80077 -0.480624 -0.0439511 -0.0824913
+43 2.2 0 0 0 -0.499868 -0.0106185 -0.108924
+44 2.3 0 0 0 -0.703301 0.124555 -0.0880158
+45 2.4 0 0 0 -0.581211 -0.244281 -0.250071
+46 2.5 1.05274 -2.86043 3.36339 -0.575104 -0.148715 -0.249092
+47 2.6 0 0 0 0.66061 -0.157649 -0.357141
+48 2.7 0 0 0 0.299971 -0.302298 -0.572714
+49 2.8 0 0 0 0.33107 -0.201699 -0.470466
+50 2.9 0 0 0 0.822686 1.08427 -0.390511
+51 3 0 0 0 0.716428 0.750998 -0.698174
+52 3.1 0.805189 0.571878 4.31938 0.121891 0.922727 -0.932582
+53 3.2 0 0 0 0.0442642 1.02537 -1.03066
+54 3.3 2.54289 -1.93701 4.88355 0.0731321 1.09091 -0.83075
+55 3.4 0 0 0 0.426589 0.821174 -0.765855
+56 3.5 0 0 0 0.445135 0.299996 -1.48972
+57 3.6 0 0 0 0.362916 -1.28673 -0.853897
+58 3.7 0.952867 -1.07044 1.04141 0.12517 -1.00353 -0.785272
+59 3.8 0.617661 0.991499 1.80973 -0.182369 -1.04057 -1.00435
+60 3.9 0.60295 -2.41888 3.98011 0.0347345 -1.01302 -0.88314
+61 4 -2.97421 -2.01531 2.98586 0.43463 -0.465643 -0.801128
+62 4.1 -3.23318 -3.31281 0.956525 0.732752 0.140718 -1.10583
+63 4.2 0 0 0 0.969872 0.298566 -0.823464
+64 4.3 0 0 0 0.7707 0.557002 -0.836549
+65 4.4 0 0 0 0.395828 0.66755 -1.53454
+66 4.5 0 0 0 0.104451 0.46777 -1.32358
+67 4.6 0 0 0 0.402084 0.464983 -1.22051
+68 4.7 0 0 0 0.352808 0.0794986 -1.31292
+69 4.8 0 0 0 0.0215512 0.284343 -0.975326
+70 4.9 0 0 0 -0.133637 0.250925 -1.33918
+71 5 0 0 0 -0.066208 0.104514 -1.27412
+72 5.1 0 0 0 -0.184391 0.479805 -1.15139
+73 5.2 0 0 0 -0.200251 0.527142 -1.34307
+74 5.3 0 0 0 0.043532 -0.0788824 -0.998406
+75 5.4 0 0 0 -0.531846 0.126289 -1.05818
+76 5.5 0 0 0 -0.259593 0.0818463 -1.58939
+77 5.6 0 0 0 -0.373828 -0.343977 -1.50908
+78 5.7 -0.294161 -1.07567 3.46536 -0.0644873 -0.424333 -1.28548
+79 5.8 0 0 0 -0.293233 -0.201133 -1.19085
+80 5.9 0.961568 -1.44949 2.42101 -0.632816 -0.0669315 -0.85119
+81 6 0 0 0 -0.0559892 -0.0194478 -1.04541
+82 6.1 0 0 0 -0.339753 0.286693 -1.24366
+83 6.2 0 0 0 -0.376208 0.444053 -1.7662
+84 6.3 0 0 0 -0.718923 0.555398 -1.93862
+85 6.4 0 0 0 -1.10631 0.263525 -1.79723
+86 6.5 0 0 0 -0.217948 -0.0489491 -2.07833
+87 6.6 0 0 0 -0.376248 -0.0588682 -2.45322
+88 6.7 -2.12742 4.22609 2.36568 -0.236703 -0.279582 -1.56434
+89 6.8 0.869072 -0.141389 3.92123 0.0540986 -0.00271606 -0.930143
+90 6.9 0 0 0 1.08829 -1.11737 -0.808187
+91 7 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
+92 7.1 0 0 0 1.03324 -0.470631 -0.486767
+93 7.2 0 0 0 0.950164 -0.112451 -0.479409
+94 7.3 -2.66121 -0.326607 7.83093 0.359 -0.482493 0.154384
+95 7.4 0 0 0 0.359089 -1.12337 0.409711
+96 7.5 -1.88971 1.34806 3.56893 0.394677 -1.0109 0.548348
+97 7.6 -1.34494 -0.896214 2.06959 0.231398 -0.728529 0.313513
+98 7.7 0 0 0 0.415681 -0.45268 0.507181
+99 7.8 0 0 0 0.259423 -0.11638 0.464208
+100 7.9 -1.97572 -1.20836 3.95731 0.252257 -0.0845701 -0.249345
+101 8 0 0 0 0.0688154 0.290386 -0.462467
+102 8.1 0.25925 -0.458269 3.33086 0.360399 -0.0409494 -0.656911
+103 8.2 0 0 0 -0.0587033 0.347698 -0.340604
+104 8.3 0 0 0 -0.377192 0.153096 -0.914654
+105 8.4 0 0 0 -0.431553 0.274996 -0.946252
+106 8.5 0 0 0 -0.898366 0.146653 -1.36383
+107 8.6 0 0 0 -0.889593 0.385951 0.125116
+108 8.7 0 0 0 -0.0139171 -0.162302 -0.0287854
+109 8.8 0 0 0 -0.266284 -0.148945 0.393533
+110 8.9 0 0 0 -0.00920376 -0.0770818 0.334642
+111 9 0 0 0 -0.0949156 0.0113352 -0.0761263
+112 9.1 0 0 0 0.0688045 0.104558 -0.101891
+113 9.2 3.79773 0.0255401 3.75032 0.419832 0.295402 0.652533
+114 9.3 0 0 0 0.594267 0.70396 0.836434
+115 9.4 0 0 0 0.174722 1.00483 1.42787
+116 9.5 0 0 0 0.0626835 0.518952 0.269158
+117 9.6 0 0 0 -0.302859 -0.265212 -0.0145578
+118 9.7 0 0 0 -0.114026 -0.201336 -0.539522
+119 9.8 0 0 0 0.104008 -0.30236 -0.0789062
+120 9.9 0 0 0 -0.0482778 -0.553118 0.45214
+121 10 0 0 0 -0.0554938 -0.402692 0.141112
+122 10.1 0 0 0 0.174338 0.556958 -0.0922154
+123 10.2 0 0 0 -1.06045 0.541565 -0.0409312
+124 10.3 0 0 0 -1.20782 0.464574 -0.413871
+125 10.4 0 0 0 -0.891701 0.327653 -0.286438
+126 10.5 0 0 0 0.231227 -0.064277 -0.89684
+127 10.6 -1.27989 -4.87365 9.40433 0.211278 0.230826 -1.23536
+128 10.7 -2.1001 -0.417817 1.17745 0.425856 0.078728 -1.44229
+129 10.8 0 0 0 0.30965 0.450884 -1.74985
+130 10.9 0 0 0 0.36735 0.990032 -1.19971
+131 11 0.253834 -1.84303 3.91828 1.01826 0.0660896 -0.481086
+132 11.1 0 0 0 0.744006 0.0906555 -0.897417
+133 11.2 0 0 0 0.339073 0.361038 -0.545084
+134 11.3 -1.9974 -0.431998 3.46296 0.611295 0.17282 0.0341483
+135 11.4 0 0 0 -0.491432 -0.958871 1.28001
+136 11.5 0 0 0 0.0431048 -1.50924 1.24037
+137 11.6 0 0 0 -0.684419 -0.0163951 1.06179
+138 11.7 0 0 0 -0.425278 -0.127741 0.757298
+139 11.8 -2.09164 0.00894897 2.22812 -0.0955178 -0.310572 0.661289
+140 11.9 0 0 0 0.156959 -0.233409 0.802568
+141 12 0 0 0 -0.05541 -0.346448 0.541571
+142 12.1 0 0 0 0.706767 0.182767 0.25767
+143 12.2 0 0 0 0.4791 0.464612 -0.212887
+144 12.3 0 0 0 0.81454 0.440323 -0.461359
+145 12.4 0 0 0 -0.110025 0.200698 -0.996706
+146 12.5 0 0 0 -0.149791 0.165599 -1.02233
+147 12.6 0 0 0 -0.170933 0.0644682 -0.866174
+148 12.7 0 0 0 -0.122869 -0.0196287 -0.801348
+149 12.8 0 0 0 -0.0693832 -0.0673091 -0.382802
+150 12.9 0 0 0 -0.0693832 -0.0673091 -0.382802
+151 13 0 0 0 -0.0693832 -0.0673091 -0.382802
+152 13.1 0 0 0 -0.0693832 -0.0673091 -0.382802
+153 13.2 0 0 0 -0.0693832 -0.0673091 -0.382802
+154 13.3 0 0 0 -0.0693832 -0.0673091 -0.382802
+155 13.4 0 0 0 -0.0693832 -0.0673091 -0.382802
+156 13.5 0 0 0 -0.000502433 0.000137492 -0.227425
+157 13.6 0 0 0 -0.000502433 0.000137492 -0.227425
+158 13.7 0 0 0 -0.000502433 0.000137492 -0.227425
+159 13.8 0 0 0 -0.000502433 0.000137492 -0.227425
+160 13.9 0 0 0 -0.000502433 0.000137492 -0.227425
+161 14 0 0 0 -0.000502433 0.000137492 -0.227425
+162 14.1 0 0 0 -0.000502433 0.000137492 -0.227425
+163 14.2 0 0 0 -0.000502433 0.000137492 -0.227425
+164 14.3 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+165 14.4 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+166 14.5 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+167 14.6 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+168 14.7 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+169 14.8 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+170 14.9 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+171 15 0 0 0 5.79042e-05 4.68687e-05 -0.00286094
+172 15.1 0 0 0 0 0 0
+173 15.2 0 0 0 0 0 0
+174 15.3 0 0 0 0 0 0
+175 15.4 0 0 0 0 0 0
+176 15.5 0 0 0 0 0 0
+177 15.6 0 0 0 0 0 0
+178 15.7 0 0 0 0 0 0
+179 15.8 0 0 0 0 0 0
+180 15.9 0 0 0 0 0 0
+181 16 0 0 0 0 0 0
diff --git a/examples/USER/misc/mop/mopz0.time.reference b/examples/USER/misc/mop/mopz0.time.reference
index 6341d22906..d6dbb2ff09 100644
--- a/examples/USER/misc/mop/mopz0.time.reference
+++ b/examples/USER/misc/mop/mopz0.time.reference
@@ -1,6 +1,3 @@
# Time-averaged data for fix mopz0t
# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
-10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264
-20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147
-30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132
-40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305
+0 1.62633 1.08234 0.844097 1.18575 -0.408792 -0.752394
diff --git a/examples/USER/misc/mop/profile.z.reference b/examples/USER/misc/mop/profile.z.reference
deleted file mode 100644
index 1e0d1bf26b..0000000000
--- a/examples/USER/misc/mop/profile.z.reference
+++ /dev/null
@@ -1,227 +0,0 @@
-# Chunk-averaged data for fix profile_z and group temp
-# Timestep Number-of-chunks Total-count
-# Chunk Coord1 Ncount density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6]
-40000 223 3292
- 1 -3.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 2 -3.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 3 -2.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 4 -2.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 5 -2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 6 -2.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 7 -2.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 8 -2.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 9 -2.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 10 -2.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 11 -2.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 12 -2.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 13 -1.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 14 -1.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 15 -1.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 16 -1.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 17 -1.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 18 -1.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 19 -1.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 20 -1.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 21 -1.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 22 -1.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 23 -0.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 24 -0.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 25 -0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 26 -0.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 27 -0.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 28 -0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 29 -0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 30 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 31 -0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 32 -0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 33 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 34 0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 35 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 36 0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 37 0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 38 0.55 0.0155 0.00170866 0.77827 -0.823106 -0.662616 -0.84909 0.0895728 -0.0915996 -0.0170938 -9.39041 -10.0498 -10.5424 -0.265868 -0.0729269 -0.626454
- 39 0.65 0.65625 0.0723425 0.805015 -0.786824 -0.81346 -0.814762 0.0155975 0.0168616 -0.0213122 -2.89739 -2.89092 -5.81642 -0.0313195 0.230066 -0.0388364
- 40 0.75 4.18625 0.461476 0.79884 -0.814511 -0.792997 -0.789012 -0.00942159 0.00597072 -0.00127992 -0.0143748 -0.0512459 -2.64067 0.0488393 0.0797603 0.0243815
- 41 0.85 9.79625 1.0799 0.79714 -0.80439 -0.79918 -0.78785 -0.00331374 0.00487411 -0.00151215 1.12418 1.08693 -0.84425 -0.00560715 -0.00540606 0.0136964
- 42 0.95 11.8853 1.31018 0.796174 -0.794167 -0.80514 -0.789215 0.00723814 -0.00234092 0.00056184 1.42901 1.47052 0.953436 0.0152978 -0.00835816 -0.0143227
- 43 1.05 9.50925 1.04826 0.790145 -0.778307 -0.798065 -0.794064 -0.00458567 0.00288496 0.00383306 1.34248 1.35909 2.2058 -0.00480159 -0.00651465 0.0107925
- 44 1.15 6.62475 0.730287 0.792109 -0.78276 -0.792956 -0.80061 -0.000304313 0.00429876 -0.000168134 1.26277 1.22489 2.4073 -0.00702209 0.0123268 0.0158178
- 45 1.25 4.843 0.533874 0.782372 -0.788056 -0.769346 -0.789713 -0.00686069 0.00712471 0.00418369 1.11904 1.10737 2.14058 -0.0215052 -0.0228293 0.0027643
- 46 1.35 3.83075 0.422287 0.79523 -0.795215 -0.781756 -0.808717 0.00249536 0.00991401 0.00380274 0.82578 0.918645 1.46731 0.0226069 0.0224161 0.0177933
- 47 1.45 3.677 0.405338 0.795643 -0.800148 -0.796298 -0.790481 -0.00645737 0.00817994 0.00550917 0.759125 0.737731 0.94736 0.0047934 -0.0525048 0.0098318
- 48 1.55 4.02825 0.444059 0.7931 -0.809145 -0.767991 -0.802164 0.00796467 -0.00254477 -0.00515821 0.711573 0.700294 0.278708 -0.00223064 0.0425578 -0.0182506
- 49 1.65 5.21025 0.574358 0.786639 -0.782146 -0.790073 -0.787698 -0.00628926 0.0029031 -0.00469372 0.731644 0.711902 -0.4288 0.0255459 0.0230297 -0.0116029
- 50 1.75 7.042 0.776283 0.790913 -0.78969 -0.794201 -0.788849 0.00258833 -0.00622832 -0.00564932 0.890595 0.855746 -0.411099 -0.0301627 0.0064535 0.0103202
- 51 1.85 8.46525 0.933177 0.792581 -0.802268 -0.785881 -0.789593 -0.0101489 -0.00231339 -0.00725399 0.995328 0.96239 0.0331328 -0.0719804 -0.00124182 0.00072388
- 52 1.95 8.65475 0.954067 0.787864 -0.781802 -0.789244 -0.792545 0.00513504 0.00406419 -0.00879172 1.00435 0.961078 0.632404 -0.0517082 -0.0159131 0.00526744
- 53 2.05 7.8595 0.866401 0.786055 -0.770225 -0.794059 -0.79388 -0.00752288 0.00623117 -0.00420196 1.00125 0.93989 1.08666 -0.0435495 0.0161905 0.0286065
- 54 2.15 6.82475 0.752334 0.77991 -0.776702 -0.775219 -0.78781 0.00471997 0.00826834 0.00277604 0.85253 0.86241 1.24674 0.0246189 0.00530171 0.0353102
- 55 2.25 5.89225 0.649539 0.781394 -0.766258 -0.795723 -0.782202 -0.00469749 7.49004e-05 -0.00738222 0.761321 0.690047 1.13698 0.0102827 0.00209006 -0.0164468
- 56 2.35 5.42025 0.597508 0.785789 -0.774668 -0.790234 -0.792466 -0.00930276 0.00394548 -0.0106206 0.655063 0.695732 0.918347 -0.0225504 -0.0119507 0.0511995
- 57 2.45 5.34525 0.58924 0.797039 -0.787684 -0.791749 -0.811683 0.00599798 0.00191556 -0.00434674 0.694615 0.671933 0.640961 -0.00323138 0.0273467 -0.0105561
- 58 2.55 5.87275 0.64739 0.794482 -0.795196 -0.793495 -0.794755 -0.0158646 -0.00938029 -0.00871214 0.665991 0.601126 0.314868 -0.0128127 0.0289784 -0.0535967
- 59 2.65 6.54775 0.721799 0.793027 -0.795599 -0.807693 -0.775789 -0.00379113 -0.00798908 0.00414433 0.687052 0.625958 0.250015 0.0223168 -0.0142519 0.0240892
- 60 2.75 7.17375 0.790807 0.789337 -0.803269 -0.779503 -0.78524 0.00170161 -0.00681561 0.00356121 0.775713 0.774137 0.355147 -0.0206119 0.0273384 0.0344849
- 61 2.85 7.55625 0.832972 0.79018 -0.795909 -0.795401 -0.77923 -0.00518976 -0.00312522 0.00106728 0.775982 0.753619 0.582624 -0.05471 0.00361953 -0.0185739
- 62 2.95 7.527 0.829748 0.7962 -0.797786 -0.802568 -0.788245 -0.00144501 0.00681308 0.00249422 0.768233 0.757786 0.735976 -0.0169325 0.0354933 -0.0135924
- 63 3.05 7.1165 0.784496 0.791519 -0.78266 -0.793301 -0.798598 -0.00508069 -0.00392219 -0.0044803 0.72029 0.727861 0.817503 0.0196124 -0.0195464 -0.000180423
- 64 3.15 6.748 0.743874 0.787019 -0.788624 -0.784329 -0.788105 -0.00409978 0.00754204 -0.00376577 0.82418 0.828474 1.02821 0.023471 0.00271621 0.019013
- 65 3.25 6.3735 0.70259 0.783471 -0.776587 -0.779256 -0.79457 0.00612107 0.0112575 -0.000948099 0.737637 0.71468 0.973695 0.037504 -0.0135665 0.0206408
- 66 3.35 6.1145 0.674039 0.788572 -0.784829 -0.790459 -0.790427 0.00916602 0.00152291 0.00176958 0.738898 0.720059 0.737 -0.0166567 -0.0248098 -0.0100902
- 67 3.45 6.084 0.670677 0.790939 -0.776032 -0.798423 -0.798362 0.00657912 0.00516364 0.00806608 0.707573 0.728111 0.646469 -0.00434771 0.0298935 0.0274583
- 68 3.55 6.2495 0.688921 0.80175 -0.78949 -0.810302 -0.805458 0.0075139 0.00779127 0.00389764 0.75039 0.720311 0.511161 0.0236026 0.00162861 -0.00166792
- 69 3.65 6.6325 0.731141 0.803451 -0.803591 -0.806982 -0.79978 -0.00461138 -0.00459482 0.00473225 0.779721 0.744737 0.552971 -0.0150463 -0.00642588 -0.0295497
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- 165 13.25 0.8055 0.0887952 0.843214 -0.810206 -0.880537 -0.838901 0.039551 -0.0997588 0.0234894 -2.39237 -2.01058 -4.14878 0.223851 0.231795 -0.352153
- 166 13.35 0.272 0.0299842 0.666721 -0.779612 -0.626689 -0.593862 -0.0393791 0.00154035 -0.00625556 -1.37505 -1.38233 -3.36414 0.00300675 -0.0372793 -0.243736
- 167 13.45 0.07925 0.00873622 0.782435 -1.07607 -0.598123 -0.673115 0.117468 0.1185 -0.0878719 -3.7526 -3.60044 -5.09311 0.910831 0.205838 -0.276478
- 168 13.55 0.0095 0.00104724 0.19248 -0.161758 -0.293769 -0.121913 0.0596029 -0.0388238 0.000461593 -0.419057 -0.823036 -1.04983 0.0273182 -0.129878 0.392706
- 169 13.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 170 13.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 171 13.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 172 13.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 173 14.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 174 14.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 175 14.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 176 14.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 177 14.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 178 14.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 179 14.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 180 14.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 181 14.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 182 14.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 183 15.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 184 15.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 185 15.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 186 15.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 187 15.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 188 15.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 189 15.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 190 15.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 191 15.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 192 15.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 193 16.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 194 16.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 195 16.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 196 16.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 197 16.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 198 16.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 199 16.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 200 16.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 201 16.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 202 16.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 203 17.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 204 17.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 205 17.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 206 17.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 207 17.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 208 17.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 209 17.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 210 17.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 211 17.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 212 17.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 213 18.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 214 18.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 215 18.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 216 18.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 217 18.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 218 18.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 219 18.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 220 18.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 221 18.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 222 18.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 223 19.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
--
GitLab
From dd64c063cf804205bfb5ea90ed1be325243814d9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 6 Sep 2018 22:28:20 -0400
Subject: [PATCH 248/332] various fixes for the manual to address breakage from
merging MESSAGE and USER-SCAFACOS packages
---
doc/src/Build_package.txt | 4 ++--
doc/src/Howto_client_server.txt | 2 +-
doc/src/Packages_details.txt | 4 ++--
doc/src/Run_options.txt | 2 +-
doc/src/commands_list.txt | 2 ++
doc/src/fix_client_md.txt | 2 +-
doc/src/fixes.txt | 1 +
doc/src/kspace_modify.txt | 2 +-
doc/src/kspace_style.txt | 4 ++--
doc/src/lammps.book | 1 +
10 files changed, 14 insertions(+), 10 deletions(-)
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 285220e6c6..f1aa4bb671 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -42,7 +42,7 @@ packages:
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MEAM"_Build_extras.html#meam,
-"MESSAGE"_#Build_extras.html#message,
+"MESSAGE"_Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
@@ -59,7 +59,7 @@ packages:
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
-"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
+"USER-SCAFACOS"_Build_extras.html#user-scafacos,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index 714c23f066..061c4efb68 100644
--- a/doc/src/Howto_client_server.txt
+++ b/doc/src/Howto_client_server.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Using LAMMPS in client/server mode
+Using LAMMPS in client/server mode :h3
Client/server coupling of two codes is where one code is the "client"
and sends request messages to a "server" code. The server responds to
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 443d78922c..b0b72f1f13 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -92,7 +92,7 @@ as contained in the file name.
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
-"USER-SCAFACOS"_#USER-SCAFACOS,
+"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@@ -1860,7 +1860,7 @@ examples/reax :ul
:line
-USER-SCAFACOS package :link(USER-SCAFACOS),h4
+USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
[Contents:]
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index 27f436ed55..1fc00bc2e3 100644
--- a/doc/src/Run_options.txt
+++ b/doc/src/Run_options.txt
@@ -176,7 +176,7 @@ Option -plog will override the name of the partition log files file.N.
:line
-[-mpicolor] color :link(mpi)
+[-mpicolor] color :link(mpicolor)
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt
index 8fae57a718..db3ef36ddf 100644
--- a/doc/src/commands_list.txt
+++ b/doc/src/commands_list.txt
@@ -89,6 +89,8 @@ Commands :h1
run
run_style
server
+ server_mc
+ server_md
set
shell
special_bonds
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
index 5b62d5617d..77f6b82c5e 100644
--- a/doc/src/fix_client_md.txt
+++ b/doc/src/fix_client_md.txt
@@ -50,7 +50,7 @@ md"_server_md.html doc page.
Note that when using LAMMPS as an MD client, your LAMMPS input script
should not normally contain force field commands, like a
-"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
+"pair_style"_pair_style.html, "bond_style"_bond_style.html, or
"kspace_style"_kspace_style.html commmand. However it is possible for
a server code to only compute a portion of the full force-field, while
LAMMPS computes the remaining part. Your LAMMPS script can also
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 7a45ed8086..f2f257b134 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -26,6 +26,7 @@ Fixes :h1
fix_bond_swap
fix_bond_react
fix_box_relax
+ fix_client_md
fix_cmap
fix_colvars
fix_controller
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 7e40323664..41973601d7 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -133,7 +133,7 @@ the code will stop with an error message. When this option is set to
For a typical application, using the automatic parameter generation
will provide simulations that are either inaccurate or slow. Using this
option is thus not recommended. For guidelines on how to obtain good
-parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
+parameters, see the "How-To"_Howto_dispersion.html discussion.
:line
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index ddf4e15703..6d8a289470 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -383,8 +383,8 @@ dimensions. The only exception is if the slab option is set with
must be periodic and the z dimension must be non-periodic.
The scafacos KSpace style will only be enabled if LAMMPS is built with
-the USER-SCAFACOS package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+the USER-SCAFACOS package. See the "Build package"_Build_package.html
+doc page for more info.
The use of ScaFaCos in LAMMPS does not yet support molecular charged
systems where the short-range Coulombic interactions between atoms in
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 72a07945e7..828863ae67 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -67,6 +67,7 @@ Howto_multiple.html
Howto_replica.html
Howto_library.html
Howto_couple.html
+Howto_client_server.html
Howto_output.html
Howto_chunk.html
Howto_2d.html
--
GitLab
From 861a7acdf0b9de61dade59ef873e1f338673a9d2 Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@votca.org>
Date: Fri, 7 Sep 2018 06:40:06 -0600
Subject: [PATCH 249/332] cmake: fix globbing in some more places
---
cmake/CMakeLists.txt | 9 ++++++---
cmake/Modules/StyleHeaderUtils.cmake | 6 +++---
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 45e6870ce8..21170a384d 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -604,7 +604,8 @@ endif()
if(PKG_MESSAGE)
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
- ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
if(BUILD_SHARED_LIBS)
add_library(cslib SHARED ${cslib_SOURCES})
@@ -754,8 +755,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
- file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
- ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
+ file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+ ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+ ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake
index d621e4c9c0..a89d098dd0 100644
--- a/cmake/Modules/StyleHeaderUtils.cmake
+++ b/cmake/Modules/StyleHeaderUtils.cmake
@@ -94,14 +94,14 @@ function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
- FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input
+ FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
- FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update
- FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force
+ FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
+ FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor
--
GitLab
From 25907c856e1463cf4986de98e61b3cafd422b3d5 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 7 Sep 2018 09:56:03 -0600
Subject: [PATCH 250/332] small doc page changes, format and content on doc
page tarballs
---
doc/src/Build_basics.txt | 4 ++++
doc/src/Howto_client_server.txt | 2 +-
doc/src/Install_tarball.txt | 6 +++++-
doc/src/Packages_details.txt | 1 +
4 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index 6924e73417..4b3a347bf1 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -292,6 +292,10 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
+NOTE: You can also download a tarball of the documention for the
+current LAMMPS version (HTML and PDF files), from the website
+"download page"_http://lammps.sandia.gov/download.html.
+
:line
Install LAMMPS after a build :h4,link(install)
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index 714c23f066..061c4efb68 100644
--- a/doc/src/Howto_client_server.txt
+++ b/doc/src/Howto_client_server.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Using LAMMPS in client/server mode
+Using LAMMPS in client/server mode :h3
Client/server coupling of two codes is where one code is the "client"
and sends request messages to a "server" code. The server responds to
diff --git a/doc/src/Install_tarball.txt b/doc/src/Install_tarball.txt
index b672c5ff25..7ba5d15ac4 100644
--- a/doc/src/Install_tarball.txt
+++ b/doc/src/Install_tarball.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Download source as a tarball :h3
+Download source and documentation as a tarball :h3
You can download a current LAMMPS tarball from the "download page"_download
of the "LAMMPS website"_lws.
@@ -22,6 +22,10 @@ few times per year, and undergo more testing before release. Patch
releases occur a couple times per month. The new contents in all
releases are listed on the "bug and feature page"_bug of the website.
+Both tarballs include LAMMPS documentation (HTML and PDF files)
+corresponding to that version. The download page also has an option
+to download the current-version LAMMPS documentation by itself.
+
Older versions of LAMMPS can also be downloaded from "this
page"_older.
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 443d78922c..1fb0549c8d 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -46,6 +46,7 @@ as contained in the file name.
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
"MEAM"_#PKG-MEAM,
+"MESSAGE"_#PKG-MESSAGE,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
"MPIIO"_#PKG-MPIIO,
--
GitLab
From 0384ef89670de96f83b0f7821c4e22484d491ed9 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 7 Sep 2018 14:00:39 -0600
Subject: [PATCH 251/332] more tweaks to client/server doc pages
---
doc/src/Howto_client_server.txt | 4 ++--
doc/src/server_mc.txt | 6 +++---
doc/src/server_md.txt | 16 +++++++++-------
3 files changed, 14 insertions(+), 12 deletions(-)
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
index 061c4efb68..aa6b8eab76 100644
--- a/doc/src/Howto_client_server.txt
+++ b/doc/src/Howto_client_server.txt
@@ -61,7 +61,7 @@ client or server.
"message"_message.html
"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
"server md"_server_md.html = LAMMPS is a server for computing MD forces
-"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
+"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
The server doc files give details of the message protocols
for data that is exchanged bewteen the client and server.
@@ -119,7 +119,7 @@ For message exchange in {mpi/one} mode:
Launch both codes in a single mpirun command:
-mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre
The two -np values determine how many procs the client and the server
run on.
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
index 53ccfc8ecd..58ca415be3 100644
--- a/doc/src/server_mc.txt
+++ b/doc/src/server_mc.txt
@@ -63,7 +63,7 @@ See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
example of how an MC driver code can use these messages.
-Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
+Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
[Client sends one of these kinds of message]:
@@ -93,9 +93,9 @@ cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
cs->send(DISPLACE,1) # msgID = 3 with 1 field
cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
-cs->send(ACCEPT,0) # msgID = 4 with no fields
+cs->send(ACCEPT,0) # msgID = 4 with no fields :pre
-cs->send(RUN,0) # msgID = 5 with no fields
+cs->send(RUN,0) # msgID = 5 with no fields :pre
:line
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
index 0db7bbe16b..753542dc75 100644
--- a/doc/src/server_md.txt
+++ b/doc/src/server_md.txt
@@ -51,9 +51,9 @@ can complete the timestep. This command could also be used with a
client code that performs energy minimization, using the server to
compute forces and energy each iteration of its minimizer.
-When using the "fix client/md" command, LAMMPS (as the client code)
-does the timestepping and receives needed energy, forces, and pressure
-values from the server code.
+When using the "fix client/md"_fix_client_md.html command, LAMMPS (as
+the client code) does the timestepping and receives needed energy,
+forces, and pressure values from the server code.
The format and content of the exchanged messages are explained here in
a conceptual sense. Python-style pseudo code for the library calls to
@@ -69,9 +69,11 @@ a quantum code (VASP) can use use these messages.
The following pseudo-code uses these values, defined as enums.
-enum{SETUP=1,STEP};
-enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
-enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre
+Define:
+
+SETUP=1, STEP=2
+DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10
+FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4 :pre
[Client sends 2 kinds of messages]:
@@ -98,7 +100,7 @@ cs->send(STEP,nfields) # msgID with nfields :pre
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
-cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box :pre
[Server replies to either kind of message]:
--
GitLab
From b488f1072e17e6f574cb45a479572783bc147fca Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 7 Sep 2018 14:22:38 -0600
Subject: [PATCH 252/332] recent package links
---
doc/src/Packages_details.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 1fb0549c8d..494f393a16 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -93,7 +93,7 @@ as contained in the file name.
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
-"USER-SCAFACOS"_#USER-SCAFACOS,
+"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
@@ -1861,7 +1861,7 @@ examples/reax :ul
:line
-USER-SCAFACOS package :link(USER-SCAFACOS),h4
+USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
[Contents:]
--
GitLab
From 3b073de3572a41f476243c3aa56ce28a9532fd6e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 9 Sep 2018 01:21:37 -0400
Subject: [PATCH 253/332] make it less likely to have people get confused by
Eigen3_DIR
---
cmake/CMakeLists.txt | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 149f9da817..80eb035fee 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -538,6 +538,13 @@ if(PKG_USER-NETCDF)
endif()
if(PKG_USER-SMD)
+ # hack alert!
+ # something defines the Eigen3_DIR variable, but it has no effect
+ # yet shows up in the TUI/GUI display as "not found".
+ # and due to not being marked as advanced, it can mislead people
+ # as the EIGEN3_INCLUDE_DIR variable which does have an effect
+ # is marked as advanced. Tested on Fedora28 with Eigen3-3.3.5 rpm.
+ mark_as_advanced(Eigen3_DIR)
option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
if(DOWNLOAD_EIGEN3)
include(ExternalProject)
--
GitLab
From 46b87518b8b62fac583e8718b9a9b3b5baf7417f Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 10 Sep 2018 00:35:55 -0400
Subject: [PATCH 254/332] cmake: use NO_MODULE for Eigen3
---
cmake/CMakeLists.txt | 10 ++--------
1 file changed, 2 insertions(+), 8 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 80eb035fee..7bfd7905f2 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -538,13 +538,6 @@ if(PKG_USER-NETCDF)
endif()
if(PKG_USER-SMD)
- # hack alert!
- # something defines the Eigen3_DIR variable, but it has no effect
- # yet shows up in the TUI/GUI display as "not found".
- # and due to not being marked as advanced, it can mislead people
- # as the EIGEN3_INCLUDE_DIR variable which does have an effect
- # is marked as advanced. Tested on Fedora28 with Eigen3-3.3.5 rpm.
- mark_as_advanced(Eigen3_DIR)
option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
if(DOWNLOAD_EIGEN3)
include(ExternalProject)
@@ -557,7 +550,8 @@ if(PKG_USER-SMD)
set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
- find_package(Eigen3)
+ find_package(Eigen3 NO_MODULE)
+ mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
--
GitLab
From 02b653c0cea83448cdeda39d231f423836d35fdf Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Sep 2018 22:22:42 -0400
Subject: [PATCH 255/332] correct end of itemized list to be compatible with
txt2rst conversion
---
doc/src/Howto_chunk.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
index 611b71dac7..82a4450d17 100644
--- a/doc/src/Howto_chunk.txt
+++ b/doc/src/Howto_chunk.txt
@@ -125,7 +125,7 @@ molecule diffusion rates. :l
As input to special functions of "equal-style
variables"_variable.html, like sum() and max() and ave(). E.g. to
find the largest cluster or fastest diffusing molecule or average
-radius-of-gyration of a set of molecules (chunks). :l :ule
+radius-of-gyration of a set of molecules (chunks). :l,ule
Other chunk commands: :h4
--
GitLab
From 3d2c7317092a9952b88ac4e6c6e16193c333093a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Sep 2018 22:32:56 -0400
Subject: [PATCH 256/332] avoid class initialization order warnings
---
src/compute_chunk_spread_atom.cpp | 2 +-
src/compute_chunk_spread_atom.h | 3 +--
src/compute_reduce_chunk.cpp | 4 ++--
3 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp
index 93a4d30a2e..c5fd27b0c1 100644
--- a/src/compute_chunk_spread_atom.cpp
+++ b/src/compute_chunk_spread_atom.cpp
@@ -37,7 +37,7 @@ enum{COMPUTE,FIX};
ComputeChunkSpreadAtom::
ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- which(NULL), argindex(NULL), ids(NULL), value2index(NULL), idchunk(NULL)
+ idchunk(NULL), ids(NULL), which(NULL), argindex(NULL), value2index(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal compute chunk/spread/atom command");
diff --git a/src/compute_chunk_spread_atom.h b/src/compute_chunk_spread_atom.h
index 9a4df080ca..80ee186450 100644
--- a/src/compute_chunk_spread_atom.h
+++ b/src/compute_chunk_spread_atom.h
@@ -35,9 +35,8 @@ class ComputeChunkSpreadAtom : public Compute {
protected:
int mode,nvalues;
char *idchunk;
-
- int *which,*argindex,*value2index;
char **ids;
+ int *which,*argindex,*value2index;
int nmax;
class ComputeChunkAtom *cchunk;
diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp
index 40e9dad8dd..beebc5f411 100644
--- a/src/compute_reduce_chunk.cpp
+++ b/src/compute_reduce_chunk.cpp
@@ -38,8 +38,8 @@ enum{COMPUTE,FIX,VARIABLE};
ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL),
- which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL)
+ which(NULL), argindex(NULL), value2index(NULL), idchunk(NULL), ids(NULL),
+ vlocal(NULL), vglobal(NULL), alocal(NULL), aglobal(NULL), varatom(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal compute reduce/chunk command");
--
GitLab
From 0305cca1df30b355f60799bed967e7456e2a3bac Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 10 Sep 2018 22:47:45 -0400
Subject: [PATCH 257/332] make certain that *_freq flags are initialized. use
-1 instead of 0 to avoid division by zero
---
src/fix.cpp | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/fix.cpp b/src/fix.cpp
index 051ac12bbe..634bc2393d 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -81,6 +81,7 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
+ global_freq = local_freq = peratom_freq = -1;
size_vector_variable = size_array_rows_variable = 0;
comm_forward = comm_reverse = comm_border = 0;
--
GitLab
From 983e8bb110a6faeab4675137ccccb51e3f986739 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 11 Sep 2018 11:36:37 -0600
Subject: [PATCH 258/332] doc page clarifications
---
doc/src/fix_shake.txt | 6 ++++--
doc/src/minimize.txt | 13 +++++++++----
2 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 77bb5794f6..5c11f96b98 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -214,8 +214,10 @@ which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
-SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
-(e.g. linear CO2 molecule). This causes numeric difficulties.
+SHAKE or RATTLE should not be used to constrain an angle at 180
+degrees (e.g. linear CO2 molecule). This causes numeric difficulties.
+You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to
+make a linear molecule rigid.
[Related commands:] none
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index 910fc7f821..73858fc249 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an
external pressure to the simulation box and allow it to shrink/expand
during the minimization.
-Only a few other fixes (typically those that apply force constraints)
-are invoked during minimization. See the doc pages for individual
-"fix"_fix.html commands to see which ones are relevant. Current
-examples of fixes that can be used include:
+Only a few other fixes (typically those that add forces) are invoked
+during minimization. See the doc pages for individual "fix"_fix.html
+commands to see which ones are relevant. Current examples of fixes
+that can be used include:
"fix addforce"_fix_addforce.html
"fix addtorque"_fix_addtorque.html
@@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for
that fix. The doc pages for individual "fix"_fix.html commands
specify if this should be done.
+NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc)
+to be held fixed while atom coordinates are being relaxed, e.g. via
+"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more
+info in the Restrictions section below.
+
:line
[Restrictions:]
--
GitLab
From 7f328d3f79bba1b3ce517084d556fccefc3e5bc4 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 11 Sep 2018 11:49:46 -0600
Subject: [PATCH 259/332] cite a good book on SLLOD thermostatting for
molecular systems
---
doc/src/Howto_nemd.txt | 11 +++++++++++
doc/src/Howto_thermostat.txt | 11 +++++++++++
doc/src/Howto_viscosity.txt | 11 +++++++++++
doc/src/fix_nvt_sllod.txt | 9 +++++++++
4 files changed, 42 insertions(+)
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
index f787801c36..0a76859dcf 100644
--- a/doc/src/Howto_nemd.txt
+++ b/doc/src/Howto_nemd.txt
@@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+generally, for both simple and complex fluids, e.g. molecular systems.
+The latter can be tricky to do correctly.
+
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
@@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the
NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the "fix flow/gauss"_fix_flow_gauss.html command.
+
+:line
+
+:link(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
index 0e2feb1869..6a0095e741 100644
--- a/doc/src/Howto_thermostat.txt
+++ b/doc/src/Howto_thermostat.txt
@@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+generally, for both simple and complex fluids, e.g. molecular systems.
+The latter can be tricky to do correctly.
+
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
langevin"_fix_langevin.html.
@@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style
custom"_thermo_style.html command. Or you can use the
"thermo_modify"_thermo_modify.html command to re-define what
temperature compute is used for default thermodynamic output.
+
+:line
+
+:link(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
index 8bcab6dd24..adfabf8279 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/src/Howto_viscosity.txt
@@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+generally, for both simple and complex fluids, e.g. molecular systems.
+The latter can be tricky to do correctly.
+
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
command, which determines grad(Vstream) in the equation above.
@@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The
time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
+
+:line
+
+:link(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 97a864a231..67c4d76417 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the "fix nvt"_fix_nh.html command.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
+use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
+generally, for both simple and complex fluids, e.g. molecular systems.
+The latter can be tricky to do correctly.
+
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
command. See, for example, discussion of the {temp} and {drag}
@@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.
:link(Daivis)
[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).
+
+:link(Daivis2)
+[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
+Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
--
GitLab
From c3ece2f0861b48d39b4f3da2350f2f969f11d40d Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 11 Sep 2018 12:44:35 -0600
Subject: [PATCH 260/332] typo in fix relax/box doc page
---
doc/src/fix_box_relax.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index 29ebeaeef3..d41607e2ed 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those
of the reference dimensions. If this is not the case, then the
converged stress tensor will not equal that specified by the user. We
can resolve this problem by periodically resetting the reference
-dimensions. The keyword {nreset_ref} controls how often this is done.
-If this keyword is not used, or is given a value of zero, then the
+dimensions. The keyword {nreset} controls how often this is done. If
+this keyword is not used, or is given a value of zero, then the
reference dimensions are set to those of the initial simulation domain
and are never changed. A value of {nstep} means that every {nstep}
minimization steps, the reference dimensions are set to those of the
--
GitLab
From b7c75b6c4efa38e5a4ec549bd7b6d7d1f9a06cd5 Mon Sep 17 00:00:00 2001
From: pmla <pete.mahler.larsen@gmail.com>
Date: Tue, 11 Sep 2018 16:41:44 -0400
Subject: [PATCH 261/332] Added compute for Polyhedral Template Matching
---
doc/src/Eqs/ptm_rmsd.jpg | Bin 0 -> 6833 bytes
doc/src/Eqs/ptm_rmsd.tex | 21 +
doc/src/compute_ptm_atom.txt | 117 ++
src/USER-PTM/LICENSE | 7 +
src/USER-PTM/alloy_types.cpp | 101 ++
src/USER-PTM/alloy_types.h | 9 +
src/USER-PTM/canonical_coloured.cpp | 167 ++
src/USER-PTM/canonical_coloured.h | 9 +
src/USER-PTM/cell.cpp | 1368 ++++++++++++++
src/USER-PTM/cell.h | 324 ++++
src/USER-PTM/compute_ptm_atom.cpp | 307 ++++
src/USER-PTM/compute_ptm_atom.h | 48 +
src/USER-PTM/config.h | 129 ++
src/USER-PTM/convex_hull_incremental.cpp | 363 ++++
src/USER-PTM/convex_hull_incremental.h | 27 +
src/USER-PTM/deformation_gradient.cpp | 37 +
src/USER-PTM/deformation_gradient.h | 142 ++
src/USER-PTM/fundamental_mappings.h | 180 ++
src/USER-PTM/graph_data.cpp | 2059 ++++++++++++++++++++++
src/USER-PTM/graph_data.h | 37 +
src/USER-PTM/graph_tools.cpp | 52 +
src/USER-PTM/graph_tools.h | 11 +
src/USER-PTM/index_ptm.cpp | 218 +++
src/USER-PTM/initialize_data.cpp | 71 +
src/USER-PTM/initialize_data.h | 61 +
src/USER-PTM/neighbour_ordering.cpp | 203 +++
src/USER-PTM/neighbour_ordering.h | 13 +
src/USER-PTM/normalize_vertices.cpp | 55 +
src/USER-PTM/normalize_vertices.h | 8 +
src/USER-PTM/polar.cpp | 337 ++++
src/USER-PTM/polar.h | 12 +
src/USER-PTM/ptm_constants.h | 174 ++
src/USER-PTM/ptm_functions.h | 27 +
src/USER-PTM/quat.cpp | 396 +++++
src/USER-PTM/quat.h | 32 +
src/USER-PTM/structure_matcher.cpp | 294 +++
src/USER-PTM/structure_matcher.h | 21 +
37 files changed, 7437 insertions(+)
create mode 100644 doc/src/Eqs/ptm_rmsd.jpg
create mode 100644 doc/src/Eqs/ptm_rmsd.tex
create mode 100644 doc/src/compute_ptm_atom.txt
create mode 100644 src/USER-PTM/LICENSE
create mode 100644 src/USER-PTM/alloy_types.cpp
create mode 100644 src/USER-PTM/alloy_types.h
create mode 100644 src/USER-PTM/canonical_coloured.cpp
create mode 100644 src/USER-PTM/canonical_coloured.h
create mode 100644 src/USER-PTM/cell.cpp
create mode 100644 src/USER-PTM/cell.h
create mode 100644 src/USER-PTM/compute_ptm_atom.cpp
create mode 100644 src/USER-PTM/compute_ptm_atom.h
create mode 100644 src/USER-PTM/config.h
create mode 100644 src/USER-PTM/convex_hull_incremental.cpp
create mode 100644 src/USER-PTM/convex_hull_incremental.h
create mode 100644 src/USER-PTM/deformation_gradient.cpp
create mode 100644 src/USER-PTM/deformation_gradient.h
create mode 100644 src/USER-PTM/fundamental_mappings.h
create mode 100644 src/USER-PTM/graph_data.cpp
create mode 100644 src/USER-PTM/graph_data.h
create mode 100644 src/USER-PTM/graph_tools.cpp
create mode 100644 src/USER-PTM/graph_tools.h
create mode 100644 src/USER-PTM/index_ptm.cpp
create mode 100644 src/USER-PTM/initialize_data.cpp
create mode 100644 src/USER-PTM/initialize_data.h
create mode 100644 src/USER-PTM/neighbour_ordering.cpp
create mode 100644 src/USER-PTM/neighbour_ordering.h
create mode 100644 src/USER-PTM/normalize_vertices.cpp
create mode 100644 src/USER-PTM/normalize_vertices.h
create mode 100644 src/USER-PTM/polar.cpp
create mode 100644 src/USER-PTM/polar.h
create mode 100644 src/USER-PTM/ptm_constants.h
create mode 100644 src/USER-PTM/ptm_functions.h
create mode 100644 src/USER-PTM/quat.cpp
create mode 100644 src/USER-PTM/quat.h
create mode 100644 src/USER-PTM/structure_matcher.cpp
create mode 100644 src/USER-PTM/structure_matcher.h
diff --git a/doc/src/Eqs/ptm_rmsd.jpg b/doc/src/Eqs/ptm_rmsd.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..2d20da706ef61194305123d5673042d2318aec23
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diff --git a/doc/src/Eqs/ptm_rmsd.tex b/doc/src/Eqs/ptm_rmsd.tex
new file mode 100644
index 0000000000..a9c29ce189
--- /dev/null
+++ b/doc/src/Eqs/ptm_rmsd.tex
@@ -0,0 +1,21 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
+
+\begin{document}
+
+\begin{equation*}
+\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+\norm{
+s[\vec{u_i} - \mean{\set{u}}]
+-
+\set{Q} \vec{v_i}
+}^2}
+\end{equation*}
+
+\end{document}
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
new file mode 100644
index 0000000000..c668eb7726
--- /dev/null
+++ b/doc/src/compute_ptm_atom.txt
@@ -0,0 +1,117 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute ptm/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID ptm/atom structures threshold :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+ptm/atom = style name of this compute command
+structures = structure types to search for
+threshold = lattice distortion threshold (RMSD) :ul
+
+[Examples:]
+
+compute 1 all ptm/atom default 0.1
+compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
+compute 1 all ptm/atom all 0 :pre
+
+[Description:]
+
+Define a computation that determines the local lattice structure
+around an atom using the PTM (Polyhedral Template Matching) method.
+The PTM method is described in "(Larsen)"_#Larsen.
+
+Currently, there are seven lattice structures PTM recognizes:
+
+fcc = 1
+hcp = 2
+bcc = 3
+ico (icosahedral) = 4
+sc (simple cubic) = 5
+dcub (diamond cubic) = 6
+dhex (diamond hexagonal) = 7
+other = 8 :ul
+
+The value of the PTM structure will be 0 for atoms not in the specified
+compute group. The choice of structures to search for can be specified using the "structures"
+argument, which is a hyphen-separated list of structure keywords.
+Two convenient pre-set options are provided:
+
+default: fcc-hcp-bcc-ico
+all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
+
+The 'default' setting detects the same structures as the Common Neighbor Analysis method.
+The 'all' setting searches for all structure types. A small performance penalty is
+incurred for the diamond structures, so it is not recommended to use this option if
+it is known that the simulation does not contain diamond structures.
+
+
+PTM identifies structures using two steps. First, a graph isomorphism test is used
+to identify potential structure matches. Next, the deviation is computed between the
+local structure (in the simulation) and a template of the ideal lattice structure.
+The deviation is calculated as:
+
+:c,image(Eqs/ptm_rmsd.jpg)
+
+Here, u and v contain the coordinates of the local and ideal structures respectively,
+s is a scale factor, and Q is a rotation. The best match is identified by the
+lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
+points.
+
+The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
+a local structure is identified as disordered. Typical values are in the range 0.1-0.15,
+but larger values may be desirable at higher temperatures.
+A value of 0 is equivalent to infinity and can be used if no threshold is desired.
+
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped). Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+{ptm/atom} style.
+
+[Output info:]
+
+This compute calculates a per-atom array, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+Results are stored in the per-atom array in the following order:
+
+type
+rmsd
+interatomic distance
+qw
+qx
+qy
+qw :ul
+
+The type is a number from 0 to 8. The rmsd is a positive real number.
+The interatomic distance is computed from the scale factor in the RMSD equation.
+The (qw,qx,qy,qz) parameters represent the orientation of the local structure
+in quaternion form. The reference coordinates for each template (from which the
+orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute centro/atom"_compute_centro_atom.html
+"compute cna/atom"_compute_cna_atom.html
+
+[Default:] none
+
+:line
+
+:link(Larsen)
+[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+
diff --git a/src/USER-PTM/LICENSE b/src/USER-PTM/LICENSE
new file mode 100644
index 0000000000..dc1e0a5e7e
--- /dev/null
+++ b/src/USER-PTM/LICENSE
@@ -0,0 +1,7 @@
+Copyright (c) 2016 PM Larsen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/src/USER-PTM/alloy_types.cpp b/src/USER-PTM/alloy_types.cpp
new file mode 100644
index 0000000000..bde51c19b1
--- /dev/null
+++ b/src/USER-PTM/alloy_types.cpp
@@ -0,0 +1,101 @@
+#include <algorithm>
+#include "ptm_constants.h"
+#include "initialize_data.h"
+
+
+#define NUM_ALLOY_TYPES 3
+static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
+ {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe},
+};
+
+static bool test_pure(int num_nbrs, int32_t* numbers)
+{
+ for (int i=1;i<num_nbrs + 1;i++)
+ if (numbers[i] != numbers[0])
+ return false;
+ return true;
+}
+
+static bool test_binary(int num_nbrs, int32_t* numbers)
+{
+ int a = numbers[0], b = -1;
+ for (int i=1;i<num_nbrs + 1;i++)
+ {
+ if (numbers[i] != a)
+ {
+ if (b == -1)
+ b = numbers[i];
+ else if (numbers[i] != b)
+ return false;
+ }
+ }
+
+ return true;
+}
+
+static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ for (int i=1;i<num_inner + 1;i++)
+ if (binary[i] == binary[0])
+ return false;
+
+ for (int i=num_inner+1;i<ref->num_nbrs+1;i++)
+ if (binary[i] != binary[0])
+ return false;
+
+ return true;
+}
+
+static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ int8_t temp[PTM_MAX_POINTS];
+ uint32_t best = 0xFFFFFFFF;
+ for (int j=0;j<ref->num_mappings;j++)
+ {
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[j][i]] = binary[i];
+
+ uint32_t code = 0;
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ code |= (temp[i] << i);
+
+ best = std::min(best, code);
+ }
+
+ return best;
+}
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ if (test_pure(ref->num_nbrs, numbers))
+ return PTM_ALLOY_PURE;
+
+ if (!test_binary(ref->num_nbrs, numbers))
+ return PTM_ALLOY_NONE;
+
+ uint32_t code = canonical_alloy_representation(ref, mapping, numbers);
+ for (int i=0;i<NUM_ALLOY_TYPES;i++)
+ if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
+ return typedata[i][1];
+
+ if (ref->type == PTM_MATCH_BCC)
+ if (test_shell_structure(ref, mapping, numbers, 8))
+ return PTM_ALLOY_B2;
+
+ if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)
+ if (test_shell_structure(ref, mapping, numbers, 4))
+ return PTM_ALLOY_SIC;
+
+ return PTM_ALLOY_NONE;
+}
+
diff --git a/src/USER-PTM/alloy_types.h b/src/USER-PTM/alloy_types.h
new file mode 100644
index 0000000000..1f2980593a
--- /dev/null
+++ b/src/USER-PTM/alloy_types.h
@@ -0,0 +1,9 @@
+#ifndef ALLOY_TYPES_H
+#define ALLOY_TYPES_H
+
+#include "initialize_data.h"
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+
+#endif
+
diff --git a/src/USER-PTM/canonical_coloured.cpp b/src/USER-PTM/canonical_coloured.cpp
new file mode 100644
index 0000000000..af446e1a95
--- /dev/null
+++ b/src/USER-PTM/canonical_coloured.cpp
@@ -0,0 +1,167 @@
+#include <string.h>
+#include <climits>
+#include <algorithm>
+#include "graph_tools.h"
+#include "ptm_constants.h"
+
+
+static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
+{
+ bool m[PTM_MAX_NBRS][PTM_MAX_NBRS];
+ memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ int8_t index[PTM_MAX_NBRS];
+ memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS);
+
+
+ int n = 0;
+ index[a] = colours[a] * num_nodes + n++;
+ if (index[a] > best_code[0])
+ return false;
+
+ bool winning = false;
+ if (index[a] < best_code[0])
+ {
+ best_code[0] = index[a];
+ winning = true;
+ }
+
+ int c = -1;
+ for (int it=1;it<2*num_edges;it++)
+ {
+ bool newvertex = index[b] == -1;
+
+ if (newvertex)
+ index[b] = colours[b] * num_nodes + n++;
+
+ if (!winning && index[b] > best_code[it])
+ return false;
+
+ if (winning || index[b] < best_code[it])
+ {
+ winning = true;
+ best_code[it] = index[b];
+ }
+
+ if (newvertex)
+ {
+ //When a new vertex is reached, take the right-most edge
+ //relative to the edge on which the vertex is reached.
+
+ c = common[a][b];
+ }
+ else if (m[b][a] == false)
+ {
+ //When an old vertex is reached on a new path, go back
+ //in the opposite direction.
+
+ c = a;
+ }
+ else
+ {
+ //When an old vertex is reached on an old path, leave the
+ //vertex on the right-most edge that has not previously
+ //been traversed in that direction.
+
+ c = common[a][b];
+ while (m[b][c] == true)
+ c = common[c][b];
+ }
+
+ m[a][b] = true;
+ a = b;
+ b = c;
+ }
+
+ if (winning)
+ {
+ memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes);
+ return true;
+ }
+
+ return false;
+}
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash)
+{
+ int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}};
+ int num_edges = 3 * num_facets / 2;
+ if (!build_facet_map(num_facets, facets, common))
+ return -1;
+
+ memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES);
+
+ bool equal = true;
+ for (int i = 1;i<num_nodes;i++)
+ if (degree[i] != degree[0] || colours[i] != colours[0])
+ equal = false;
+
+ if (equal)
+ {
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]);
+ }
+ else
+ {
+ uint32_t best_degree = 0;
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ best_degree = std::max(best_degree, ((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0));
+ best_degree = std::max(best_degree, ((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8));
+ best_degree = std::max(best_degree, ((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16));
+ }
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ if (best_degree == (((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, a, b);
+
+ if (best_degree == (((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, b, c);
+
+ if (best_degree == (((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, c, a);
+ }
+ }
+
+ for (int i = num_nodes-1;i>=0;i--)
+ canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1;
+ canonical_labelling[0] = 0;
+
+ uint64_t hash = 0;
+ for (int i = 0;i<2 * num_edges;i++)
+ {
+ uint64_t e = best_code[i];
+ e += i % 8;
+ e &= 0xF;
+ e <<= (4 * i) % 64;
+ hash ^= e;
+ }
+
+ *p_hash = hash;
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/USER-PTM/canonical_coloured.h b/src/USER-PTM/canonical_coloured.h
new file mode 100644
index 0000000000..4a7b5f5a4a
--- /dev/null
+++ b/src/USER-PTM/canonical_coloured.h
@@ -0,0 +1,9 @@
+#ifndef CANONICAL_COLOURED_H
+#define CANONICAL_COLOURED_H
+
+#include <stdint.h>
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
+
+#endif
+
diff --git a/src/USER-PTM/cell.cpp b/src/USER-PTM/cell.cpp
new file mode 100644
index 0000000000..f88e310b74
--- /dev/null
+++ b/src/USER-PTM/cell.cpp
@@ -0,0 +1,1368 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file cell.cc
+ * \brief Function implementations for the voronoicell and related classes. */
+
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include "config.h"
+#include "cell.h"
+
+namespace voro {
+
+inline void voro_fatal_error(const char *p,int status) {
+ fprintf(stderr,"voro++: %s\n",p);
+ exit(status);
+ //return -1;//status;
+}
+
+/** Constructs a Voronoi cell and sets up the initial memory. */
+voronoicell_base::voronoicell_base() :
+ current_vertices(init_vertices), current_vertex_order(init_vertex_order),
+ current_delete_size(init_delete_size), current_delete2_size(init_delete2_size),
+ ed(new int*[current_vertices]), nu(new int[current_vertices]),
+ pts(new double[3*current_vertices]), mem(new int[current_vertex_order]),
+ mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]),
+ ds(new int[current_delete_size]), stacke(ds+current_delete_size),
+ ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size),
+ current_marginal(init_marginal), marg(new int[current_marginal]) {
+ int i;
+ for(i=0;i<3;i++) {
+ mem[i]=init_n_vertices;mec[i]=0;
+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
+ }
+ mem[3]=init_3_vertices;mec[3]=0;
+ mep[3]=new int[init_3_vertices*7];
+ for(i=4;i<current_vertex_order;i++) {
+ mem[i]=init_n_vertices;mec[i]=0;
+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
+ }
+}
+
+/** The voronoicell destructor deallocates all the dynamic memory. */
+voronoicell_base::~voronoicell_base() {
+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mep[i];
+ delete [] marg;
+ delete [] ds2;delete [] ds;
+ delete [] mep;delete [] mec;
+ delete [] mem;delete [] pts;
+ delete [] nu;delete [] ed;
+}
+
+/** Ensures that enough memory is allocated prior to carrying out a copy.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] vb a pointered to the class to be copied. */
+template<class vc_class>
+void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) {
+ while(current_vertex_order<vb->current_vertex_order) add_memory_vorder(vc);
+ for(int i=0;i<current_vertex_order;i++) while(mem[i]<vb->mec[i]) add_memory(vc,i,ds2);
+ while(current_vertices<vb->p) add_memory_vertices(vc);
+}
+
+/** Increases the memory storage for a particular vertex order, by increasing
+ * the size of the of the corresponding mep array. If the arrays already exist,
+ * their size is doubled; if they don't exist, then new ones of size
+ * init_n_vertices are allocated. The routine also ensures that the pointers in
+ * the ed array are updated, by making use of the back pointers. For the cases
+ * where the back pointer has been temporarily overwritten in the marginal
+ * vertex code, the auxiliary delete stack is scanned to find out how to update
+ * the ed value. If the template has been instantiated with the neighbor
+ * tracking turned on, then the routine also reallocates the corresponding mne
+ * array.
+ * \param[in] i the order of the vertex memory to be increased. */
+template<class vc_class>
+void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) {
+ int s=(i<<1)+1;
+ if(mem[i]==0) {
+ vc.n_allocate(i,init_n_vertices);
+ mep[i]=new int[init_n_vertices*s];
+ mem[i]=init_n_vertices;
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Order %d vertex memory created\n",i);
+#endif
+ } else {
+ int j=0,k,*l;
+ mem[i]<<=1;
+ if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]);
+#endif
+ l=new int[s*mem[i]];
+ int m=0;
+ vc.n_allocate_aux1(i);
+ while(j<s*mec[i]) {
+ k=mep[i][j+(i<<1)];
+ if(k>=0) {
+ ed[k]=l+j;
+ vc.n_set_to_aux1_offset(k,m);
+ } else {
+ int *dsp;
+ for(dsp=ds2;dsp<stackp2;dsp++) {
+ if(ed[*dsp]==mep[i]+j) {
+ ed[*dsp]=l+j;
+ vc.n_set_to_aux1_offset(*dsp,m);
+ break;
+ }
+ }
+ if(dsp==stackp2) voro_fatal_error("Couldn't relocate dangling pointer",VOROPP_INTERNAL_ERROR);
+#if VOROPP_VERBOSE >=3
+ fputs("Relocated dangling pointer",stderr);
+#endif
+ }
+ for(k=0;k<s;k++,j++) l[j]=mep[i][j];
+ for(k=0;k<i;k++,m++) vc.n_copy_to_aux1(i,m);
+ }
+ delete [] mep[i];
+ mep[i]=l;
+ vc.n_switch_to_aux1(i);
+ }
+}
+
+/** Doubles the maximum number of vertices allowed, by reallocating the ed, nu,
+ * and pts arrays. If the allocation exceeds the absolute maximum set in
+ * max_vertices, then the routine exits with a fatal error. If the template has
+ * been instantiated with the neighbor tracking turned on, then the routine
+ * also reallocates the ne array. */
+template<class vc_class>
+void voronoicell_base::add_memory_vertices(vc_class &vc) {
+
+printf("nope: %d\n", current_vertices);
+exit(3);
+
+ int i=(current_vertices<<1),j,**pp,*pnu;
+ if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Vertex memory scaled up to %d\n",i);
+#endif
+ double *ppts;
+ pp=new int*[i];
+ for(j=0;j<current_vertices;j++) pp[j]=ed[j];
+ delete [] ed;ed=pp;
+ vc.n_add_memory_vertices(i);
+ pnu=new int[i];
+ for(j=0;j<current_vertices;j++) pnu[j]=nu[j];
+ delete [] nu;nu=pnu;
+ ppts=new double[3*i];
+ for(j=0;j<3*current_vertices;j++) ppts[j]=pts[j];
+ delete [] pts;pts=ppts;
+ current_vertices=i;
+}
+
+/** Doubles the maximum allowed vertex order, by reallocating mem, mep, and mec
+ * arrays. If the allocation exceeds the absolute maximum set in
+ * max_vertex_order, then the routine causes a fatal error. If the template has
+ * been instantiated with the neighbor tracking turned on, then the routine
+ * also reallocates the mne array. */
+template<class vc_class>
+void voronoicell_base::add_memory_vorder(vc_class &vc) {
+ int i=(current_vertex_order<<1),j,*p1,**p2;
+ if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
+#endif
+ p1=new int[i];
+ for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];while(j<i) p1[j++]=0;
+ delete [] mem;mem=p1;
+ p2=new int*[i];
+ for(j=0;j<current_vertex_order;j++) p2[j]=mep[j];
+ delete [] mep;mep=p2;
+ p1=new int[i];
+ for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];while(j<i) p1[j++]=0;
+ delete [] mec;mec=p1;
+ vc.n_add_memory_vorder(i);
+ current_vertex_order=i;
+}
+
+/** Doubles the size allocation of the main delete stack. If the allocation
+ * exceeds the absolute maximum set in max_delete_size, then routine causes a
+ * fatal error. */
+void voronoicell_base::add_memory_ds(int *&stackp) {
+ current_delete_size<<=1;
+ if(current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size);
+#endif
+ int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds;
+ while(dsp<stackp) *(dsnp++)=*(dsp++);
+ delete [] ds;ds=dsn;stackp=dsnp;
+ stacke=ds+current_delete_size;
+}
+
+/** Doubles the size allocation of the auxiliary delete stack. If the
+ * allocation exceeds the absolute maximum set in max_delete2_size, then the
+ * routine causes a fatal error. */
+void voronoicell_base::add_memory_ds2(int *&stackp2) {
+ current_delete2_size<<=1;
+ if(current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size);
+#endif
+ int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2;
+ while(dsp<stackp2) *(dsnp++)=*(dsp++);
+ delete [] ds2;ds2=dsn;stackp2=dsnp;
+ stacke2=ds2+current_delete2_size;
+}
+
+/** Initializes a Voronoi cell as a rectangular box with the given dimensions.
+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
+void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
+ for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
+ mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
+ *pts=xmin;pts[1]=ymin;pts[2]=zmin;
+ pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
+ pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
+ pts[9]=xmax;pts[10]=ymax;pts[11]=zmin;
+ pts[12]=xmin;pts[13]=ymin;pts[14]=zmax;
+ pts[15]=xmax;pts[16]=ymin;pts[17]=zmax;
+ pts[18]=xmin;pts[19]=ymax;pts[20]=zmax;
+ pts[21]=xmax;pts[22]=ymax;pts[23]=zmax;
+ int *q=mep[3];
+ *q=1;q[1]=4;q[2]=2;q[3]=2;q[4]=1;q[5]=0;q[6]=0;
+ q[7]=3;q[8]=5;q[9]=0;q[10]=2;q[11]=1;q[12]=0;q[13]=1;
+ q[14]=0;q[15]=6;q[16]=3;q[17]=2;q[18]=1;q[19]=0;q[20]=2;
+ q[21]=2;q[22]=7;q[23]=1;q[24]=2;q[25]=1;q[26]=0;q[27]=3;
+ q[28]=6;q[29]=0;q[30]=5;q[31]=2;q[32]=1;q[33]=0;q[34]=4;
+ q[35]=4;q[36]=1;q[37]=7;q[38]=2;q[39]=1;q[40]=0;q[41]=5;
+ q[42]=7;q[43]=2;q[44]=4;q[45]=2;q[46]=1;q[47]=0;q[48]=6;
+ q[49]=5;q[50]=3;q[51]=6;q[52]=2;q[53]=1;q[54]=0;q[55]=7;
+ *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
+ ed[4]=q+28;ed[5]=q+35;ed[6]=q+42;ed[7]=q+49;
+ *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=nu[6]=nu[7]=3;
+}
+
+/** Starting from a point within the current cutting plane, this routine attempts
+ * to find an edge to a point outside the cutting plane. This prevents the plane
+ * routine from .
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in,out] up */
+template<class vc_class>
+inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) {
+ int i,lp,lw,*j(ds2),*stackp2(ds2);
+ double l;
+ *(stackp2++)=up;
+ while(j<stackp2) {
+ up=*(j++);
+ for(i=0;i<nu[up];i++) {
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ if(lw==-1) return true;
+ else if(lw==0) add_to_stack(vc,lp,stackp2);
+ }
+ }
+ return false;
+}
+
+/** Adds a point to the auxiliary delete stack if it is not already there.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] lp the index of the point to add.
+ * \param[in,out] stackp2 a pointer to the end of the stack entries. */
+template<class vc_class>
+inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) {
+ for(int *k(ds2);k<stackp2;k++) if(*k==lp) return;
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=lp;
+}
+
+/** Cuts the Voronoi cell by a particle whose center is at a separation of
+ * (x,y,z) from the cell center. The value of rsq should be initially set to
+ * \f$x^2+y^2+z^2\f$.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] (x,y,z) the normal vector to the plane.
+ * \param[in] rsq the distance along this vector of the plane.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely, true otherwise. */
+template<class vc_class>
+bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) {
+ int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp;
+ int us=0,ls=0,qs,iqs,cs,uw,qw,lw;
+ int *edp,*edd;
+ double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false;
+
+ // Initialize the safe testing routine
+ n_marg=0;px=x;py=y;pz=z;prsq=rsq;
+
+ // Test approximately sqrt(n)/4 points for their proximity to the plane
+ // and keep the one which is closest
+ uw=m_test(up,u);
+
+ // Starting from an initial guess, we now move from vertex to vertex,
+ // to try and find an edge which intersects the cutting plane,
+ // or a vertex which is on the plane
+ try {
+ if(uw==1) {
+
+ // The test point is inside the cutting plane.
+ us=0;
+ do {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ us++;
+ } while (us<nu[up]);
+
+ if(us==nu[up]) {
+ return false;
+ }
+
+ ls=ed[up][nu[up]+us];
+ while(lw==1) {
+ if(++count>=p) throw true;
+ u=l;up=lp;
+ for(us=0;us<ls;us++) {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ }
+ if(us==ls) {
+ us++;
+ while(us<nu[up]) {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ us++;
+ }
+ if(us==nu[up]) {
+ return false;
+ }
+ }
+ ls=ed[up][nu[up]+us];
+ }
+
+ // If the last point in the iteration is within the
+ // plane, we need to do the complicated setup
+ // routine. Otherwise, we use the regular iteration.
+ if(lw==0) {
+ up=lp;
+ complicated_setup=true;
+ } else complicated_setup=false;
+ } else if(uw==-1) {
+ us=0;
+ do {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ us++;
+ } while (us<nu[up]);
+ if(us==nu[up]) return true;
+
+ while(qw==-1) {
+ qs=ed[up][nu[up]+us];
+ if(++count>=p) throw true;
+ u=q;up=qp;
+ for(us=0;us<qs;us++) {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ }
+ if(us==qs) {
+ us++;
+ while(us<nu[up]) {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ us++;
+ }
+ if(us==nu[up]) return true;
+ }
+ }
+ if(qw==1) {
+ lp=up;ls=us;l=u;
+ up=qp;us=ed[lp][nu[lp]+ls];u=q;
+ complicated_setup=false;
+ } else {
+ up=qp;
+ complicated_setup=true;
+ }
+ } else {
+
+ // Our original test point was on the plane, so we
+ // automatically head for the complicated setup
+ // routine
+ complicated_setup=true;
+ }
+ }
+ catch(bool except) {
+ // This routine is a fall-back, in case floating point errors
+ // cause the usual search routine to fail. In the fall-back
+ // routine, we just test every edge to find one straddling
+ // the plane.
+#if VOROPP_VERBOSE >=1
+ fputs("Bailed out of convex calculation\n",stderr);
+#endif
+ qw=1;lw=0;
+ for(qp=0;qp<p;qp++) {
+ qw=m_test(qp,q);
+ if(qw==1) {
+
+ // The point is inside the cutting space. Now
+ // see if we can find a neighbor which isn't.
+ for(us=0;us<nu[qp];us++) {
+ lp=ed[qp][us];
+ if(lp<qp) {
+ lw=m_test(lp,l);
+ if(lw!=1) break;
+ }
+ }
+ if(us<nu[qp]) {
+ up=qp;
+ if(lw==0) {
+ complicated_setup=true;
+ } else {
+ complicated_setup=false;
+ u=q;
+ ls=ed[up][nu[up]+us];
+ }
+ break;
+ }
+ } else if(qw==-1) {
+
+ // The point is outside the cutting space. See
+ // if we can find a neighbor which isn't.
+ for(ls=0;ls<nu[qp];ls++) {
+ up=ed[qp][ls];
+ if(up<qp) {
+ uw=m_test(up,u);
+ if(uw!=-1) break;
+ }
+ }
+ if(ls<nu[qp]) {
+ if(uw==0) {
+ up=qp;
+ complicated_setup=true;
+ } else {
+ complicated_setup=false;
+ lp=qp;l=q;
+ us=ed[lp][nu[lp]+ls];
+ }
+ break;
+ }
+ } else {
+
+ // The point is in the plane, so we just
+ // proceed with the complicated setup routine
+ up=qp;
+ complicated_setup=true;
+ break;
+ }
+ }
+ if(qp==p) return qw==-1?true:false;
+ }
+
+ // We're about to add the first point of the new facet. In either
+ // routine, we have to add a point, so first check there's space for
+ // it.
+ if(p==current_vertices) add_memory_vertices(vc);
+
+ if(complicated_setup) {
+
+ // We want to be strict about reaching the conclusion that the
+ // cell is entirely within the cutting plane. It's not enough
+ // to find a vertex that has edges which are all inside or on
+ // the plane. If the vertex has neighbors that are also on the
+ // plane, we should check those too.
+ if(!search_for_outside_edge(vc,up)) return false;
+
+ // The search algorithm found a point which is on the cutting
+ // plane. We leave that point in place, and create a new one at
+ // the same location.
+ pts[3*p]=pts[3*up];
+ pts[3*p+1]=pts[3*up+1];
+ pts[3*p+2]=pts[3*up+2];
+
+ // Search for a collection of edges of the test vertex which
+ // are outside of the cutting space. Begin by testing the
+ // zeroth edge.
+ i=0;
+ lp=*ed[up];
+ lw=m_test(lp,l);
+ if(lw!=-1) {
+
+ // The first edge is either inside the cutting space,
+ // or lies within the cutting plane. Test the edges
+ // sequentially until we find one that is outside.
+ rp=lw;
+ do {
+ i++;
+
+ // If we reached the last edge with no luck
+ // then all of the vertices are inside
+ // or on the plane, so the cell is completely
+ // deleted
+ if(i==nu[up]) return false;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ } while (lw!=-1);
+ j=i+1;
+
+ // We found an edge outside the cutting space. Keep
+ // moving through these edges until we find one that's
+ // inside or on the plane.
+ while(j<nu[up]) {
+ lp=ed[up][j];
+ lw=m_test(lp,l);
+ if(lw!=-1) break;
+ j++;
+ }
+
+ // Compute the number of edges for the new vertex. In
+ // general it will be the number of outside edges
+ // found, plus two. But we need to recognize the
+ // special case when all but one edge is outside, and
+ // the remaining one is on the plane. For that case we
+ // have to reduce the edge count by one to prevent
+ // doubling up.
+ if(j==nu[up]&&i==1&&rp==0) {
+ nu[p]=nu[up];
+ double_edge=true;
+ } else nu[p]=j-i+2;
+ k=1;
+
+ // Add memory for the new vertex if needed, and
+ // initialize
+ while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
+ vc.n_set_pointer(p,nu[p]);
+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
+ ed[p][nu[p]<<1]=p;
+
+ // Copy the edges of the original vertex into the new
+ // one. Delete the edges of the original vertex, and
+ // update the relational table.
+ us=cycle_down(i,up);
+ while(i<j) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ qs=i==nu[up]?0:i;
+ } else {
+
+ // In this case, the zeroth edge is outside the cutting
+ // plane. Begin by searching backwards from the last
+ // edge until we find an edge which isn't outside.
+ i=nu[up]-1;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ while(lw==-1) {
+ i--;
+
+ // If i reaches zero, then we have a point in
+ // the plane all of whose edges are outside
+ // the cutting space, so we just exit
+ if(i==0) return true;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ }
+
+ // Now search forwards from zero
+ j=1;
+ qp=ed[up][j];
+ qw=m_test(qp,q);
+ while(qw==-1) {
+ j++;
+ qp=ed[up][j];
+ qw=m_test(qp,l);
+ }
+
+ // Compute the number of edges for the new vertex. In
+ // general it will be the number of outside edges
+ // found, plus two. But we need to recognize the
+ // special case when all but one edge is outside, and
+ // the remaining one is on the plane. For that case we
+ // have to reduce the edge count by one to prevent
+ // doubling up.
+ if(i==j&&qw==0) {
+ double_edge=true;
+ nu[p]=nu[up];
+ } else {
+ nu[p]=nu[up]-i+j+1;
+ }
+
+ // Add memory to store the vertex if it doesn't exist
+ // already
+ k=1;
+ while(nu[p]>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
+
+ // Copy the edges of the original vertex into the new
+ // one. Delete the edges of the original vertex, and
+ // update the relational table.
+ vc.n_set_pointer(p,nu[p]);
+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
+ ed[p][nu[p]<<1]=p;
+ us=i++;
+ while(i<nu[up]) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ i=0;
+ while(i<j) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ qs=j;
+ }
+ if(!double_edge) {
+ vc.n_copy(p,k,up,qs);
+ vc.n_set(p,0,p_id);
+ } else vc.n_copy(p,0,up,qs);
+
+ // Add this point to the auxiliary delete stack
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=up;
+
+ // Look at the edges on either side of the group that was
+ // detected. We're going to commence facet computation by
+ // moving along one of them. We are going to end up coming back
+ // along the other one.
+ cs=k;
+ qp=up;q=u;
+ i=ed[up][us];
+ us=ed[up][nu[up]+us];
+ up=i;
+ ed[qp][nu[qp]<<1]=-p;
+
+ } else {
+
+ // The search algorithm found an intersected edge between the
+ // points lp and up. Create a new vertex between them which
+ // lies on the cutting plane. Since u and l differ by at least
+ // the tolerance, this division should never screw up.
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=up;
+ r=u/(u-l);l=1-r;
+ pts[3*p]=pts[3*lp]*r+pts[3*up]*l;
+ pts[3*p+1]=pts[3*lp+1]*r+pts[3*up+1]*l;
+ pts[3*p+2]=pts[3*lp+2]*r+pts[3*up+2]*l;
+
+ // This point will always have three edges. Connect one of them
+ // to lp.
+ nu[p]=3;
+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
+ vc.n_set_pointer(p,3);
+ vc.n_set(p,0,p_id);
+ vc.n_copy(p,1,up,us);
+ vc.n_copy(p,2,lp,ls);
+ ed[p]=mep[3]+7*mec[3]++;
+ ed[p][6]=p;
+ ed[up][us]=-1;
+ ed[lp][ls]=p;
+ ed[lp][nu[lp]+ls]=1;
+ ed[p][1]=lp;
+ ed[p][nu[p]+1]=ls;
+ cs=2;
+
+ // Set the direction to move in
+ qs=cycle_up(us,up);
+ qp=up;q=u;
+ }
+
+ // When the code reaches here, we have initialized the first point, and
+ // we have a direction for moving it to construct the rest of the facet
+ cp=p;rp=p;p++;
+ while(qp!=up||qs!=us) {
+
+ // We're currently tracing round an intersected facet. Keep
+ // moving around it until we find a point or edge which
+ // intersects the plane.
+ lp=ed[qp][qs];
+ lw=m_test(lp,l);
+
+ if(lw==1) {
+
+ // The point is still in the cutting space. Just add it
+ // to the delete stack and keep moving.
+ qs=cycle_up(ed[qp][nu[qp]+qs],lp);
+ qp=lp;
+ q=l;
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=qp;
+
+ } else if(lw==-1) {
+
+ // The point is outside of the cutting space, so we've
+ // found an intersected edge. Introduce a regular point
+ // at the point of intersection. Connect it to the
+ // point we just tested. Also connect it to the previous
+ // new point in the facet we're constructing.
+ if(p==current_vertices) add_memory_vertices(vc);
+ r=q/(q-l);l=1-r;
+ pts[3*p]=pts[3*lp]*r+pts[3*qp]*l;
+ pts[3*p+1]=pts[3*lp+1]*r+pts[3*qp+1]*l;
+ pts[3*p+2]=pts[3*lp+2]*r+pts[3*qp+2]*l;
+ nu[p]=3;
+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
+ ls=ed[qp][qs+nu[qp]];
+ vc.n_set_pointer(p,3);
+ vc.n_set(p,0,p_id);
+ vc.n_copy(p,1,qp,qs);
+ vc.n_copy(p,2,lp,ls);
+ ed[p]=mep[3]+7*mec[3]++;
+ *ed[p]=cp;
+ ed[p][1]=lp;
+ ed[p][3]=cs;
+ ed[p][4]=ls;
+ ed[p][6]=p;
+ ed[lp][ls]=p;
+ ed[lp][nu[lp]+ls]=1;
+ ed[cp][cs]=p;
+ ed[cp][nu[cp]+cs]=0;
+ ed[qp][qs]=-1;
+ qs=cycle_up(qs,qp);
+ cp=p++;
+ cs=2;
+ } else {
+
+ // We've found a point which is on the cutting plane.
+ // We're going to introduce a new point right here, but
+ // first we need to figure out the number of edges it
+ // has.
+ if(p==current_vertices) add_memory_vertices(vc);
+
+ // If the previous vertex detected a double edge, our
+ // new vertex will have one less edge.
+ k=double_edge?0:1;
+ qs=ed[qp][nu[qp]+qs];
+ qp=lp;
+ iqs=qs;
+
+ // Start testing the edges of the current point until
+ // we find one which isn't outside the cutting space
+ do {
+ k++;
+ qs=cycle_up(qs,qp);
+ lp=ed[qp][qs];
+ lw=m_test(lp,l);
+ } while (lw==-1);
+
+ // Now we need to find out whether this marginal vertex
+ // we are on has been visited before, because if that's
+ // the case, we need to add vertices to the existing
+ // new vertex, rather than creating a fresh one. We also
+ // need to figure out whether we're in a case where we
+ // might be creating a duplicate edge.
+ j=-ed[qp][nu[qp]<<1];
+ if(qp==up&&qs==us) {
+
+ // If we're heading into the final part of the
+ // new facet, then we never worry about the
+ // duplicate edge calculation.
+ new_double_edge=false;
+ if(j>0) k+=nu[j];
+ } else {
+ if(j>0) {
+
+ // This vertex was visited before, so
+ // count those vertices to the ones we
+ // already have.
+ k+=nu[j];
+
+ // The only time when we might make a
+ // duplicate edge is if the point we're
+ // going to move to next is also a
+ // marginal point, so test for that
+ // first.
+ if(lw==0) {
+
+ // Now see whether this marginal point
+ // has been visited before.
+ i=-ed[lp][nu[lp]<<1];
+ if(i>0) {
+
+ // Now see if the last edge of that other
+ // marginal point actually ends up here.
+ if(ed[i][nu[i]-1]==j) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ } else {
+
+ // That marginal point hasn't been visited
+ // before, so we probably don't have to worry
+ // about duplicate edges, except in the
+ // case when that's the way into the end
+ // of the facet, because that way always creates
+ // an edge.
+ if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ }
+ } else new_double_edge=false;
+ } else {
+
+ // The vertex hasn't been visited
+ // before, but let's see if it's
+ // marginal
+ if(lw==0) {
+
+ // If it is, we need to check
+ // for the case that it's a
+ // small branch, and that we're
+ // heading right back to where
+ // we came from
+ i=-ed[lp][nu[lp]<<1];
+ if(i==cp) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ } else new_double_edge=false;
+ }
+ }
+
+ // k now holds the number of edges of the new vertex
+ // we are forming. Add memory for it if it doesn't exist
+ // already.
+ while(k>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[k]==mem[k]) add_memory(vc,k,stackp2);
+
+ // Now create a new vertex with order k, or augment
+ // the existing one
+ if(j>0) {
+
+ // If we're augmenting a vertex but we don't
+ // actually need any more edges, just skip this
+ // routine to avoid memory confusion
+ if(nu[j]!=k) {
+ // Allocate memory and copy the edges
+ // of the previous instance into it
+ vc.n_set_aux1(k);
+ edp=mep[k]+((k<<1)+1)*mec[k]++;
+ i=0;
+ while(i<nu[j]) {
+ vc.n_copy_aux1(j,i);
+ edp[i]=ed[j][i];
+ edp[k+i]=ed[j][nu[j]+i];
+ i++;
+ }
+ edp[k<<1]=j;
+
+ // Remove the previous instance with
+ // fewer vertices from the memory
+ // structure
+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
+ if(edd!=ed[j]) {
+ for(lw=0;lw<=(nu[j]<<1);lw++) ed[j][lw]=edd[lw];
+ vc.n_set_aux2_copy(j,nu[j]);
+ vc.n_copy_pointer(edd[nu[j]<<1],j);
+ ed[edd[nu[j]<<1]]=ed[j];
+ }
+ vc.n_set_to_aux1(j);
+ ed[j]=edp;
+ } else i=nu[j];
+ } else {
+
+ // Allocate a new vertex of order k
+ vc.n_set_pointer(p,k);
+ ed[p]=mep[k]+((k<<1)+1)*mec[k]++;
+ ed[p][k<<1]=p;
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=qp;
+ pts[3*p]=pts[3*qp];
+ pts[3*p+1]=pts[3*qp+1];
+ pts[3*p+2]=pts[3*qp+2];
+ ed[qp][nu[qp]<<1]=-p;
+ j=p++;
+ i=0;
+ }
+ nu[j]=k;
+
+ // Unless the previous case was a double edge, connect
+ // the first available edge of the new vertex to the
+ // last one in the facet
+ if(!double_edge) {
+ ed[j][i]=cp;
+ ed[j][nu[j]+i]=cs;
+ vc.n_set(j,i,p_id);
+ ed[cp][cs]=j;
+ ed[cp][nu[cp]+cs]=i;
+ i++;
+ }
+
+ // Copy in the edges of the underlying vertex,
+ // and do one less if this was a double edge
+ qs=iqs;
+ while(i<(new_double_edge?k:k-1)) {
+ qs=cycle_up(qs,qp);
+ lp=ed[qp][qs];ls=ed[qp][nu[qp]+qs];
+ vc.n_copy(j,i,qp,qs);
+ ed[j][i]=lp;
+ ed[j][nu[j]+i]=ls;
+ ed[lp][ls]=j;
+ ed[lp][nu[lp]+ls]=i;
+ ed[qp][qs]=-1;
+ i++;
+ }
+ qs=cycle_up(qs,qp);
+ cs=i;
+ cp=j;
+ vc.n_copy(j,new_double_edge?0:cs,qp,qs);
+
+ // Update the double_edge flag, to pass it
+ // to the next instance of this routine
+ double_edge=new_double_edge;
+ }
+ }
+
+ // Connect the final created vertex to the initial one
+ ed[cp][cs]=rp;
+ *ed[rp]=cp;
+ ed[cp][nu[cp]+cs]=0;
+ ed[rp][nu[rp]]=cs;
+
+ // Delete points: first, remove any duplicates
+ dsp=ds;
+ while(dsp<stackp) {
+ j=*dsp;
+ if(ed[j][nu[j]]!=-1) {
+ ed[j][nu[j]]=-1;
+ dsp++;
+ } else *dsp=*(--stackp);
+ }
+
+ // Add the points in the auxiliary delete stack,
+ // and reset their back pointers
+ for(dsp=ds2;dsp<stackp2;dsp++) {
+ j=*dsp;
+ ed[j][nu[j]<<1]=j;
+ if(ed[j][nu[j]]!=-1) {
+ ed[j][nu[j]]=-1;
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=j;
+ }
+ }
+
+ // Scan connections and add in extras
+ for(dsp=ds;dsp<stackp;dsp++) {
+ cp=*dsp;
+ for(edp=ed[cp];edp<ed[cp]+nu[cp];edp++) {
+ qp=*edp;
+ if(qp!=-1&&ed[qp][nu[qp]]!=-1) {
+ if(stackp==stacke) {
+ int dis=stackp-dsp;
+ add_memory_ds(stackp);
+ dsp=ds+dis;
+ }
+ *(stackp++)=qp;
+ ed[qp][nu[qp]]=-1;
+ }
+ }
+ }
+ up=0;
+
+ // Delete them from the array structure
+ while(stackp>ds) {
+ --p;
+ while(ed[p][nu[p]]==-1) {
+ j=nu[p];
+ edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]);
+ while(edp<ed[p]+(j<<1)+1) *(edp++)=*(edd++);
+ vc.n_set_aux2_copy(p,j);
+ vc.n_copy_pointer(ed[p][(j<<1)],p);
+ ed[ed[p][(j<<1)]]=ed[p];
+ --p;
+ }
+ up=*(--stackp);
+ if(up<p) {
+
+ // Vertex management
+ pts[3*up]=pts[3*p];
+ pts[3*up+1]=pts[3*p+1];
+ pts[3*up+2]=pts[3*p+2];
+
+ // Memory management
+ j=nu[up];
+ edp=ed[up];edd=(mep[j]+((j<<1)+1)*--mec[j]);
+ while(edp<ed[up]+(j<<1)+1) *(edp++)=*(edd++);
+ vc.n_set_aux2_copy(up,j);
+ vc.n_copy_pointer(ed[up][j<<1],up);
+ vc.n_copy_pointer(up,p);
+ ed[ed[up][j<<1]]=ed[up];
+
+ // Edge management
+ ed[up]=ed[p];
+ nu[up]=nu[p];
+ for(i=0;i<nu[up];i++) ed[ed[up][i]][ed[up][nu[up]+i]]=up;
+ ed[up][nu[up]<<1]=up;
+ } else up=p++;
+ }
+
+ // Check for any vertices of zero order
+ if(*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR);
+
+ // Collapse any order 2 vertices and exit
+ return collapse_order2(vc);
+}
+
+/** During the creation of a new facet in the plane routine, it is possible
+ * that some order two vertices may arise. This routine removes them.
+ * Suppose an order two vertex joins c and d. If there's a edge between
+ * c and d already, then the order two vertex is just removed; otherwise,
+ * the order two vertex is removed and c and d are joined together directly.
+ * It is possible this process will create order two or order one vertices,
+ * and the routine is continually run until all of them are removed.
+ * \return False if the vertex removal was unsuccessful, indicative of the cell
+ * reducing to zero volume and disappearing; true if the vertex removal
+ * was successful. */
+template<class vc_class>
+inline bool voronoicell_base::collapse_order2(vc_class &vc) {
+ if(!collapse_order1(vc)) return false;
+ int a,b,i,j,k,l;
+ while(mec[2]>0) {
+
+ // Pick a order 2 vertex and read in its edges
+ i=--mec[2];
+ j=mep[2][5*i];k=mep[2][5*i+1];
+ if(j==k) {
+#if VOROPP_VERBOSE >=1
+ fputs("Order two vertex joins itself",stderr);
+#endif
+ return false;
+ }
+
+ // Scan the edges of j to see if joins k
+ for(l=0;l<nu[j];l++) {
+ if(ed[j][l]==k) break;
+ }
+
+ // If j doesn't already join k, join them together.
+ // Otherwise delete the connection to the current
+ // vertex from j and k.
+ a=mep[2][5*i+2];b=mep[2][5*i+3];i=mep[2][5*i+4];
+ if(l==nu[j]) {
+ ed[j][a]=k;
+ ed[k][b]=j;
+ ed[j][nu[j]+a]=b;
+ ed[k][nu[k]+b]=a;
+ } else {
+ if(!delete_connection(vc,j,a,false)) return false;
+ if(!delete_connection(vc,k,b,true)) return false;
+ }
+
+ // Compact the memory
+ --p;
+ if(up==i) up=0;
+ if(p!=i) {
+ if(up==p) up=i;
+ pts[3*i]=pts[3*p];
+ pts[3*i+1]=pts[3*p+1];
+ pts[3*i+2]=pts[3*p+2];
+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
+ vc.n_copy_pointer(i,p);
+ ed[i]=ed[p];
+ nu[i]=nu[p];
+ ed[i][nu[i]<<1]=i;
+ }
+
+ // Collapse any order 1 vertices if they were created
+ if(!collapse_order1(vc)) return false;
+ }
+ return true;
+}
+
+/** Order one vertices can potentially be created during the order two collapse
+ * routine. This routine keeps removing them until there are none left.
+ * \return False if the vertex removal was unsuccessful, indicative of the cell
+ * having zero volume and disappearing; true if the vertex removal was
+ * successful. */
+template<class vc_class>
+inline bool voronoicell_base::collapse_order1(vc_class &vc) {
+ int i,j,k;
+ while(mec[1]>0) {
+ up=0;
+#if VOROPP_VERBOSE >=1
+ fputs("Order one collapse\n",stderr);
+#endif
+ i=--mec[1];
+ j=mep[1][3*i];k=mep[1][3*i+1];
+ i=mep[1][3*i+2];
+ if(!delete_connection(vc,j,k,false)) return false;
+ --p;
+ if(up==i) up=0;
+ if(p!=i) {
+ if(up==p) up=i;
+ pts[3*i]=pts[3*p];
+ pts[3*i+1]=pts[3*p+1];
+ pts[3*i+2]=pts[3*p+2];
+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
+ vc.n_copy_pointer(i,p);
+ ed[i]=ed[p];
+ nu[i]=nu[p];
+ ed[i][nu[i]<<1]=i;
+ }
+ }
+ return true;
+}
+
+/** This routine deletes the kth edge of vertex j and reorganizes the memory.
+ * If the neighbor computation is enabled, we also have to supply an handedness
+ * flag to decide whether to preserve the plane on the left or right of the
+ * connection.
+ * \return False if a zero order vertex was formed, indicative of the cell
+ * disappearing; true if the vertex removal was successful. */
+template<class vc_class>
+inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) {
+ int q=hand?k:cycle_up(k,j);
+ int i=nu[j]-1,l,*edp,*edd,m;
+#if VOROPP_VERBOSE >=1
+ if(i<1) {
+ fputs("Zero order vertex formed\n",stderr);
+ return false;
+ }
+#endif
+ if(mec[i]==mem[i]) add_memory(vc,i,ds2);
+ vc.n_set_aux1(i);
+ for(l=0;l<q;l++) vc.n_copy_aux1(j,l);
+ while(l<i) {
+ vc.n_copy_aux1_shift(j,l);
+ l++;
+ }
+ edp=mep[i]+((i<<1)+1)*mec[i]++;
+ edp[i<<1]=j;
+ for(l=0;l<k;l++) {
+ edp[l]=ed[j][l];
+ edp[l+i]=ed[j][l+nu[j]];
+ }
+ while(l<i) {
+ m=ed[j][l+1];
+ edp[l]=m;
+ k=ed[j][l+nu[j]+1];
+ edp[l+i]=k;
+ ed[m][nu[m]+k]--;
+ l++;
+ }
+
+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
+ for(l=0;l<=(nu[j]<<1);l++) ed[j][l]=edd[l];
+ vc.n_set_aux2_copy(j,nu[j]);
+ vc.n_set_to_aux2(edd[nu[j]<<1]);
+ vc.n_set_to_aux1(j);
+ ed[edd[nu[j]<<1]]=edd;
+ ed[j]=edp;
+ nu[j]=i;
+ return true;
+}
+
+/** Calculates the areas of each face of the Voronoi cell and prints the
+ * results to an output stream.
+ * \param[out] v the vector to store the results in. */
+void voronoicell_base::face_areas(std::vector<double> &v) {
+ double area;
+ v.clear();
+ int i,j,k,l,m,n;
+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ area=0;
+ ed[i][j]=-1-k;
+ l=cycle_up(ed[i][nu[i]+j],k);
+ m=ed[k][l];ed[k][l]=-1-m;
+ while(m!=i) {
+ n=cycle_up(ed[k][nu[k]+l],m);
+ ux=pts[3*k]-pts[3*i];
+ uy=pts[3*k+1]-pts[3*i+1];
+ uz=pts[3*k+2]-pts[3*i+2];
+ vx=pts[3*m]-pts[3*i];
+ vy=pts[3*m+1]-pts[3*i+1];
+ vz=pts[3*m+2]-pts[3*i+2];
+ wx=uy*vz-uz*vy;
+ wy=uz*vx-ux*vz;
+ wz=ux*vy-uy*vx;
+ area+=sqrt(wx*wx+wy*wy+wz*wz);
+ k=m;l=n;
+ m=ed[k][l];ed[k][l]=-1-m;
+ }
+ v.push_back(0.125*area);
+ }
+ }
+ reset_edges();
+}
+
+/** Several routines in the class that gather cell-based statistics internally
+ * track their progress by flipping edges to negative so that they know what
+ * parts of the cell have already been tested. This function resets them back
+ * to positive. When it is called, it assumes that every edge in the routine
+ * should have already been flipped to negative, and it bails out with an
+ * internal error if it encounters a positive edge. */
+inline void voronoicell_base::reset_edges() {
+ int i,j;
+ for(i=0;i<p;i++) for(j=0;j<nu[i];j++) {
+ if(ed[i][j]>=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR);
+ ed[i][j]=-1-ed[i][j];
+ }
+}
+
+/** Checks to see if a given vertex is inside, outside or within the test
+ * plane. If the point is far away from the test plane, the routine immediately
+ * returns whether it is inside or outside. If the routine is close the the
+ * plane and within the specified tolerance, then the special check_marginal()
+ * routine is called.
+ * \param[in] n the vertex to test.
+ * \param[out] ans the result of the scalar product used in evaluating the
+ * location of the point.
+ * \return -1 if the point is inside the plane, 1 if the point is outside the
+ * plane, or 0 if the point is within the plane. */
+inline int voronoicell_base::m_test(int n,double &ans) {
+ double *pp=pts+n+(n<<1);
+ ans=*(pp++)*px;
+ ans+=*(pp++)*py;
+ ans+=*pp*pz-prsq;
+ if(ans<-tolerance2) {
+ return -1;
+ } else if(ans>tolerance2) {
+ return 1;
+ }
+ return check_marginal(n,ans);
+}
+
+/** Checks to see if a given vertex is inside, outside or within the test
+ * plane, for the case when the point has been detected to be very close to the
+ * plane. The routine ensures that the returned results are always consistent
+ * with previous tests, by keeping a table of any marginal results. The routine
+ * first sees if the vertex is in the table, and if it finds a previously
+ * computed result it uses that. Otherwise, it computes a result for this
+ * vertex and adds it the table.
+ * \param[in] n the vertex to test.
+ * \param[in] ans the result of the scalar product used in evaluating
+ * the location of the point.
+ * \return -1 if the point is inside the plane, 1 if the point is outside the
+ * plane, or 0 if the point is within the plane. */
+int voronoicell_base::check_marginal(int n,double &ans) {
+ int i;
+ for(i=0;i<n_marg;i+=2) if(marg[i]==n) return marg[i+1];
+ if(n_marg==current_marginal) {
+ current_marginal<<=1;
+ if(current_marginal>max_marginal)
+ voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i);
+#endif
+ int *pmarg=new int[current_marginal];
+ for(int j=0;j<n_marg;j++) pmarg[j]=marg[j];
+ delete [] marg;
+ marg=pmarg;
+ }
+ marg[n_marg++]=n;
+ marg[n_marg++]=ans>tolerance?1:(ans<-tolerance?-1:0);
+ return marg[n_marg-1];
+}
+
+/** This initializes the class to be a rectangular box. It calls the base class
+ * initialization routine to set up the edge and vertex information, and then
+ * sets up the neighbor information, with initial faces being assigned ID
+ * numbers from -1 to -6.
+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
+void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
+ init_base(xmin,xmax,ymin,ymax,zmin,zmax);
+ int *q=mne[3];
+ *q=-5;q[1]=-3;q[2]=-1;
+ q[3]=-5;q[4]=-2;q[5]=-3;
+ q[6]=-5;q[7]=-1;q[8]=-4;
+ q[9]=-5;q[10]=-4;q[11]=-2;
+ q[12]=-6;q[13]=-1;q[14]=-3;
+ q[15]=-6;q[16]=-3;q[17]=-2;
+ q[18]=-6;q[19]=-4;q[20]=-1;
+ q[21]=-6;q[22]=-2;q[23]=-4;
+ *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
+ ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21;
+}
+
+/** This routine checks to make sure the neighbor information of each face is
+ * consistent. */
+void voronoicell_neighbor::check_facets() {
+ int i,j,k,l,m,q;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ ed[i][j]=-1-k;
+ q=ne[i][j];
+ l=cycle_up(ed[i][nu[i]+j],k);
+ do {
+ m=ed[k][l];
+ ed[k][l]=-1-m;
+ if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q);
+ l=cycle_up(ed[k][nu[k]+l],m);
+ k=m;
+ } while (k!=i);
+ }
+ }
+ reset_edges();
+}
+
+/** The class constructor allocates memory for storing neighbor information. */
+voronoicell_neighbor::voronoicell_neighbor() {
+ int i;
+ mne=new int*[current_vertex_order];
+ ne=new int*[current_vertices];
+ for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i];
+ mne[3]=new int[init_3_vertices*3];
+ for(i=4;i<current_vertex_order;i++) mne[i]=new int[init_n_vertices*i];
+}
+
+/** The class destructor frees the dynamically allocated memory for storing
+ * neighbor information. */
+voronoicell_neighbor::~voronoicell_neighbor() {
+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mne[i];
+ delete [] mne;
+ delete [] ne;
+}
+
+/** Computes a vector list of neighbors. */
+void voronoicell_neighbor::neighbors(std::vector<int> &v) {
+ v.clear();
+ int i,j,k,l,m;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ v.push_back(ne[i][j]);
+ ed[i][j]=-1-k;
+ l=cycle_up(ed[i][nu[i]+j],k);
+ do {
+ m=ed[k][l];
+ ed[k][l]=-1-m;
+ l=cycle_up(ed[k][nu[k]+l],m);
+ k=m;
+ } while (k!=i);
+ }
+ }
+ reset_edges();
+}
+
+// Explicit instantiation
+template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int);
+template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*);
+
+}
+
diff --git a/src/USER-PTM/cell.h b/src/USER-PTM/cell.h
new file mode 100644
index 0000000000..51a0cbb9ef
--- /dev/null
+++ b/src/USER-PTM/cell.h
@@ -0,0 +1,324 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file cell.hh
+ * \brief Header file for the voronoicell and related classes. */
+
+#ifndef VOROPP_CELL_HH
+#define VOROPP_CELL_HH
+
+#include <vector>
+#include <cstdio>
+
+#include "config.h"
+
+namespace voro {
+
+/** \brief A class representing a single Voronoi cell.
+ *
+ * This class represents a single Voronoi cell, as a collection of vertices
+ * that are connected by edges. The class contains routines for initializing
+ * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
+ * It the contains routines for recomputing the cell based on cutting it
+ * by a plane, which forms the key routine for the Voronoi cell computation.
+ * It contains numerous routine for computing statistics about the Voronoi cell,
+ * and it can output the cell in several formats.
+ *
+ * This class is not intended for direct use, but forms the base of the
+ * voronoicell and voronoicell_neighbor classes, which extend it based on
+ * whether neighboring particle ID information needs to be tracked. */
+class voronoicell_base {
+ public:
+ /** This holds the current size of the arrays ed and nu, which
+ * hold the vertex information. If more vertices are created
+ * than can fit in this array, then it is dynamically extended
+ * using the add_memory_vertices routine. */
+ int current_vertices;
+ /** This holds the current maximum allowed order of a vertex,
+ * which sets the size of the mem, mep, and mec arrays. If a
+ * vertex is created with more vertices than this, the arrays
+ * are dynamically extended using the add_memory_vorder routine.
+ */
+ int current_vertex_order;
+ /** This sets the size of the main delete stack. */
+ int current_delete_size;
+ /** This sets the size of the auxiliary delete stack. */
+ int current_delete2_size;
+ /** This sets the total number of vertices in the current cell.
+ */
+ int p;
+ /** This is the index of particular point in the cell, which is
+ * used to start the tracing routines for plane intersection
+ * and cutting. These routines will work starting from any
+ * point, but it's often most efficient to start from the last
+ * point considered, since in many cases, the cell construction
+ * algorithm may consider many planes with similar vectors
+ * concurrently. */
+ int up;
+ /** This is a two dimensional array that holds information
+ * about the edge connections of the vertices that make up the
+ * cell. The two dimensional array is not allocated in the
+ * usual method. To account for the fact the different vertices
+ * have different orders, and thus require different amounts of
+ * storage, the elements of ed[i] point to one-dimensional
+ * arrays in the mep[] array of different sizes.
+ *
+ * More specifically, if vertex i has order m, then ed[i]
+ * points to a one-dimensional array in mep[m] that has 2*m+1
+ * entries. The first m elements hold the neighboring edges, so
+ * that the jth edge of vertex i is held in ed[i][j]. The next
+ * m elements hold a table of relations which is redundant but
+ * helps speed up the computation. It satisfies the relation
+ * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
+ * pointer, so that ed[i+2*m]=i. The back pointers are used
+ * when rearranging the memory. */
+ int **ed;
+ /** This array holds the order of the vertices in the Voronoi
+ * cell. This array is dynamically allocated, with its current
+ * size held by current_vertices. */
+ int *nu;
+ /** This in an array with size 3*current_vertices for holding
+ * the positions of the vertices. */
+ double *pts;
+ voronoicell_base();
+ virtual ~voronoicell_base();
+ void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void init_octahedron_base(double l);
+ void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
+ void translate(double x,double y,double z);
+ double volume();
+ double max_radius_squared();
+ double total_edge_distance();
+ double surface_area();
+ void centroid(double &cx,double &cy,double &cz);
+ int number_of_faces();
+ int number_of_edges();
+ void vertex_orders(std::vector<int> &v);
+ void vertices(std::vector<double> &v);
+ void vertices(double x,double y,double z,std::vector<double> &v);
+ void face_areas(std::vector<double> &v);
+ void face_orders(std::vector<int> &v);
+ void face_freq_table(std::vector<int> &v);
+ void face_vertices(std::vector<int> &v);
+ void face_perimeters(std::vector<double> &v);
+ void normals(std::vector<double> &v);
+ template<class vc_class>
+ bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
+ bool plane_intersects(double x,double y,double z,double rsq);
+ bool plane_intersects_guess(double x,double y,double z,double rsq);
+ void construct_relations();
+ void check_relations();
+ void check_duplicates();
+ /** Returns a list of IDs of neighboring particles
+ * corresponding to each face.
+ * \param[out] v a reference to a vector in which to return the
+ * results. If no neighbor information is
+ * available, a blank vector is returned. */
+ virtual void neighbors(std::vector<int> &v) {v.clear();}
+ /** This a virtual function that is overridden by a routine to
+ * print the neighboring particle IDs for a given vertex. By
+ * default, when no neighbor information is available, the
+ * routine does nothing.
+ * \param[in] i the vertex to consider. */
+ /** This is a simple inline function for picking out the index
+ * of the next edge counterclockwise at the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return 0 if a=nu[p]-1, or a+1 otherwise. */
+ inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
+ /** This is a simple inline function for picking out the index
+ * of the next edge clockwise from the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return nu[p]-1 if a=0, or a-1 otherwise. */
+ inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
+ protected:
+ /** This a one dimensional array that holds the current sizes
+ * of the memory allocations for them mep array.*/
+ int *mem;
+ /** This is a one dimensional array that holds the current
+ * number of vertices of order p that are stored in the mep[p]
+ * array. */
+ int *mec;
+ /** This is a two dimensional array for holding the information
+ * about the edges of the Voronoi cell. mep[p] is a
+ * one-dimensional array for holding the edge information about
+ * all vertices of order p, with each vertex holding 2*p+1
+ * integers of information. The total number of vertices held
+ * on mep[p] is stored in mem[p]. If the space runs out, the
+ * code allocates more using the add_memory() routine. */
+ int **mep;
+ inline void reset_edges();
+ template<class vc_class>
+ void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
+ void copy(voronoicell_base* vb);
+ private:
+ /** This is the delete stack, used to store the vertices which
+ * are going to be deleted during the plane cutting procedure.
+ */
+ int *ds,*stacke;
+ /** This is the auxiliary delete stack, which has size set by
+ * current_delete2_size. */
+ int *ds2,*stacke2;
+ /** This stores the current memory allocation for the marginal
+ * cases. */
+ int current_marginal;
+ /** This stores the total number of marginal points which are
+ * currently in the buffer. */
+ int n_marg;
+ /** This array contains a list of the marginal points, and also
+ * the outcomes of the marginal tests. */
+ int *marg;
+ /** The x coordinate of the normal vector to the test plane. */
+ double px;
+ /** The y coordinate of the normal vector to the test plane. */
+ double py;
+ /** The z coordinate of the normal vector to the test plane. */
+ double pz;
+ /** The magnitude of the normal vector to the test plane. */
+ double prsq;
+ template<class vc_class>
+ void add_memory(vc_class &vc,int i,int *stackp2);
+ template<class vc_class>
+ void add_memory_vertices(vc_class &vc);
+ template<class vc_class>
+ void add_memory_vorder(vc_class &vc);
+ void add_memory_ds(int *&stackp);
+ void add_memory_ds2(int *&stackp2);
+ template<class vc_class>
+ inline bool collapse_order1(vc_class &vc);
+ template<class vc_class>
+ inline bool collapse_order2(vc_class &vc);
+ template<class vc_class>
+ inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
+ template<class vc_class>
+ inline bool search_for_outside_edge(vc_class &vc,int &up);
+ template<class vc_class>
+ inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
+ inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
+ inline void normals_search(std::vector<double> &v,int i,int j,int k);
+ inline bool search_edge(int l,int &m,int &k);
+ inline int m_test(int n,double &ans);
+ int check_marginal(int n,double &ans);
+ friend class voronoicell;
+ friend class voronoicell_neighbor;
+};
+
+/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
+ * with neighbor information.
+ *
+ * This class is an extension of the voronoicell_base class, in cases when the
+ * IDs of neighboring particles associated with each face of the Voronoi cell.
+ * It contains additional data structures mne and ne for storing this
+ * information. */
+class voronoicell_neighbor : public voronoicell_base {
+ public:
+ using voronoicell_base::nplane;
+ /** This two dimensional array holds the neighbor information
+ * associated with each vertex. mne[p] is a one dimensional
+ * array which holds all of the neighbor information for
+ * vertices of order p. */
+ int **mne;
+ /** This is a two dimensional array that holds the neighbor
+ * information associated with each vertex. ne[i] points to a
+ * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
+ * neighbor information associated with the jth edge of vertex
+ * i. It is set to the ID number of the plane that made the
+ * face that is clockwise from the jth edge. */
+ int **ne;
+ voronoicell_neighbor();
+ ~voronoicell_neighbor();
+ void operator=(voronoicell_neighbor &c);
+ /** Cuts the Voronoi cell by a particle whose center is at a
+ * separation of (x,y,z) from the cell center. The value of rsq
+ * should be initially set to \f$x^2+y^2+z^2\f$.
+ * \param[in] (x,y,z) the normal vector to the plane.
+ * \param[in] rsq the distance along this vector of the plane.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool nplane(double x,double y,double z,double rsq,int p_id) {
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This routine calculates the modulus squared of the vector
+ * before passing it to the main nplane() routine with full
+ * arguments.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool nplane(double x,double y,double z,int p_id) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This version of the plane routine just makes up the plane
+ * ID to be zero. It will only be referenced if neighbor
+ * tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] rsq the modulus squared of the vector.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z,double rsq) {
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ /** Cuts a Voronoi cell using the influence of a particle at
+ * (x,y,z), first calculating the modulus squared of this
+ * vector before passing it to the main nplane() routine. Zero
+ * is supplied as the plane ID, which will be ignored unless
+ * neighbor tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void check_facets();
+ virtual void neighbors(std::vector<int> &v);
+
+ private:
+ int *paux1;
+ int *paux2;
+ inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
+ inline void n_add_memory_vertices(int i) {
+ int **pp=new int*[i];
+ for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
+ delete [] ne;ne=pp;
+ }
+ inline void n_add_memory_vorder(int i) {
+ int **p2=new int*[i];
+ for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
+ delete [] mne;mne=p2;
+ }
+ inline void n_set_pointer(int p,int n) {
+ ne[p]=mne[n]+n*mec[n];
+ }
+ inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
+ inline void n_set(int a,int b,int c) {ne[a][b]=c;}
+ inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
+ inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
+ inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
+ inline void n_set_aux2_copy(int a,int b) {
+ paux2=mne[b]+b*mec[b];
+ for(int i=0;i<b;i++) ne[a][i]=paux2[i];
+ }
+ inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
+ inline void n_set_to_aux1(int j) {ne[j]=paux1;}
+ inline void n_set_to_aux2(int j) {ne[j]=paux2;}
+ inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
+ inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
+ inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
+ inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
+ friend class voronoicell_base;
+};
+
+}
+
+#endif
+
diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
new file mode 100644
index 0000000000..b6b4a9786c
--- /dev/null
+++ b/src/USER-PTM/compute_ptm_atom.cpp
@@ -0,0 +1,307 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed
+under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: PM Larsen (MIT)
+------------------------------------------------------------------------- */
+
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include "atom.h"
+#include "comm.h"
+#include "compute_ptm_atom.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include "ptm_functions.h"
+
+#define MAX_NEIGHBORS 30
+#define NUM_COLUMNS 7
+#define UNKNOWN 0
+#define OTHER 8
+
+using namespace LAMMPS_NS;
+
+static const char cite_user_ptm_package[] =
+ "USER-PTM package:\n\n"
+ "@Article{larsen2016ptm,\n"
+ " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, "
+ "Jakob},\n"
+ " title={Robust structural identification via polyhedral template "
+ "matching},\n"
+ " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n"
+ " year={2016},\n"
+ " number={5},\n"
+ " volume={24},\n"
+ " pages={055007},\n"
+ " DOI = {10.1088/0965-0393/24/5/055007}"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
+ : Compute(lmp, narg, arg), list(NULL), output(NULL) {
+ if (narg != 5)
+ error->all(FLERR, "Illegal compute ptm/atom command");
+
+ char *structures = arg[3];
+ char *ptr = structures;
+
+ const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc",
+ "dcub", "dhex", "all", "default"};
+ int32_t flags[] = {
+ PTM_CHECK_FCC,
+ PTM_CHECK_HCP,
+ PTM_CHECK_BCC,
+ PTM_CHECK_ICO,
+ PTM_CHECK_SC,
+ PTM_CHECK_DCUB,
+ PTM_CHECK_DHEX,
+ PTM_CHECK_ALL,
+ PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
+
+ input_flags = 0;
+ while (*ptr != '\0') {
+
+ bool found = false;
+ for (int i = 0; i < 9; i++) {
+ int len = strlen(strings[i]);
+ if (strncmp(ptr, strings[i], len) == 0) {
+ input_flags |= flags[i];
+ ptr += len;
+ found = true;
+ break;
+ }
+ }
+
+ if (!found)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ if (*ptr == '\0')
+ break;
+
+ if (*ptr != '-')
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ ptr++;
+ }
+
+ double threshold = force->numeric(FLERR, arg[4]);
+ if (threshold < 0.0)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (threshold is negative)");
+ rmsd_threshold = threshold;
+ if (rmsd_threshold == 0)
+ rmsd_threshold = INFINITY;
+
+ peratom_flag = 1;
+ size_peratom_cols = NUM_COLUMNS;
+ create_attribute = 1;
+ nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); }
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init() {
+ if (force->pair == NULL)
+ error->all(FLERR, "Compute ptm/atom requires a pair style be defined");
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "ptm/atom") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute ptm/atom defined");
+
+ // need an occasional full neighbor list
+
+ int irequest = neighbor->request(this, instance_me);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; }
+
+/* ---------------------------------------------------------------------- */
+
+typedef struct {
+ int index;
+ double d;
+} ptmnbr_t;
+
+static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
+ return a.d < b.d;
+}
+
+static int get_neighbors(double *pos, int jnum, int *jlist, double **x,
+ double (*nbr)[3]) {
+
+ ptmnbr_t *nbr_order = new ptmnbr_t[jnum];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ int j = jlist[jj];
+ j &= NEIGHMASK;
+
+ double dx = pos[0] - x[j][0];
+ double dy = pos[1] - x[j][1];
+ double dz = pos[2] - x[j][2];
+ double rsq = dx * dx + dy * dy + dz * dz;
+
+ nbr_order[jj].index = j;
+ nbr_order[jj].d = rsq;
+ }
+
+ std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare);
+ int num_nbrs = std::min(MAX_NEIGHBORS, jnum);
+
+ nbr[0][0] = nbr[0][1] = nbr[0][2] = 0;
+ for (int jj = 0; jj < num_nbrs; jj++) {
+
+ int j = nbr_order[jj].index;
+ nbr[jj + 1][0] = x[j][0] - pos[0];
+ nbr[jj + 1][1] = x[j][1] - pos[1];
+ nbr[jj + 1][2] = x[j][2] - pos[2];
+ }
+
+ delete[] nbr_order;
+ return num_nbrs;
+}
+
+void ComputePTMAtom::compute_peratom() {
+ // PTM global initialization. If already initialized this function does
+ // nothing.
+ ptm_initialize_global();
+
+ // initialize PTM local storage
+ ptm_local_handle_t local_handle = ptm_initialize_local();
+
+ invoked_peratom = update->ntimestep;
+
+ // grow arrays if necessary
+ if (atom->nmax > nmax) {
+ memory->destroy(output);
+ nmax = atom->nmax;
+
+ memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output");
+ array_atom = output;
+ }
+
+ // invoke full neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ int inum = list->inum;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int ii = 0; ii < inum; ii++) {
+
+ int i = ilist[ii];
+ output[i][0] = UNKNOWN;
+ if (!(mask[i] & groupbit))
+ continue;
+
+ double *pos = x[i];
+
+ int *jlist = firstneigh[i];
+ int jnum = numneigh[i];
+ if (jnum <= 0)
+ continue;
+
+ // get neighbours ordered by increasing distance
+ double nbr[MAX_NEIGHBORS + 1][3];
+ int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr);
+
+ // check that we have enough neighbours for the desired structure types
+ int32_t flags = 0;
+ if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC))
+ flags |= PTM_CHECK_SC;
+ if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC))
+ flags |= PTM_CHECK_FCC;
+ if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP))
+ flags |= PTM_CHECK_HCP;
+ if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO))
+ flags |= PTM_CHECK_ICO;
+ if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC))
+ flags |= PTM_CHECK_BCC;
+ if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB))
+ flags |= PTM_CHECK_DCUB;
+ if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX))
+ flags |= PTM_CHECK_DHEX;
+
+ // now run PTM
+ int8_t mapping[MAX_NEIGHBORS + 1];
+ int32_t type, alloy_type;
+ double scale, rmsd, interatomic_distance, lattice_constant;
+ double q[4], F[9], F_res[3], U[9], P[9];
+ ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type,
+ &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping,
+ &interatomic_distance, &lattice_constant);
+
+ if (rmsd > rmsd_threshold) {
+ type = PTM_MATCH_NONE;
+ }
+
+ // printf("%d type=%d rmsd=%f\n", i, type, rmsd);
+
+ if (type == PTM_MATCH_NONE)
+ type = OTHER;
+
+ output[i][0] = type;
+ output[i][1] = rmsd;
+ output[i][2] = interatomic_distance;
+ output[i][3] = q[0];
+ output[i][4] = q[1];
+ output[i][5] = q[2];
+ output[i][6] = q[3];
+ }
+
+ // printf("finished ptm analysis\n");
+ ptm_uninitialize_local(local_handle);
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputePTMAtom::memory_usage() {
+ double bytes = nmax * NUM_COLUMNS * sizeof(double);
+ bytes += nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/USER-PTM/compute_ptm_atom.h
new file mode 100644
index 0000000000..5c10e0c443
--- /dev/null
+++ b/src/USER-PTM/compute_ptm_atom.h
@@ -0,0 +1,48 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(ptm/atom,ComputePTMAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_PTM_ATOM_H
+#define LMP_COMPUTE_PTM_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePTMAtom : public Compute {
+ public:
+ ComputePTMAtom(class LAMMPS *, int, char **);
+ ~ComputePTMAtom();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_peratom();
+ double memory_usage();
+
+ private:
+ int nmax;
+ int32_t input_flags;
+ double rmsd_threshold;
+ class NeighList *list;
+ double **output;
+};
+
+}
+
+#endif
+#endif
+
diff --git a/src/USER-PTM/config.h b/src/USER-PTM/config.h
new file mode 100644
index 0000000000..eba69b3373
--- /dev/null
+++ b/src/USER-PTM/config.h
@@ -0,0 +1,129 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file config.hh
+ * \brief Master configuration file for setting various compile-time options. */
+
+#ifndef VOROPP_CONFIG_HH
+#define VOROPP_CONFIG_HH
+
+namespace voro {
+
+// These constants set the initial memory allocation for the Voronoi cell
+/** The initial memory allocation for the number of vertices. */
+const int init_vertices=256;
+/** The initial memory allocation for the maximum vertex order. */
+const int init_vertex_order=64;
+/** The initial memory allocation for the number of regular vertices of order
+ * 3. */
+const int init_3_vertices=256;
+/** The initial memory allocation for the number of vertices of higher order.
+ */
+const int init_n_vertices=8;
+/** The initial buffer size for marginal cases used by the suretest class. */
+const int init_marginal=64;
+/** The initial size for the delete stack. */
+const int init_delete_size=256;
+/** The initial size for the auxiliary delete stack. */
+const int init_delete2_size=256;
+/** The initial size for the wall pointer array. */
+const int init_wall_size=32;
+/** The default initial size for the ordering class. */
+const int init_ordering_size=4096;
+/** The initial size of the pre_container chunk index. */
+const int init_chunk_size=256;
+
+// If the initial memory is too small, the program dynamically allocates more.
+// However, if the limits below are reached, then the program bails out.
+/** The maximum memory allocation for the number of vertices. */
+const int max_vertices=16777216;
+/** The maximum memory allocation for the maximum vertex order. */
+const int max_vertex_order=2048;
+/** The maximum memory allocation for the any particular order of vertex. */
+const int max_n_vertices=16777216;
+/** The maximum buffer size for marginal cases used by the suretest class. */
+const int max_marginal=16777216;
+/** The maximum size for the delete stack. */
+const int max_delete_size=16777216;
+/** The maximum size for the auxiliary delete stack. */
+const int max_delete2_size=16777216;
+/** The maximum amount of particle memory allocated for a single region. */
+const int max_particle_memory=16777216;
+/** The maximum size for the wall pointer array. */
+const int max_wall_size=2048;
+/** The maximum size for the ordering class. */
+const int max_ordering_size=67108864;
+/** The maximum size for the pre_container chunk index. */
+const int max_chunk_size=65536;
+
+/** The chunk size in the pre_container classes. */
+const int pre_container_chunk_size=1024;
+
+#ifndef VOROPP_VERBOSE
+/** Voro++ can print a number of different status and debugging messages to
+ * notify the user of special behavior, and this macro sets the amount which
+ * are displayed. At level 0, no messages are printed. At level 1, messages
+ * about unusual cases during cell construction are printed, such as when the
+ * plane routine bails out due to floating point problems. At level 2, general
+ * messages about memory expansion are printed. At level 3, technical details
+ * about memory management are printed. */
+#define VOROPP_VERBOSE 0
+#endif
+
+/** If a point is within this distance of a cutting plane, then the code
+ * assumes that point exactly lies on the plane. */
+const double tolerance=1e-11;
+
+/** If a point is within this distance of a cutting plane, then the code stores
+ * whether this point is inside, outside, or exactly on the cutting plane in
+ * the marginal cases buffer, to prevent the test giving a different result on
+ * a subsequent evaluation due to floating point rounding errors. */
+const double tolerance2=2e-11;
+
+/** The square of the tolerance, used when deciding whether some squared
+ * quantities are large enough to be used. */
+const double tolerance_sq=tolerance*tolerance;
+
+/** A large number that is used in the computation. */
+const double large_number=1e30;
+
+/** A radius to use as a placeholder when no other information is available. */
+const double default_radius=0.5;
+
+/** The maximum number of shells of periodic images to test over. */
+const int max_unit_voro_shells=10;
+
+/** A guess for the optimal number of particles per block, used to set up the
+ * container grid. */
+const double optimal_particles=5.6;
+
+/** If this is set to 1, then the code reports any instances of particles being
+ * put outside of the container geometry. */
+#define VOROPP_REPORT_OUT_OF_BOUNDS 0
+
+/** Voro++ returns this status code if there is a file-related error, such as
+ * not being able to open file. */
+#define VOROPP_FILE_ERROR 1
+
+/** Voro++ returns this status code if there is a memory allocation error, if
+ * one of the safe memory limits is exceeded. */
+#define VOROPP_MEMORY_ERROR 2
+
+/** Voro++ returns this status code if there is any type of internal error, if
+ * it detects that representation of the Voronoi cell is inconsistent. This
+ * status code will generally indicate a bug, and the developer should be
+ * contacted. */
+#define VOROPP_INTERNAL_ERROR 3
+
+/** Voro++ returns this status code if it could not interpret the command line
+ * arguments passed to the command line utility. */
+#define VOROPP_CMD_LINE_ERROR 4
+
+}
+
+#endif
diff --git a/src/USER-PTM/convex_hull_incremental.cpp b/src/USER-PTM/convex_hull_incremental.cpp
new file mode 100644
index 0000000000..bfe173cc02
--- /dev/null
+++ b/src/USER-PTM/convex_hull_incremental.cpp
@@ -0,0 +1,363 @@
+#include <cmath>
+#include <cfloat>
+#include <string.h>
+#include <cassert>
+#include <algorithm>
+#include "convex_hull_incremental.h"
+#include "ptm_constants.h"
+
+
+#define VISIBLE 1
+#define INVISIBLE 2
+#define BOTH 3
+#define TOLERANCE 1E-8
+
+static double norm_squared(double* p)
+{
+ double x = p[0];
+ double y = p[1];
+ double z = p[2];
+
+ return x*x + y*y + z*z;
+}
+
+static double dot_product(const double* a, const double* b)
+{
+ return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
+}
+
+static void cross_product(double* a, double* b, double* c)
+{
+ c[0] = a[1] * b[2] - a[2] * b[1];
+ c[1] = a[2] * b[0] - a[0] * b[2];
+ c[2] = a[0] * b[1] - a[1] * b[0];
+}
+
+static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal)
+{
+ double u[3] = { points[b][0] - points[a][0],
+ points[b][1] - points[a][1],
+ points[b][2] - points[a][2] };
+
+ double v[3] = { points[c][0] - points[a][0],
+ points[c][1] - points[a][1],
+ points[c][2] - points[a][2] };
+
+ cross_product(u, v, plane_normal);
+ double norm = sqrt(norm_squared(plane_normal));
+ plane_normal[0] /= norm;
+ plane_normal[1] /= norm;
+ plane_normal[2] /= norm;
+}
+
+static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross)
+{
+ return plane_cross[0] * (plane_point[0] - w[0])
+ + plane_cross[1] * (plane_point[1] - w[1])
+ + plane_cross[2] * (plane_point[2] - w[2]);
+}
+
+static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index)
+{
+ for (int j=0;j<3;j++)
+ {
+ double dmin = DBL_MAX, dmax = -DBL_MAX;
+ int imin = 0, imax = 0;
+
+ for (int i = 0;i<num_points;i++)
+ {
+ double d = points[i][j];
+ if (d < dmin)
+ {
+ dmin = d;
+ imin = i;
+ }
+ if (d > dmax)
+ {
+ dmax = d;
+ imax = i;
+ }
+ }
+
+ if (imin == imax)
+ return false; //degenerate point set
+
+ min_index[j] = imin;
+ max_index[j] = imax;
+ }
+
+ return true;
+}
+
+static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c)
+{
+ const double* x1 = points[a];
+ const double* x2 = points[b];
+
+ double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]};
+ double ns_x2x1 = norm_squared(x2x1);
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b)
+ continue;
+
+ const double* x0 = points[i];
+
+ double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]};
+ double dot = dot_product(x1x0, x2x1);
+ double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1;
+
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_c = bi;
+ return max_dist > TOLERANCE;
+}
+
+static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d)
+{
+ double plane_normal[3];
+ calculate_plane_normal(points, a, b, c, plane_normal);
+
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b || i == c)
+ continue;
+
+ const double* x0 = points[i];
+ double dist = fabs(point_plane_distance(x0, points[a], plane_normal));
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_d = bi;
+ return max_dist > TOLERANCE;
+}
+
+static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices)
+{
+ int min_index[3] = {0};
+ int max_index[3] = {0};
+ if (!calc_max_extent(num_points, points, min_index, max_index))
+ return -1;
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<3;i++)
+ {
+ int a = min_index[i], b = max_index[i];
+ double delta[3] = { points[a][0] - points[b][0],
+ points[a][1] - points[b][1],
+ points[a][2] - points[b][2] };
+ double dist = norm_squared(delta);
+ if (dist > max_dist)
+ {
+ bi = i;
+ max_dist = dist;
+ }
+ }
+
+ //first two points are (a, b)
+ int a = min_index[bi], b = max_index[bi], c = -1, d = -1;
+
+ if (!find_third_point(num_points, points, a, b, &c))
+ return -2;
+
+ if (!find_fourth_point(num_points, points, a, b, c, &d))
+ return -3;
+
+ initial_vertices[0] = a;
+ initial_vertices[1] = b;
+ initial_vertices[2] = c;
+ initial_vertices[3] = d;
+ return 0;
+}
+
+static bool visible(const double* w, const double* plane_point, const double* plane_normal)
+{
+ return point_plane_distance(w, plane_point, plane_normal) > 0;
+}
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre)
+{
+ calculate_plane_normal(points, a, b, c, plane_normal);
+ if (visible(barycentre, points[a], plane_normal))
+ {
+ plane_normal[0] = -plane_normal[0];
+ plane_normal[1] = -plane_normal[1];
+ plane_normal[2] = -plane_normal[2];
+
+ facet[0] = b;
+ facet[1] = a;
+ facet[2] = c;
+ }
+ else
+ {
+ facet[0] = a;
+ facet[1] = b;
+ facet[2] = c;
+ }
+}
+
+static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre)
+{
+ memset(processed, 0, PTM_MAX_POINTS * sizeof(bool));
+ memset(barycentre, 0, 3 * sizeof(double));
+ int ret = initial_simplex(num_points, points, initial_vertices);
+ if (ret != 0)
+ return ret;
+
+ for (int i = 0;i<4;i++)
+ {
+ int a = initial_vertices[i];
+ processed[a] = true;
+
+ barycentre[0] += points[a][0];
+ barycentre[1] += points[a][1];
+ barycentre[2] += points[a][2];
+ }
+ barycentre[0] /= 4;
+ barycentre[1] /= 4;
+ barycentre[2] /= 4;
+
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre);
+ add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre);
+ return 0;
+}
+
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3])
+{
+ assert( num_points == PTM_NUM_POINTS_FCC
+ || num_points == PTM_NUM_POINTS_HCP
+ || num_points == PTM_NUM_POINTS_BCC
+ || num_points == PTM_NUM_POINTS_ICO
+ || num_points == PTM_NUM_POINTS_SC
+ || num_points == PTM_NUM_POINTS_DCUB
+ || num_points == PTM_NUM_POINTS_DHEX);
+
+ int ret = 0;
+ int num_prev = ch->num_prev;
+ ch->num_prev = num_points;
+ if (!ch->ok || 0)
+ {
+ ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre);
+ if (ret != 0)
+ return ret;
+
+ ch->num_facets = 4;
+ num_prev = 0;
+ }
+
+ for (int i = num_prev;i<num_points;i++)
+ {
+ if (ch->processed[i])
+ continue;
+ ch->processed[i] = true;
+
+ int num_to_add = 0;
+ int8_t to_add[PTM_MAX_FACETS][3];
+ int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS];
+ memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS);
+ for (int j = 0;j<ch->num_facets;j++)
+ {
+ int a = ch->facets[j][0];
+ int b = ch->facets[j][1];
+ int c = ch->facets[j][2];
+
+ int u = 0, v = 0, w = 0;
+
+ double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]);
+ bool vis = distance > TOLERANCE;
+ if (vis)
+ {
+ u = edge_visible[a][b] |= VISIBLE;
+ edge_visible[b][a] |= VISIBLE;
+
+ v = edge_visible[b][c] |= VISIBLE;
+ edge_visible[c][b] |= VISIBLE;
+
+ w = edge_visible[c][a] |= VISIBLE;
+ edge_visible[a][c] |= VISIBLE;
+
+ memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t));
+ memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double));
+ ch->num_facets--;
+ j--;
+ }
+ else
+ {
+ u = edge_visible[a][b] |= INVISIBLE;
+ edge_visible[b][a] |= INVISIBLE;
+
+ v = edge_visible[b][c] |= INVISIBLE;
+ edge_visible[c][b] |= INVISIBLE;
+
+ w = edge_visible[c][a] |= INVISIBLE;
+ edge_visible[a][c] |= INVISIBLE;
+ }
+
+ if (u == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = a;
+ to_add[num_to_add][2] = b;
+ num_to_add++;
+ }
+
+ if (v == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = b;
+ to_add[num_to_add][2] = c;
+ num_to_add++;
+ }
+
+ if (w == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = c;
+ to_add[num_to_add][2] = a;
+ num_to_add++;
+ }
+ }
+
+ for (int j = 0;j<num_to_add;j++)
+ {
+ if (ch->num_facets >= PTM_MAX_FACETS)
+ return -4;
+
+ add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++;
+ }
+ }
+
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = ch->facets[i][0];
+ int b = ch->facets[i][1];
+ int c = ch->facets[i][2];
+ if (a == 0 || b == 0 || c == 0)
+ return 1; //central atom contained in convex hull
+
+ simplex[i][0] = a - 1;
+ simplex[i][1] = b - 1;
+ simplex[i][2] = c - 1;
+ }
+
+ return ret;
+}
+
diff --git a/src/USER-PTM/convex_hull_incremental.h b/src/USER-PTM/convex_hull_incremental.h
new file mode 100644
index 0000000000..d384a0457e
--- /dev/null
+++ b/src/USER-PTM/convex_hull_incremental.h
@@ -0,0 +1,27 @@
+#ifndef CONVEX_HULL_INCREMENTAL_H
+#define CONVEX_HULL_INCREMENTAL_H
+
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int8_t facets[PTM_MAX_FACETS][3];
+ double plane_normal[PTM_MAX_FACETS][3];
+ bool processed[PTM_MAX_POINTS];
+ int initial_vertices[4];
+ double barycentre[3];
+ int num_facets;
+ int num_prev;
+ bool ok;
+
+} convexhull_t;
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
+
+#endif
+
diff --git a/src/USER-PTM/deformation_gradient.cpp b/src/USER-PTM/deformation_gradient.cpp
new file mode 100644
index 0000000000..9a86dff6a3
--- /dev/null
+++ b/src/USER-PTM/deformation_gradient.cpp
@@ -0,0 +1,37 @@
+#include "deformation_gradient.h"
+
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
+{
+ for (int i = 0;i<3;i++)
+ {
+ for (int j = 0;j<3;j++)
+ {
+ double acc = 0.0;
+ for (int k = 0;k<num_points;k++)
+ acc += penrose[k][j] * normalized[mapping[k]][i];
+
+ F[i*3 + j] = acc;
+ }
+ }
+
+ res[0] = 0;
+ res[1] = 0;
+ res[2] = 0;
+
+ for (int k = 0;k<num_points;k++)
+ {
+ for (int i = 0;i<3;i++)
+ {
+ double acc = 0.0;
+ for (int j = 0;j<3;j++)
+ {
+ acc += F[i*3 + j] * ideal_points[k][j];
+ }
+
+ double delta = acc - normalized[mapping[k]][i];
+ res[i] += delta * delta;
+ }
+ }
+}
+
diff --git a/src/USER-PTM/deformation_gradient.h b/src/USER-PTM/deformation_gradient.h
new file mode 100644
index 0000000000..059a06fdec
--- /dev/null
+++ b/src/USER-PTM/deformation_gradient.h
@@ -0,0 +1,142 @@
+#ifndef DEFORMATION_GRADIENT_H
+#define DEFORMATION_GRADIENT_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
+
+//sc
+#define k_sc 0.5
+const double penrose_sc[PTM_NUM_POINTS_SC][3] = {
+ {0, 0, 0},
+ {0, 0, -k_sc},
+ {0, 0, k_sc},
+ {0, -k_sc, 0},
+ {0, k_sc, 0},
+ {-k_sc, 0, 0},
+ {k_sc, 0, 0},
+ };
+
+//fcc
+#define k_fcc 0.17677669529663678216
+const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = {
+ {0, 0, 0},
+ {0, k_fcc, k_fcc},
+ {0, -k_fcc, -k_fcc},
+ {0, k_fcc, -k_fcc},
+ {0, -k_fcc, k_fcc},
+ {k_fcc, 0, k_fcc},
+ {-k_fcc, 0, -k_fcc},
+ {k_fcc, 0, -k_fcc},
+ {-k_fcc, 0, k_fcc},
+ {k_fcc, k_fcc, -0},
+ {-k_fcc, -k_fcc, 0},
+ {k_fcc, -k_fcc, 0},
+ {-k_fcc, k_fcc, -0},
+ };
+
+//hcp
+#define k_hcp 0.17677669529663678216
+const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = {
+ {0, 0, 0},
+ {k_hcp, 0, k_hcp},
+ {-k_hcp/3, -4*k_hcp/3, -k_hcp/3},
+ {k_hcp, k_hcp, 0},
+ {-k_hcp/3, -k_hcp/3, -4*k_hcp/3},
+ {0, k_hcp, k_hcp},
+ {-4*k_hcp/3, -k_hcp/3, -k_hcp/3},
+ {-k_hcp, k_hcp, -0},
+ {0, k_hcp, -k_hcp},
+ {k_hcp, 0, -k_hcp},
+ {k_hcp, -k_hcp, 0},
+ {-k_hcp, 0, k_hcp},
+ {0, -k_hcp, k_hcp},
+ };
+
+//ico
+#define k_ico 0.13143277802974323576
+#define phi 1.61803398874989490253
+//((1.0 + sqrt(5)) / 2)
+const double penrose_ico[PTM_NUM_POINTS_ICO][3] = {
+ {0, 0, 0},
+ {0, k_ico, phi*k_ico},
+ {0, -k_ico, -phi*k_ico},
+ {0, k_ico, -phi*k_ico},
+ {0, -k_ico, phi*k_ico},
+ {-k_ico, -phi*k_ico, -0},
+ {k_ico, phi*k_ico, 0},
+ {k_ico, -phi*k_ico, 0},
+ {-k_ico, phi*k_ico, -0},
+ {-phi*k_ico, 0, -k_ico},
+ {phi*k_ico, 0, k_ico},
+ {phi*k_ico, 0, -k_ico},
+ {-phi*k_ico, 0, k_ico},
+ };
+
+//bcc
+#define k_bcc 0.11543038598460284017
+const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = {
+ {0, 0, 0},
+ {-k_bcc, -k_bcc, -k_bcc},
+ {k_bcc, k_bcc, k_bcc},
+ {k_bcc, -k_bcc, -k_bcc},
+ {-k_bcc, k_bcc, k_bcc},
+ {-k_bcc, k_bcc, -k_bcc},
+ {k_bcc, -k_bcc, k_bcc},
+ {-k_bcc, -k_bcc, k_bcc},
+ {k_bcc, k_bcc, -k_bcc},
+ {0, 0, -2*k_bcc},
+ {0, 0, 2*k_bcc},
+ {0, -2*k_bcc, 0},
+ {0, 2*k_bcc, 0},
+ {-2*k_bcc, 0, 0},
+ {2*k_bcc, 0, -0},
+ };
+
+//dcub
+#define kdcub 0.07095369570691034689
+const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = {
+ { 0, 0, 0 },
+ { -kdcub, kdcub, kdcub },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, -2 * kdcub, 0 },
+ { -2 * kdcub, 0, -2 * kdcub },
+ { 0, -2 * kdcub, -2 * kdcub },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ };
+
+
+#define kdhex 0.04730246380471011397
+const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
+ { 0, 0, 0 },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { -kdcub, kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -kdhex, -4 * kdhex, -kdhex },
+ { -4 * kdhex, -kdhex, -kdhex },
+ { -kdhex, -kdhex, -4 * kdhex },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ };
+#endif
+
+
diff --git a/src/USER-PTM/fundamental_mappings.h b/src/USER-PTM/fundamental_mappings.h
new file mode 100644
index 0000000000..9030d3a2b2
--- /dev/null
+++ b/src/USER-PTM/fundamental_mappings.h
@@ -0,0 +1,180 @@
+#ifndef FUNDAMENTAL_MAPPINGS_H
+#define FUNDAMENTAL_MAPPINGS_H
+
+#include <stdint.h>
+
+#define NUM_CUBIC_MAPPINGS 24
+#define NUM_ICO_MAPPINGS 60
+#define NUM_HEX_MAPPINGS 6
+#define NUM_DCUB_MAPPINGS 12
+#define NUM_DHEX_MAPPINGS 3
+
+const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6},
+ {0, 2, 1, 4, 3, 5, 6},
+ {0, 2, 1, 3, 4, 6, 5},
+ {0, 1, 2, 4, 3, 6, 5},
+ {0, 3, 4, 5, 6, 1, 2},
+ {0, 5, 6, 2, 1, 4, 3},
+ {0, 6, 5, 1, 2, 4, 3},
+ {0, 4, 3, 5, 6, 2, 1},
+ {0, 5, 6, 1, 2, 3, 4},
+ {0, 4, 3, 6, 5, 1, 2},
+ {0, 3, 4, 6, 5, 2, 1},
+ {0, 6, 5, 2, 1, 3, 4},
+ {0, 3, 4, 2, 1, 5, 6},
+ {0, 6, 5, 3, 4, 1, 2},
+ {0, 1, 2, 5, 6, 4, 3},
+ {0, 4, 3, 1, 2, 5, 6},
+ {0, 5, 6, 3, 4, 2, 1},
+ {0, 1, 2, 6, 5, 3, 4},
+ {0, 2, 1, 5, 6, 3, 4},
+ {0, 5, 6, 4, 3, 1, 2},
+ {0, 3, 4, 1, 2, 6, 5},
+ {0, 2, 1, 6, 5, 4, 3},
+ {0, 6, 5, 4, 3, 2, 1},
+ {0, 4, 3, 2, 1, 6, 5} };
+
+const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9},
+ {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11},
+ {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7},
+ {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5},
+ {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2},
+ {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6},
+ {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3},
+ {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9},
+ {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8},
+ {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1},
+ {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10},
+ {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11},
+ {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2},
+ {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5},
+ {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12},
+ {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4},
+ {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} };
+
+const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14},
+ {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14},
+ {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13},
+ {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13},
+ {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10},
+ {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11},
+ {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11},
+ {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9},
+ {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12},
+ {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10},
+ {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9},
+ {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12},
+ {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14},
+ {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10},
+ {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11},
+ {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14},
+ {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9},
+ {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12},
+ {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12},
+ {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11},
+ {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} };
+
+const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4},
+ {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4},
+ {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5},
+ {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1},
+ {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5},
+ {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12},
+ {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12},
+ {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1},
+ {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9},
+ {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8},
+ {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9},
+ {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8},
+ {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8},
+ {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9},
+ {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3},
+ {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5},
+ {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6},
+ {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4},
+ {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2},
+ {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3},
+ {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10},
+ {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10},
+ {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1},
+ {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2},
+ {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7},
+ {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5},
+ {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9},
+ {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2},
+ {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10},
+ {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7},
+ {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7},
+ {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12},
+ {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6},
+ {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12},
+ {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3},
+ {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10},
+ {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3},
+ {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6},
+ {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9},
+ {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3},
+ {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8},
+ {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2},
+ {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5},
+ {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4},
+ {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11},
+ {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1},
+ {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11},
+ {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11},
+ {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6},
+ {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11},
+ {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7},
+ {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11},
+ {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} };
+
+const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7},
+ {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9},
+ {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10},
+ {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} };
+
+const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12},
+ {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6},
+ {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8},
+ {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13},
+ {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10},
+ {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11},
+ {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15},
+ {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7},
+ {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5},
+ {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9},
+ {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} };
+
+const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
+ {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
+
+#endif
+
diff --git a/src/USER-PTM/graph_data.cpp b/src/USER-PTM/graph_data.cpp
new file mode 100644
index 0000000000..aea2e59eac
--- /dev/null
+++ b/src/USER-PTM/graph_data.cpp
@@ -0,0 +1,2059 @@
+#include "graph_data.h"
+
+
+int8_t automorphisms[65][17] = {
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1},
+ { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1},
+ { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1},
+ { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1},
+ { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1},
+ { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1},
+ { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1},
+ { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1},
+ { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1},
+ { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1},
+ { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1},
+ { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1},
+ { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1},
+ { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1},
+ { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1},
+ { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1},
+ { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1},
+ { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1},
+ { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+};
+
+graph_t graphs_sc[NUM_SC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}},
+
+};
+
+graph_t graphs_ico[NUM_ICO_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}},
+
+};
+
+graph_t graphs_fcc[NUM_FCC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{7,
+0,
+1,
+5,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+};
+
+graph_t graphs_hcp[NUM_HCP_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{6,
+0,
+6,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{7,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{9,
+0,
+8,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{12,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{13,
+0,
+10,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{14,
+0,
+12,
+10,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{15,
+0,
+22,
+10,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+};
+
+graph_t graphs_bcc[NUM_BCC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}},
+
+{7,
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+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}},
+
+{8,
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+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
+
+{9,
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+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{10,
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+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
+
+{11,
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+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
+
+{12,
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+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
+
+{13,
+0,
+0,
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+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{13,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{14,
+0,
+55,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{15,
+0,
+59,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{16,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{17,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{18,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{19,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{20,
+0,
+61,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{21,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{22,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{23,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+};
+
diff --git a/src/USER-PTM/graph_data.h b/src/USER-PTM/graph_data.h
new file mode 100644
index 0000000000..3a8a5c7ae7
--- /dev/null
+++ b/src/USER-PTM/graph_data.h
@@ -0,0 +1,37 @@
+#ifndef GRAPH_DATA_H
+#define GRAPH_DATA_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int id;
+ uint64_t hash;
+ int automorphism_index;
+ int num_automorphisms;
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ int8_t facets[PTM_MAX_FACETS][3];
+} graph_t;
+
+#define NUM_SC_GRAPHS 1
+#define NUM_ICO_GRAPHS 1
+#define NUM_FCC_GRAPHS 8
+#define NUM_HCP_GRAPHS 16
+#define NUM_BCC_GRAPHS 218
+#define NUM_DCUB_GRAPHS 12
+#define NUM_DHEX_GRAPHS 24
+
+extern int8_t automorphisms[][PTM_MAX_POINTS];
+
+extern graph_t graphs_sc[NUM_SC_GRAPHS];
+extern graph_t graphs_fcc[NUM_FCC_GRAPHS];
+extern graph_t graphs_hcp[NUM_HCP_GRAPHS];
+extern graph_t graphs_ico[NUM_ICO_GRAPHS];
+extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
+extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
+extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
+
+#endif
+
diff --git a/src/USER-PTM/graph_tools.cpp b/src/USER-PTM/graph_tools.cpp
new file mode 100644
index 0000000000..864e921b51
--- /dev/null
+++ b/src/USER-PTM/graph_tools.cpp
@@ -0,0 +1,52 @@
+#include <string.h>
+#include <algorithm>
+#include "graph_tools.h"
+#include "ptm_constants.h"
+
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
+{
+ memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //assert(common[a][b] == -1);
+ //assert(common[b][c] == -1);
+ //assert(common[c][a] == -1);
+ if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1)
+ return false;
+
+ common[a][b] = c;
+ common[b][c] = a;
+ common[c][a] = b;
+ }
+
+ return true;
+}
+
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree)
+{
+ memset(degree, 0, sizeof(int8_t) * num_nodes);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ degree[a]++;
+ degree[b]++;
+ degree[c]++;
+ }
+
+ int8_t max_degree = 0;
+ for (int i = 0;i<num_nodes;i++)
+ max_degree = std::max(max_degree, degree[i]);
+
+ return max_degree;
+}
+
diff --git a/src/USER-PTM/graph_tools.h b/src/USER-PTM/graph_tools.h
new file mode 100644
index 0000000000..791a44f9a6
--- /dev/null
+++ b/src/USER-PTM/graph_tools.h
@@ -0,0 +1,11 @@
+#ifndef GRAPH_TOOLS_H
+#define GRAPH_TOOLS_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
+
+#endif
+
diff --git a/src/USER-PTM/index_ptm.cpp b/src/USER-PTM/index_ptm.cpp
new file mode 100644
index 0000000000..2683323ac5
--- /dev/null
+++ b/src/USER-PTM/index_ptm.cpp
@@ -0,0 +1,218 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "convex_hull_incremental.h"
+#include "graph_data.h"
+#include "deformation_gradient.h"
+#include "alloy_types.h"
+#include "neighbour_ordering.h"
+#include "normalize_vertices.h"
+#include "quat.h"
+#include "polar.h"
+#include "initialize_data.h"
+#include "structure_matcher.h"
+#include "ptm_functions.h"
+#include "ptm_constants.h"
+
+
+//todo: verify that c == norm(template[1])
+static double calculate_interatomic_distance(int type, double scale)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))};
+ return c[type] / scale;
+}
+
+static double calculate_lattice_constant(int type, double interatomic_distance)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)};
+ return c[type] * interatomic_distance;
+}
+
+static int rotate_into_fundamental_zone(int type, double* q)
+{
+ if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
+ if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
+ if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
+ return -1;
+}
+
+static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ if (topological_ordering)
+ {
+ double normalized_points[PTM_MAX_INPUT_POINTS][3];
+ normalize_vertices(num_points, unpermuted_points, normalized_points);
+ int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
+ if (ret != 0)
+ topological_ordering = false;
+ }
+
+ if (!topological_ordering)
+ for (int i=0;i<num_points;i++)
+ ordering[i] = i;
+
+ for (int i=0;i<num_points;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+}
+
+static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ *p_type = PTM_MATCH_NONE;
+ if (p_alloy_type != NULL)
+ *p_alloy_type = PTM_ALLOY_NONE;
+
+ if (mapping != NULL)
+ memset(mapping, -1, num_points * sizeof(int8_t));
+
+ const refdata_t* ref = res->ref_struct;
+ if (ref == NULL)
+ return;
+
+ *p_type = ref->type;
+ if (p_alloy_type != NULL && unpermuted_numbers != NULL)
+ *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
+
+ int bi = rotate_into_fundamental_zone(ref->type, res->q);
+ int8_t temp[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[bi][i]] = res->mapping[i];
+
+ memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t));
+
+ if (F != NULL && F_res != NULL)
+ {
+ double scaled_points[PTM_MAX_INPUT_POINTS][3];
+
+ subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
+ for (int i = 0;i<ref->num_nbrs + 1;i++)
+ {
+ scaled_points[i][0] *= res->scale;
+ scaled_points[i][1] *= res->scale;
+ scaled_points[i][2] *= res->scale;
+ }
+ calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
+
+ if (P != NULL && U != NULL)
+ polar_decomposition_3x3(F, false, U, P);
+ }
+
+ if (mapping != NULL)
+ for (int i=0;i<ref->num_nbrs + 1;i++)
+ mapping[i] = ordering[res->mapping[i]];
+
+ double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale);
+ double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance);
+
+ if (p_interatomic_distance != NULL)
+ *p_interatomic_distance = interatomic_distance;
+
+ if (p_lattice_constant != NULL)
+ *p_lattice_constant = lattice_constant;
+
+ *p_rmsd = res->rmsd;
+ *p_scale = res->scale;
+ memcpy(q, res->q, 4 * sizeof(double));
+}
+
+
+extern bool ptm_initialized;
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
+ int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ assert(ptm_initialized);
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ if (flags & PTM_CHECK_SC)
+ assert(num_points >= PTM_NUM_POINTS_SC);
+
+ if (flags & PTM_CHECK_BCC)
+ assert(num_points >= PTM_NUM_POINTS_BCC);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ assert(num_points >= PTM_NUM_POINTS_FCC);
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ assert(num_points >= PTM_NUM_POINTS_DCUB);
+
+ int ret = 0;
+ result_t res;
+ res.ref_struct = NULL;
+ res.rmsd = INFINITY;
+
+ int8_t ordering[PTM_MAX_INPUT_POINTS];
+ double points[PTM_MAX_POINTS][3];
+ int32_t numbers[PTM_MAX_POINTS];
+
+ int8_t dordering[PTM_MAX_INPUT_POINTS];
+ double dpoints[PTM_MAX_POINTS][3];
+ int32_t dnumbers[PTM_MAX_POINTS];
+
+ convexhull_t ch;
+ double ch_points[PTM_MAX_INPUT_POINTS][3];
+
+ if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
+ {
+ int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
+ order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
+ normalize_vertices(num_lpoints, points, ch_points);
+ ch.ok = false;
+
+ if (flags & PTM_CHECK_SC)
+ ret = match_general(&structure_sc, ch_points, points, &ch, &res);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
+
+ if (flags & PTM_CHECK_BCC)
+ ret = match_general(&structure_bcc, ch_points, points, &ch, &res);
+ }
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ {
+ ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
+ if (ret == 0)
+ {
+ normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
+ ch.ok = false;
+
+ ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
+ }
+ }
+
+ if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX))
+ {
+ output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+ else
+ {
+ output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/USER-PTM/initialize_data.cpp b/src/USER-PTM/initialize_data.cpp
new file mode 100644
index 0000000000..6c177bfb70
--- /dev/null
+++ b/src/USER-PTM/initialize_data.cpp
@@ -0,0 +1,71 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "initialize_data.h"
+
+
+static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
+{
+ double plane_normal[3];
+ double origin[3] = {0, 0, 0};
+
+ for (int i = 0;i<num_facets;i++)
+ add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
+}
+
+static int initialize_graphs(const refdata_t* s, int8_t* colours)
+{
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
+ assert(_max_degree <= s->max_degree);
+
+ make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
+ int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
+ if (ret != 0)
+ return ret;
+ }
+
+ return PTM_NO_ERROR;
+}
+
+bool ptm_initialized = false;
+int ptm_initialize_global()
+{
+ if (ptm_initialized)
+ return PTM_NO_ERROR;
+
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+
+ int ret = initialize_graphs(&structure_sc, colours);
+ ret |= initialize_graphs(&structure_fcc, colours);
+ ret |= initialize_graphs(&structure_hcp, colours);
+ ret |= initialize_graphs(&structure_ico, colours);
+ ret |= initialize_graphs(&structure_bcc, colours);
+ ret |= initialize_graphs(&structure_dcub, dcolours);
+ ret |= initialize_graphs(&structure_dhex, dcolours);
+
+ if (ret == PTM_NO_ERROR)
+ ptm_initialized = true;
+
+ return ret;
+}
+
+ptm_local_handle_t ptm_initialize_local()
+{
+ assert(ptm_initialized);
+ return (ptm_local_handle_t)voronoi_initialize_local();
+}
+
+void ptm_uninitialize_local(ptm_local_handle_t ptr)
+{
+ voronoi_uninitialize_local(ptr);
+}
+
diff --git a/src/USER-PTM/initialize_data.h b/src/USER-PTM/initialize_data.h
new file mode 100644
index 0000000000..644dfea8c4
--- /dev/null
+++ b/src/USER-PTM/initialize_data.h
@@ -0,0 +1,61 @@
+#ifndef INITIALIZE_DATA_H
+#define INITIALIZE_DATA_H
+
+
+#include "graph_data.h"
+#include "graph_tools.h"
+#include "deformation_gradient.h"
+#include "fundamental_mappings.h"
+#include "neighbour_ordering.h"
+#include "canonical_coloured.h"
+#include "convex_hull_incremental.h"
+
+
+typedef struct
+{
+ int type;
+ int num_nbrs;
+ int num_facets;
+ int max_degree;
+ int num_graphs;
+ int num_mappings;
+ graph_t* graphs;
+ const double (*points)[3];
+ const double (*penrose)[3];
+ const int8_t (*mapping)[PTM_MAX_POINTS];
+} refdata_t;
+
+
+//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc };
+const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc };
+const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc };
+const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp };
+const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico };
+const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc };
+const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
+const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct ptm_local_handle* ptm_local_handle_t;
+ptm_local_handle_t ptm_initialize_local();
+void ptm_uninitialize_local(ptm_local_handle_t ptr);
+
+int ptm_initialize_global();
+
+//------------------------------------
+// global initialization switch
+//------------------------------------
+extern bool ptm_initialized;
+
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#endif
+
diff --git a/src/USER-PTM/neighbour_ordering.cpp b/src/USER-PTM/neighbour_ordering.cpp
new file mode 100644
index 0000000000..8e8b016cfc
--- /dev/null
+++ b/src/USER-PTM/neighbour_ordering.cpp
@@ -0,0 +1,203 @@
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
+#include <cassert>
+#include <algorithm>
+#include "ptm_constants.h"
+#include "cell.h"
+using namespace voro;
+
+
+
+typedef struct
+{
+ double area;
+ double dist;
+ int index;
+} sorthelper_t;
+
+static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
+{
+ if (a.area > b.area)
+ return true;
+
+ if (a.area < b.area)
+ return false;
+
+ if (a.dist < b.dist)
+ return true;
+
+ return false;
+}
+
+//todo: change voronoi code to return errors rather than exiting
+static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
+{
+ const double k = 1000 * max_norm; //todo: reduce this constant
+ v->init(-k,k,-k,k,-k,k);
+
+ for (int i=1;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ v->nplane(x,y,z,normsq[i],i);
+ }
+
+ v->neighbors(nbr_indices);
+ v->face_areas(face_areas);
+ return 0;
+}
+
+int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
+
+ double max_norm = 0;
+ double points[PTM_MAX_INPUT_POINTS][3];
+ double normsq[PTM_MAX_INPUT_POINTS];
+ for (int i = 0;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ points[i][0] = x;
+ points[i][1] = y;
+ points[i][2] = z;
+
+ normsq[i] = x*x + y*y + z*z;
+ max_norm = std::max(max_norm, normsq[i]);
+#ifdef DEBUG
+ printf("point %d: %f\t%f\t%f\t%f\n", i, x, y, z, x*x + y*y + z*z);
+#endif
+ }
+
+ max_norm = sqrt(max_norm);
+
+ std::vector<int> nbr_indices(num_points + 6);
+ std::vector<double> face_areas(num_points + 6);
+ int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas);
+ if (ret != 0)
+ return ret;
+
+ double areas[PTM_MAX_INPUT_POINTS];
+ memset(areas, 0, num_points * sizeof(double));
+ areas[0] = INFINITY;
+ for (size_t i=0;i<nbr_indices.size();i++)
+ {
+ int index = nbr_indices[i];
+ if (index > 0)
+ areas[index] = face_areas[i];
+ }
+
+ sorthelper_t data[PTM_MAX_INPUT_POINTS];
+ for (int i=0;i<num_points;i++)
+ {
+ assert(areas[i] == areas[i]);
+ data[i].area = areas[i];
+ data[i].dist = normsq[i];
+ data[i].index = i;
+ }
+
+ std::sort(data, data + num_points, &sorthelper_compare);
+
+#ifdef DEBUG
+ for (int i=0;i<num_points;i++)
+ printf("%d %f\n", data[i].index, data[i].area);
+#endif
+
+ for (int i=0;i<num_points;i++)
+ ordering[i] = data[i].index;
+
+ return ret;
+}
+
+void* voronoi_initialize_local()
+{
+ voronoicell_neighbor* ptr = new voronoicell_neighbor;
+ return (void*)ptr;
+}
+
+void voronoi_uninitialize_local(void* _ptr)
+{
+ voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
+ delete ptr;
+}
+
+
+typedef struct
+{
+ double dist;
+ int p;
+ int index;
+} diamond_t;
+
+static bool diamond_compare(diamond_t const& a, diamond_t const& b)
+{
+ return a.dist < b.dist;
+}
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ diamond_t data[4 * (PTM_MAX_INPUT_POINTS - 5)];
+ int index = 0;
+ for (int i=5;i<num_points;i++)
+ {
+ for (int j=1;j<5;j++)
+ {
+ double dx = unpermuted_points[i][0] - unpermuted_points[j][0];
+ double dy = unpermuted_points[i][1] - unpermuted_points[j][1];
+ double dz = unpermuted_points[i][2] - unpermuted_points[j][2];
+
+ double d = dx*dx + dy*dy + dz*dz;
+
+ data[index].p = j - 1;
+ data[index].index = i;
+ data[index].dist = d;
+ index++;
+ }
+ }
+ int n = index;
+
+ std::sort(data, data + n, &diamond_compare);
+
+ for (index=0;index<5;index++)
+ ordering[index] = index;
+
+ int num_found = 0;
+ bool hit[PTM_MAX_INPUT_POINTS] = {0};
+ int counts[4] = {0};
+ for (int i=0;i<n;i++)
+ {
+ int p = data[i].p;
+ int q = data[i].index;
+ if (hit[q] || counts[p] >= 3)
+ continue;
+
+ ordering[1 + 4 + 3 * p + counts[p]] = q;
+ counts[p]++;
+ index++;
+ num_found++;
+ if (num_found >= 12)
+ break;
+ }
+
+ if (num_found != 12)
+ return -1;
+
+ for (int i=0;i<PTM_NUM_NBRS_DCUB+1;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+
+ return 0;
+}
+
diff --git a/src/USER-PTM/neighbour_ordering.h b/src/USER-PTM/neighbour_ordering.h
new file mode 100644
index 0000000000..33160caa4f
--- /dev/null
+++ b/src/USER-PTM/neighbour_ordering.h
@@ -0,0 +1,13 @@
+#ifndef NEIGHBOUR_ORDERING_H
+#define NEIGHBOUR_ORDERING_H
+
+int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers);
+
+void* voronoi_initialize_local();
+void voronoi_uninitialize_local(void* ptr);
+
+#endif
+
diff --git a/src/USER-PTM/normalize_vertices.cpp b/src/USER-PTM/normalize_vertices.cpp
new file mode 100644
index 0000000000..61dca5006f
--- /dev/null
+++ b/src/USER-PTM/normalize_vertices.cpp
@@ -0,0 +1,55 @@
+#include <cmath>
+
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
+{
+ //calculate barycentre
+ double sum[3] = {0, 0, 0};
+ for (int i=0;i<num;i++)
+ {
+ sum[0] += points[i][0];
+ sum[1] += points[i][1];
+ sum[2] += points[i][2];
+ }
+
+ sum[0] /= num;
+ sum[1] /= num;
+ sum[2] /= num;
+
+ //subtract barycentre
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] = points[i][0] - sum[0];
+ normalized[i][1] = points[i][1] - sum[1];
+ normalized[i][2] = points[i][2] - sum[2];
+ }
+}
+
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
+{
+ subtract_barycentre(num, points, normalized);
+
+ //calculate mean length
+ double scale = 0.0;
+ for (int i=1;i<num;i++)
+ {
+ double x = normalized[i][0];
+ double y = normalized[i][1];
+ double z = normalized[i][2];
+
+ double norm = sqrt(x*x + y*y + z*z);
+ scale += norm;
+ }
+ scale /= num;
+
+ //scale vertices such that mean length is 1
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] /= scale;
+ normalized[i][1] /= scale;
+ normalized[i][2] /= scale;
+ }
+
+ return scale;
+}
+
diff --git a/src/USER-PTM/normalize_vertices.h b/src/USER-PTM/normalize_vertices.h
new file mode 100644
index 0000000000..e18990cd9b
--- /dev/null
+++ b/src/USER-PTM/normalize_vertices.h
@@ -0,0 +1,8 @@
+#ifndef NORMALIZE_VERTICES_H
+#define NORMALIZE_VERTICES_H
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
+
+#endif
+
diff --git a/src/USER-PTM/polar.cpp b/src/USER-PTM/polar.cpp
new file mode 100644
index 0000000000..fdb759a1f3
--- /dev/null
+++ b/src/USER-PTM/polar.cpp
@@ -0,0 +1,337 @@
+/*******************************************************************************
+ * -/_|:|_|_\-
+ *
+ * This code is a modification of D.L. Theobald's QCP rotation code.
+ * It has been adapted to calculate the polar decomposition of a 3x3 matrix
+ * Adaption by P.M. Larsen
+ *
+ * Original Author(s): Douglas L. Theobald
+ * Department of Biochemistry
+ * MS 009
+ * Brandeis University
+ * 415 South St
+ * Waltham, MA 02453
+ * USA
+ *
+ * dtheobald@brandeis.edu
+ *
+ * Pu Liu
+ * Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
+ * 665 Stockton Drive
+ * Exton, PA 19341
+ * USA
+ *
+ * pliu24@its.jnj.com
+ *
+ *
+ * If you use this QCP rotation calculation method in a publication, please
+ * reference:
+ *
+ * Douglas L. Theobald (2005)
+ * "Rapid calculation of RMSD using a quaternion-based characteristic
+ * polynomial."
+ * Acta Crystallographica A 61(4):478-480.
+ *
+ * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
+ * "Fast determination of the optimal rotational matrix for macromolecular
+ * superpositions."
+ * Journal of Computational Chemistry 31(7):1561-1563.
+ *
+ *
+ * Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without modification, are permitted
+ * provided that the following conditions are met:
+ *
+ * * Redistributions of source code must retain the above copyright notice, this list of
+ * conditions and the following disclaimer.
+ * * Redistributions in binary form must reproduce the above copyright notice, this list
+ * of conditions and the following disclaimer in the documentation and/or other materials
+ * provided with the distribution.
+ * * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to
+ * endorse or promote products derived from this software without specific prior written
+ * permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Source: started anew.
+ *
+ * Change History:
+ * 2009/04/13 Started source
+ * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr
+ * If trying all rows of the adjoint still gives too small
+ * qsqr, then just return identity matrix. (DLT)
+ * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct()
+ * invalid mem access
+ * 2011/02/21 Made CenterCoords use weights
+ * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h
+ * Also changed some functions to static
+ * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error
+ * 2012/07/26 minor changes to comments and main.c, more info (v.1.4)
+ *
+ * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
+ * for use in Polyhedral Template Matching.
+ *
+ ******************************************************************************/
+
+#include <cmath>
+#include <algorithm>
+#include <string.h>
+#include "quat.h"
+
+
+static void matmul_3x3(double* A, double* x, double* b)
+{
+ b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
+ b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6];
+ b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6];
+
+ b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7];
+ b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7];
+ b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7];
+
+ b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8];
+ b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8];
+ b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8];
+}
+
+static double matrix_determinant_3x3(double* A)
+{
+ return A[0] * (A[4]*A[8] - A[5]*A[7])
+ - A[1] * (A[3]*A[8] - A[5]*A[6])
+ + A[2] * (A[3]*A[7] - A[4]*A[6]);
+}
+
+static void flip_matrix(double* A)
+{
+ for (int i=0;i<9;i++)
+ A[i] = -A[i];
+}
+
+static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt)
+{
+ const double evecprec = 1e-6;
+ const double evalprec = 1e-11;
+
+ double Sxx = A[0], Sxy = A[1], Sxz = A[2],
+ Syx = A[3], Syy = A[4], Syz = A[5],
+ Szx = A[6], Szy = A[7], Szz = A[8];
+
+ double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz,
+ Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz,
+ Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx;
+
+ double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2;
+
+ double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
+ double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
+ double SxzpSzx = Sxz + Szx;
+ double SyzpSzy = Syz + Szy;
+ double SxypSyx = Sxy + Syx;
+ double SyzmSzy = Syz - Szy;
+ double SxzmSzx = Sxz - Szx;
+ double SxymSyx = Sxy - Syx;
+ double SxxpSyy = Sxx + Syy;
+ double SxxmSyy = Sxx - Syy;
+ double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
+
+ double C[3];
+ C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
+ + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
+ + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz))
+ + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz));
+
+ C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz);
+ C[2] = -2.0 * fnorm_squared;
+
+ //Newton-Raphson
+ double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0;
+ if (mxEigenV > evalprec)
+ {
+ for (int i=0;i<50;i++)
+ {
+ double oldg = mxEigenV;
+ double x2 = mxEigenV*mxEigenV;
+ double b = (x2 + C[2])*mxEigenV;
+ double a = b + C[1];
+ double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a));
+ mxEigenV -= delta;
+ if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
+ break;
+ }
+ }
+ else
+ {
+ mxEigenV = 0.0;
+ }
+
+ (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV));
+
+ double a11 = SxxpSyy + Szz - mxEigenV;
+ double a12 = SyzmSzy;
+ double a13 = -SxzmSzx;
+ double a14 = SxymSyx;
+
+ double a21 = SyzmSzy;
+ double a22 = SxxmSyy - Szz -mxEigenV;
+ double a23 = SxypSyx;
+ double a24 = SxzpSzx;
+
+ double a31 = a13;
+ double a32 = a23;
+ double a33 = Syy - Sxx - Szz - mxEigenV;
+ double a34 = SyzpSzy;
+
+ double a41 = a14;
+ double a42 = a24;
+ double a43 = a34;
+ double a44 = Szz - SxxpSyy - mxEigenV;
+
+ double a3344_4334 = a33 * a44 - a43 * a34;
+ double a3244_4234 = a32 * a44 - a42 * a34;
+ double a3243_4233 = a32 * a43 - a42 * a33;
+ double a3143_4133 = a31 * a43 - a41 * a33;
+ double a3144_4134 = a31 * a44 - a41 * a34;
+ double a3142_4132 = a31 * a42 - a41 * a32;
+ double a1324_1423 = a13 * a24 - a14 * a23;
+ double a1224_1422 = a12 * a24 - a14 * a22;
+ double a1223_1322 = a12 * a23 - a13 * a22;
+ double a1124_1421 = a11 * a24 - a14 * a21;
+ double a1123_1321 = a11 * a23 - a13 * a21;
+ double a1122_1221 = a11 * a22 - a12 * a21;
+
+ double q[4][4];
+ q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233;
+ q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
+ q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132;
+ q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132;
+
+ q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
+ q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133;
+ q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
+ q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132;
+
+ q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
+ q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321;
+ q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
+ q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221;
+
+ q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
+ q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321;
+ q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
+ q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
+
+ double qsqr[4];
+ for (int i=0;i<4;i++)
+ qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3];
+
+ int bi = 0;
+ double max = 0;
+ for (int i=0;i<4;i++)
+ {
+ if (qsqr[i] > max)
+ {
+ bi = i;
+ max = qsqr[i];
+ }
+ }
+
+ bool too_small = false;
+ if (qsqr[bi] < evecprec)
+ {
+ //if qsqr is still too small, return the identity rotation.
+ q[bi][0] = 1;
+ q[bi][1] = 0;
+ q[bi][2] = 0;
+ q[bi][3] = 0;
+ too_small = true;
+ }
+ else
+ {
+ double normq = sqrt(qsqr[bi]);
+ q[bi][0] /= normq;
+ q[bi][1] /= normq;
+ q[bi][2] /= normq;
+ q[bi][3] /= normq;
+ }
+
+ memcpy(qopt, q[bi], 4 * sizeof(double));
+ return !too_small;
+}
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P)
+{
+ double A[9];
+ memcpy(A, _A, 9 * sizeof(double));
+
+ double det = matrix_determinant_3x3(A);
+ if (det < 0)
+ flip_matrix(A);
+
+ double q[4];
+ double nrmsdsq = 0;
+ optimal_quaternion(A, true, -1, &nrmsdsq, q);
+ q[0] = -q[0];
+ quaternion_to_rotation_matrix(q, U);
+
+ if (det < 0)
+ flip_matrix(U);
+
+ double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]};
+
+ if (right_sided)
+ matmul_3x3(UT, _A, P);
+ else
+ matmul_3x3(_A, UT, P);
+
+ return 0;
+}
+
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation)
+{
+ A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0;
+
+ for (int i = 0; i < num; ++i)
+ {
+ double x1 = coords1[i][0];
+ double y1 = coords1[i][1];
+ double z1 = coords1[i][2];
+
+ double x2 = coords2[permutation[i]][0];
+ double y2 = coords2[permutation[i]][1];
+ double z2 = coords2[permutation[i]][2];
+
+ A[0] += x1 * x2;
+ A[1] += x1 * y2;
+ A[2] += x1 * z2;
+
+ A[3] += y1 * x2;
+ A[4] += y1 * y2;
+ A[5] += y1 * z2;
+
+ A[6] += z1 * x2;
+ A[7] += z1 * y2;
+ A[8] += z1 * z2;
+ }
+}
+
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U)
+{
+ optimal_quaternion(A, false, E0, p_nrmsdsq, q);
+ quaternion_to_rotation_matrix(q, U);
+ return 0;
+}
+
diff --git a/src/USER-PTM/polar.h b/src/USER-PTM/polar.h
new file mode 100644
index 0000000000..3ec025b806
--- /dev/null
+++ b/src/USER-PTM/polar.h
@@ -0,0 +1,12 @@
+#ifndef POLAR_H
+#define POLAR_H
+
+#include <stdint.h>
+#include <stdbool.h>
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
+
+#endif
+
diff --git a/src/USER-PTM/ptm_constants.h b/src/USER-PTM/ptm_constants.h
new file mode 100644
index 0000000000..f868f51e84
--- /dev/null
+++ b/src/USER-PTM/ptm_constants.h
@@ -0,0 +1,174 @@
+#ifndef PTM_CONSTANTS_H
+#define PTM_CONSTANTS_H
+
+//------------------------------------
+// definitions
+//------------------------------------
+#define PTM_NO_ERROR 0
+
+
+#define PTM_CHECK_FCC (1 << 0)
+#define PTM_CHECK_HCP (1 << 1)
+#define PTM_CHECK_BCC (1 << 2)
+#define PTM_CHECK_ICO (1 << 3)
+#define PTM_CHECK_SC (1 << 4)
+#define PTM_CHECK_DCUB (1 << 5)
+#define PTM_CHECK_DHEX (1 << 6)
+#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)
+#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX)
+
+#define PTM_MATCH_NONE 0
+#define PTM_MATCH_FCC 1
+#define PTM_MATCH_HCP 2
+#define PTM_MATCH_BCC 3
+#define PTM_MATCH_ICO 4
+#define PTM_MATCH_SC 5
+#define PTM_MATCH_DCUB 6
+#define PTM_MATCH_DHEX 7
+
+#define PTM_ALLOY_NONE 0
+#define PTM_ALLOY_PURE 1
+#define PTM_ALLOY_L10 2
+#define PTM_ALLOY_L12_CU 3
+#define PTM_ALLOY_L12_AU 4
+#define PTM_ALLOY_B2 5
+#define PTM_ALLOY_SIC 6
+
+
+#define PTM_MAX_INPUT_POINTS 35
+#define PTM_MAX_NBRS 16
+#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1)
+#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4
+#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6
+
+
+//------------------------------------
+// number of neighbours
+//------------------------------------
+#define PTM_NUM_NBRS_FCC 12
+#define PTM_NUM_NBRS_HCP 12
+#define PTM_NUM_NBRS_BCC 14
+#define PTM_NUM_NBRS_ICO 12
+#define PTM_NUM_NBRS_SC 6
+#define PTM_NUM_NBRS_DCUB 16
+#define PTM_NUM_NBRS_DHEX 16
+
+#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1)
+#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1)
+#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1)
+#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1)
+#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1)
+#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1)
+#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1)
+
+const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX};
+
+//------------------------------------
+// template structures
+//------------------------------------
+
+//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1
+
+const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. },
+ { 0. , 0.707106781187, 0.707106781187 },
+ { 0. , -0.707106781187, -0.707106781187 },
+ { 0. , 0.707106781187, -0.707106781187 },
+ { 0. , -0.707106781187, 0.707106781187 },
+ { 0.707106781187, 0. , 0.707106781187 },
+ { -0.707106781187, 0. , -0.707106781187 },
+ { 0.707106781187, 0. , -0.707106781187 },
+ { -0.707106781187, 0. , 0.707106781187 },
+ { 0.707106781187, 0.707106781187, 0. },
+ { -0.707106781187, -0.707106781187, 0. },
+ { 0.707106781187, -0.707106781187, 0. },
+ { -0.707106781187, 0.707106781187, 0. } };
+
+const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. },
+ { 0.707106781186, 0. , 0.707106781186 },
+ { -0.235702260395, -0.942809041583, -0.235702260395 },
+ { 0.707106781186, 0.707106781186, 0. },
+ { -0.235702260395, -0.235702260395, -0.942809041583 },
+ { 0. , 0.707106781186, 0.707106781186 },
+ { -0.942809041583, -0.235702260395, -0.235702260395 },
+ { -0.707106781186, 0.707106781186, 0. },
+ { 0. , 0.707106781186, -0.707106781186 },
+ { 0.707106781186, 0. , -0.707106781186 },
+ { 0.707106781186, -0.707106781186, 0. },
+ { -0.707106781186, 0. , 0.707106781186 },
+ { 0. , -0.707106781186, 0.707106781186 } };
+
+const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. },
+ { -0.541451884327, -0.541451884327, -0.541451884327 },
+ { 0.541451884327, 0.541451884327, 0.541451884327 },
+ { 0.541451884327, -0.541451884327, -0.541451884327 },
+ { -0.541451884327, 0.541451884327, 0.541451884327 },
+ { -0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0.541451884327, -0.541451884327, 0.541451884327 },
+ { -0.541451884327, -0.541451884327, 0.541451884327 },
+ { 0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0. , 0. , -1.082903768655 },
+ { 0. , 0. , 1.082903768655 },
+ { 0. , -1.082903768655, 0. },
+ { 0. , 1.082903768655, 0. },
+ { -1.082903768655, 0. , 0. },
+ { 1.082903768655, 0. , 0. } };
+
+const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. },
+ { 0. , 0.525731112119, 0.850650808352 },
+ { 0. , -0.525731112119, -0.850650808352 },
+ { 0. , 0.525731112119, -0.850650808352 },
+ { 0. , -0.525731112119, 0.850650808352 },
+ { -0.525731112119, -0.850650808352, 0. },
+ { 0.525731112119, 0.850650808352, 0. },
+ { 0.525731112119, -0.850650808352, 0. },
+ { -0.525731112119, 0.850650808352, 0. },
+ { -0.850650808352, 0. , -0.525731112119 },
+ { 0.850650808352, 0. , 0.525731112119 },
+ { 0.850650808352, 0. , -0.525731112119 },
+ { -0.850650808352, 0. , 0.525731112119 } };
+
+const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. },
+ { 0. , 0. , -1. },
+ { 0. , 0. , 1. },
+ { 0. , -1. , 0. },
+ { 0. , 1. , 0. },
+ { -1. , 0. , 0. },
+ { 1. , 0. , 0. } };
+
+const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, -0.782983254107, 0. },
+ { -0.782983254107, 0. , -0.782983254107 },
+ { 0. , -0.782983254107, -0.782983254107 },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. } };
+
+const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.260994418036, -1.043977672142, -0.260994418036 },
+ { -1.043977672142, -0.260994418036, -0.260994418036 },
+ { -0.260994418036, -0.260994418036, -1.043977672142 },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 } };
+#endif
+
diff --git a/src/USER-PTM/ptm_functions.h b/src/USER-PTM/ptm_functions.h
new file mode 100644
index 0000000000..69141a37c4
--- /dev/null
+++ b/src/USER-PTM/ptm_functions.h
@@ -0,0 +1,27 @@
+#ifndef PTM_FUNCTIONS_H
+#define PTM_FUNCTIONS_H
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "initialize_data.h"
+#include "ptm_constants.h"
+
+
+//------------------------------------
+// function declarations
+//------------------------------------
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
diff --git a/src/USER-PTM/quat.cpp b/src/USER-PTM/quat.cpp
new file mode 100644
index 0000000000..f55aff3d2b
--- /dev/null
+++ b/src/USER-PTM/quat.cpp
@@ -0,0 +1,396 @@
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+
+
+#define SIGN(x) (x >= 0 ? 1 : -1)
+#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
+#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
+
+
+#define SQRT_2 1.4142135623730951454746218587388284504414
+#define HALF_SQRT_2 0.7071067811865474617150084668537601828575
+
+#define PHI 1.6180339887498949025257388711906969547272
+#define HALF_PHI 0.8090169943749474512628694355953484773636
+
+#define INV_PHI 0.6180339887498947915034364086750429123640
+#define HALF_INV_PHI 0.3090169943749473957517182043375214561820
+
+#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089
+#define SQRT_2_3 0.8164965809277260344600790631375275552273
+#define SQRT_1_6 0.4082482904638630172300395315687637776136
+
+
+double generator_cubic[24][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 },
+ {HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {0, HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, HALF_SQRT_2, HALF_SQRT_2 },
+ {0, -HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, -HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } };
+
+double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 } };
+
+double generator_hcp[6][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6},
+ {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6},
+ {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} };
+
+double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5} };
+
+double generator_icosahedral[60][4] = { {1, 0, 0, 0},
+ {HALF_PHI, -HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, -HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, HALF_INV_PHI},
+ {HALF_PHI, 0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, 0, -HALF_INV_PHI, 0.5},
+ {HALF_PHI, -HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, 0.5},
+ {HALF_PHI, HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0.5, 0, HALF_INV_PHI},
+ {0.5, HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, HALF_PHI, HALF_INV_PHI, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, 0.5, 0.5, -0.5},
+ {0.5, 0.5, -0.5, 0.5},
+ {0.5, 0.5, -0.5, -0.5},
+ {0.5, HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, 0, HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, HALF_PHI, HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, HALF_INV_PHI},
+ {0.5, -HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, -HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, -0.5, 0.5, 0.5},
+ {0.5, -0.5, 0.5, -0.5},
+ {0.5, -0.5, -0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0.5, -HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, -HALF_PHI, HALF_INV_PHI, 0},
+ {HALF_INV_PHI, -HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, 0, -0.5, -HALF_PHI},
+ {HALF_INV_PHI, -0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, 0, 0.5, -HALF_PHI},
+ {HALF_INV_PHI, -HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, -0.5, HALF_PHI, 0},
+ {HALF_INV_PHI, 0, -0.5, HALF_PHI},
+ {HALF_INV_PHI, HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0, 0.5, HALF_PHI},
+ {HALF_INV_PHI, 0.5, HALF_PHI, 0},
+ {0, 1, 0, 0},
+ {0, HALF_PHI, -0.5, HALF_INV_PHI},
+ {0, HALF_PHI, -0.5, -HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, -HALF_INV_PHI},
+ {0, 0.5, HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, HALF_INV_PHI, HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, HALF_PHI},
+ {0, HALF_INV_PHI, -HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, -HALF_PHI, -0.5},
+ {0, HALF_INV_PHI, HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, HALF_PHI, -0.5},
+ {0, 0, 1, 0},
+ {0, 0, 0, 1} };
+
+static void quat_rot(double* r, double* a, double* b)
+{
+ b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]);
+ b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]);
+ b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]);
+ b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]);
+}
+
+static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q)
+{
+ double max = 0.0;
+ int i = 0, bi = -1;
+ for (i=0;i<num_generators;i++)
+ {
+ double* g = generator[i];
+ double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]);
+ if (t > max)
+ {
+ max = t;
+ bi = i;
+ }
+ }
+
+ double f[4];
+ quat_rot(q, generator[bi], f);
+ memcpy(q, &f, 4 * sizeof(double));
+ if (q[0] < 0)
+ {
+ q[0] = -q[0];
+ q[1] = -q[1];
+ q[2] = -q[2];
+ q[3] = -q[3];
+ }
+
+ return bi;
+}
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q);
+}
+
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q);
+}
+
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q);
+}
+
+int rotate_quaternion_into_hcp_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q);
+}
+
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q);
+}
+
+double quat_dot(double* a, double* b)
+{
+ return a[0] * b[0]
+ + a[1] * b[1]
+ + a[2] * b[2]
+ + a[3] * b[3];
+}
+
+double quat_size(double* q)
+{
+ return sqrt(quat_dot(q, q));
+}
+
+void normalize_quaternion(double* q)
+{
+ double size = quat_size(q);
+
+ q[0] /= size;
+ q[1] /= size;
+ q[2] /= size;
+ q[3] /= size;
+}
+
+void rotation_matrix_to_quaternion(double* u, double* q)
+{
+ double r11 = u[0];
+ double r12 = u[1];
+ double r13 = u[2];
+ double r21 = u[3];
+ double r22 = u[4];
+ double r23 = u[5];
+ double r31 = u[6];
+ double r32 = u[7];
+ double r33 = u[8];
+
+ q[0] = (1.0 + r11 + r22 + r33) / 4.0;
+ q[1] = (1.0 + r11 - r22 - r33) / 4.0;
+ q[2] = (1.0 - r11 + r22 - r33) / 4.0;
+ q[3] = (1.0 - r11 - r22 + r33) / 4.0;
+
+ q[0] = sqrt(MAX(0, q[0]));
+ q[1] = sqrt(MAX(0, q[1]));
+ q[2] = sqrt(MAX(0, q[2]));
+ q[3] = sqrt(MAX(0, q[3]));
+
+ double m0 = MAX(q[0], q[1]);
+ double m1 = MAX(q[2], q[3]);
+ double max = MAX(m0, m1);
+
+ int i = 0;
+ for (i=0;i<4;i++)
+ if (q[i] == max)
+ break;
+
+ if (i == 0)
+ {
+ q[1] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r13 - r31);
+ q[3] *= SIGN(r21 - r12);
+ }
+ else if (i == 1)
+ {
+ q[0] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r13 + r31);
+ }
+ else if (i == 2)
+ {
+ q[0] *= SIGN(r13 - r31);
+ q[1] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r32 + r23);
+ }
+ else if (i == 3)
+ {
+ q[0] *= SIGN(r21 - r12);
+ q[1] *= SIGN(r31 + r13);
+ q[2] *= SIGN(r32 + r23);
+ }
+
+ normalize_quaternion(q);
+}
+
+void quaternion_to_rotation_matrix(double* q, double* u)
+{
+ double a = q[0];
+ double b = q[1];
+ double c = q[2];
+ double d = q[3];
+
+ u[0] = a*a + b*b - c*c - d*d;
+ u[1] = 2*b*c - 2*a*d;
+ u[2] = 2*b*d + 2*a*c;
+
+ u[3] = 2*b*c + 2*a*d;
+ u[4] = a*a - b*b + c*c - d*d;
+ u[5] = 2*c*d - 2*a*b;
+
+ u[6] = 2*b*d - 2*a*c;
+ u[7] = 2*c*d + 2*a*b;
+ u[8] = a*a - b*b - c*c + d*d;
+}
+
+double quat_quick_misorientation(double* q1, double* q2)
+{
+ double t = quat_dot(q1, q2);
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_misorientation(double* q1, double* q2)
+{
+ return acos(quat_quick_misorientation(q1, q2));
+}
+
+
+double quat_quick_disorientation_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_hcp(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_hcp_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_hcp(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_hcp(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1));
+}
+
+double quat_quick_disorientation_icosahedral(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_icosahedral_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_icosahedral(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_icosahedral(q0, q1));
+}
+
diff --git a/src/USER-PTM/quat.h b/src/USER-PTM/quat.h
new file mode 100644
index 0000000000..725086322c
--- /dev/null
+++ b/src/USER-PTM/quat.h
@@ -0,0 +1,32 @@
+#ifndef QUAT_H
+#define QUAT_H
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
+int rotate_quaternion_into_hcp_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q);
+
+void normalize_quaternion(double* q);
+void quaternion_to_rotation_matrix(double* q, double* U);
+void rotation_matrix_to_quaternion(double* u, double* q);
+double quat_dot(double* a, double* b);
+double quat_quick_misorientation(double* q1, double* q2);
+double quat_misorientation(double* q1, double* q2);
+
+double quat_quick_disorientation_cubic(double* q0, double* q1);
+double quat_disorientation_cubic(double* q0, double* q1);
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_quick_disorientation_hcp(double* q0, double* q1);
+double quat_disorientation_hcp(double* q0, double* q1);
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_quick_disorientation_icosahedral(double* q0, double* q1);
+double quat_disorientation_icosahedral(double* q0, double* q1);
+
+#endif
+
+
+
+
diff --git a/src/USER-PTM/structure_matcher.cpp b/src/USER-PTM/structure_matcher.cpp
new file mode 100644
index 0000000000..dad8e3599a
--- /dev/null
+++ b/src/USER-PTM/structure_matcher.cpp
@@ -0,0 +1,294 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "convex_hull_incremental.h"
+#include "canonical_coloured.h"
+#include "graph_data.h"
+#include "graph_tools.h"
+#include "normalize_vertices.h"
+#include "polar.h"
+#include "structure_matcher.h"
+#include "ptm_constants.h"
+
+
+static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
+ double G1, double G2, double E0, double* q, double* p_scale)
+{
+ double A0[9];
+ InnerProduct(A0, num_points, ideal_points, normalized, mapping);
+
+ double nrmsdsq, rot[9];
+ FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot);
+
+ double k0 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ for (int j=0;j<3;j++)
+ {
+ double v = 0.0;
+ for (int k=0;k<3;k++)
+ v += rot[j*3+k] * ideal_points[i][k];
+
+ k0 += v * normalized[mapping[i]][j];
+ }
+ }
+
+ double scale = k0 / G2;
+ *p_scale = scale;
+ return sqrt(fabs(G1 - scale*k0) / num_points);
+}
+
+static void check_graphs( const refdata_t* s,
+ uint64_t hash,
+ int8_t* canonical_labelling,
+ double (*normalized)[3],
+ result_t* res)
+{
+ int num_points = s->num_nbrs + 1;
+ const double (*ideal_points)[3] = s->points;
+ int8_t inverse_labelling[PTM_MAX_POINTS];
+ int8_t mapping[PTM_MAX_POINTS];
+
+ for (int i=0; i<num_points; i++)
+ inverse_labelling[ canonical_labelling[i] ] = i;
+
+ double G1 = 0, G2 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ double x1 = ideal_points[i][0];
+ double y1 = ideal_points[i][1];
+ double z1 = ideal_points[i][2];
+
+ double x2 = normalized[i][0];
+ double y2 = normalized[i][1];
+ double z2 = normalized[i][2];
+
+ G1 += x1 * x1 + y1 * y1 + z1 * z1;
+ G2 += x2 * x2 + y2 * y2 + z2 * z2;
+ }
+ double E0 = (G1 + G2) / 2;
+
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ if (hash != s->graphs[i].hash)
+ continue;
+
+ graph_t* gref = &s->graphs[i];
+ for (int j = 0;j<gref->num_automorphisms;j++)
+ {
+ for (int k=0;k<num_points;k++)
+ mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ];
+
+ double q[4], scale = 0;
+ double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale);
+ if (rmsd < res->rmsd)
+ {
+ res->rmsd = rmsd;
+ res->scale = scale;
+ res->ref_struct = s;
+ memcpy(res->q, q, 4 * sizeof(double));
+ memcpy(res->mapping, mapping, sizeof(int8_t) * num_points);
+ }
+ }
+ }
+}
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res)
+{
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != s->num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree);
+ if (max_degree > s->max_degree)
+ return PTM_NO_ERROR;
+
+ if (s->type == PTM_MATCH_SC)
+ for (int i = 0;i<s->num_nbrs;i++)
+ if (degree[i] != 4)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(s->num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ check_graphs(s, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_fcc.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_fcc.max_degree;
+
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_dcub.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_dcub.max_degree;
+
+
+ int8_t facets[PTM_MAX_FACETS][3];
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ //check for facets with multiple inner atoms
+ bool inverted[4] = {false, false, false, false};
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int n = 0;
+ for (int j=0;j<3;j++)
+ {
+ if (facets[i][j] <= 3)
+ {
+ inverted[facets[i][j]] = true;
+ n++;
+ }
+ }
+ if (n > 1)
+ return PTM_NO_ERROR;
+ }
+
+ int num_inverted = 0;
+ for (int i=0;i<4;i++)
+ num_inverted += inverted[i] ? 1 : 0;
+
+ if (ch->num_facets != num_facets + 2 * num_inverted)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ int num_found = 0;
+ int8_t toadd[4][3];
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+ if (a <= 3 || b <= 3 || c <= 3)
+ continue;
+
+ int i0 = (a - 4) / 3;
+ int i1 = (b - 4) / 3;
+ int i2 = (c - 4) / 3;
+
+ if (i0 == i1 && i0 == i2)
+ {
+ if (num_found + num_inverted >= 4)
+ return PTM_NO_ERROR;
+
+ toadd[num_found][0] = a;
+ toadd[num_found][1] = b;
+ toadd[num_found][2] = c;
+ num_found++;
+
+ memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t));
+ ch->num_facets--;
+ i--;
+ }
+ }
+
+ if (num_found + num_inverted != 4)
+ return PTM_NO_ERROR;
+
+ for (int i=0;i<num_found;i++)
+ {
+ int a = toadd[i][0];
+ int b = toadd[i][1];
+ int c = toadd[i][2];
+
+ int i0 = (a - 4) / 3;
+
+ facets[ch->num_facets][0] = i0;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = i0;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = i0;
+ ch->num_facets++;
+ }
+
+ _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res);
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/USER-PTM/structure_matcher.h b/src/USER-PTM/structure_matcher.h
new file mode 100644
index 0000000000..25e80a94e1
--- /dev/null
+++ b/src/USER-PTM/structure_matcher.h
@@ -0,0 +1,21 @@
+#ifndef STRUCTURE_MATCHER_H
+#define STRUCTURE_MATCHER_H
+
+#include "initialize_data.h"
+#include "ptm_constants.h"
+
+typedef struct
+{
+ double rmsd;
+ double scale;
+ double q[4]; //rotation in quaternion form (rigid body transformation)
+ int8_t mapping[PTM_MAX_POINTS];
+ const refdata_t* ref_struct;
+} result_t;
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res);
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+
+#endif
+
--
GitLab
From 83b6d6ae960ce0e7f8edb32d95edb3540ae5f764 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Wed, 12 Sep 2018 17:47:16 +0300
Subject: [PATCH 262/332] small modifications of potential #839
---
doc/src/pair_coul_shield.txt | 8 ++++-
doc/src/pair_ilp_graphene_hbn.txt | 20 ++++++-----
doc/src/pair_kolmogorov_crespi_full.txt | 34 +++++++++++--------
potentials/BNCH.ILP | 2 +-
potentials/CH.KC | 4 +--
potentials/CH_taper.KC | 10 ++++++
src/USER-MISC/pair_ilp_graphene_hbn.cpp | 27 +++++++--------
src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 27 +++++++--------
8 files changed, 76 insertions(+), 56 deletions(-)
create mode 100644 potentials/CH_taper.KC
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 19f69688d5..517cb47740 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -38,7 +38,7 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
-"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
+"(Leven1)"_#Leven2, "(Leven2)"_#Leven3 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
@@ -82,5 +82,11 @@ LAMMPS"_Section_start.html#start_2_3 section for more info.
:line
+:link(Leven2)
+[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+:link(Leven3)
+[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+
:link(Maaravi1)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 127b8e9103..dd175b3b4f 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -31,7 +31,7 @@ pair_coeff 2 2 coul/shield 0.69 :pre
[Description:]
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
-potential (ILP) potential as described in "(Leven)"_#Leven and
+potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven and
"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
in "(Kolmogorov)"_#Kolmogorov2.
@@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2.
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
-equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
+equation can be found in "(Leven)"_#Leven1 and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
@@ -62,9 +62,10 @@ are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang.
-These parameters provide a good description in both short- and long-range interaction regime.
-While the old ILP parameters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for long-range interaction regime.
-This feature is essential for simulations in high pressure regime (i.e., interlayer distance smaller than the equilibrium distance).
+These parameters provide a good description in both short- and long-range interaction regimes.
+While the old ILP parameters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are
+only suitable for long-range interaction regime. This feature is essential for simulations
+in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance).
The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
@@ -110,14 +111,17 @@ units, if your simulation does not use {metal} units.
:line
+:link(Leven1)
+[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
:link(Leven)
-[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
+[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi2)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
:link(Kolmogorov2)
-[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
:link(Ouyang)
-[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
+[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 10bb8a5224..09f0aaaed0 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
-pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
+pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
-pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
-pair_coeff * * rebo CH.airebo C C
-pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
+pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
+pair_coeff * * rebo CH.airebo C H
+pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
[Description:]
@@ -38,24 +38,30 @@ forces and to include all the pairs to build the neighbor list for
calculating the normals. Energies are shifted so that they go
continuously to zero at the cutoff assuming that the exponential part of
{Vij} (first term) decays sufficiently fast. This shift is achieved by
-the last term in the equation for {Vij} above.
+the last term in the equation for {Vij} above. This is essential only
+when the tapper function is turned off. The formula of taper function
+can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
NOTE: This potential is intended for interactions between two different
graphene layers. Therefore, to avoid interaction within the same layers,
each layer should have a separate molecule id and is recommended to use
"full" atom style in the data file.
-The parameter file (e.g. CC.KC), is intended for use with {metal}
+The parameter file (e.g. CH.KC), is intended for use with {metal}
"units"_units.html, with energies in meV. Two additional parameters, {S},
and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
-NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC) is presented in "(Ouyang)"_#Ouyang.
-The parameters in CH.KC provides a good description in both short- and long-range interaction regime.
-While the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime.
-This feature is essential for simulations in high pressure regime (i.e., interlayer distance smaller than the equilibrium distance).
-The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang.
+NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC (without the taper function)
+and CH_taper.KC (with the taper function) are presented in "(Ouyang)"_#Ouyang1.
+The energy for the KC potential with the taper function goes continuously to zero at the cutoff.
+The parameters in both CH.KC and CH_taper.KC provide a good description in
+both short- and long-range interaction regimes. While the original parameters (CC.KC)
+published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime.
+This feature is essential for simulations in high pressure regime
+(i.e., the interlayer distance is smaller than the equilibrium distance).
+The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
@@ -81,7 +87,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
-The CC.KC potential file provided with LAMMPS (see the potentials
+The CH.KC potential file provided with LAMMPS (see the potentials
folder) are parameterized for metal units. You can use this potential
with any LAMMPS units, but you would need to create your own custom
CC.KC potential file with all coefficients converted to the appropriate
@@ -102,5 +108,5 @@ units.
:link(Kolmogorov1)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
-:link(Ouyang)
-[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
+:link(Ouyang1)
+[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
diff --git a/potentials/BNCH.ILP b/potentials/BNCH.ILP
index 3f38b5e35a..6ca56ca186 100644
--- a/potentials/BNCH.ILP
+++ b/potentials/BNCH.ILP
@@ -1,6 +1,6 @@
# Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions
#
-# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
+# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
diff --git a/potentials/CH.KC b/potentials/CH.KC
index 2005472395..1b4f7503ea 100644
--- a/potentials/CH.KC
+++ b/potentials/CH.KC
@@ -1,6 +1,6 @@
-# Refined parameters for Kolmogorov-Crespi Potential
+# Refined parameters for Kolmogorov-Crespi Potential without taper function
#
-# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018).
+# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
#
# z0 C0 C2 C4 C delta lambda A S rcut
C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0
diff --git a/potentials/CH_taper.KC b/potentials/CH_taper.KC
new file mode 100644
index 0000000000..0f08b2e6dd
--- /dev/null
+++ b/potentials/CH_taper.KC
@@ -0,0 +1,10 @@
+# Refined parameters for Kolmogorov-Crespi Potential with taper function
+#
+# Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018).
+#
+# z0 C0 C2 C4 C delta lambda A S rcut
+C C 3.416084 20.021583 10.9055107 4.2756354 1.0010836E-2 0.8447122 2.9360584 14.3132588 1.0 2.0
+C H 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 1.5
+H H 2.187478 3.915802E-5 5.0896431E-5 3.6657827 1.5373722446 0.9633581 0.4249989 1.570737E-4 1.0 1.2
+H C 2.849054 72.557245 1.0164169E-2 65.923312 8.7962504E-5 0.3349237 3.0402632 14.7533201 1.0 2.2
+
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 30ee2e7a5a..7c637e4faf 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -249,11 +249,9 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
f[i][2] += fkcz - fprod1[2]*Tap;
- if (newton_pair || j < nlocal) {
- f[j][0] -= fkcx + fprod2[0]*Tap;
- f[j][1] -= fkcy + fprod2[1]*Tap;
- f[j][2] -= fkcz + fprod2[2]*Tap;
- }
+ f[j][0] -= fkcx + fprod2[0]*Tap;
+ f[j][1] -= fkcy + fprod2[1]*Tap;
+ f[j][2] -= fkcz + fprod2[2]*Tap;
// calculate the forces acted on the neighbors of atom i from atom j
ILP_neighs_i = ILP_firstneigh[i];
@@ -274,15 +272,13 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag)
for (ll = 0; ll < ILP_numneigh[j]; ll++) {
l = ILP_neighs_j[ll];
if (l == j) continue;
- if (newton_pair || l < nlocal) {
- // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
- dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
- dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
- dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
- f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
- f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
- f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
- }
+ // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
+ dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
+ dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
+ dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
+ f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
+ f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
+ f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
if (eflag) {
@@ -729,7 +725,8 @@ void PairILPGrapheneHBN::ILP_neigh()
ILP_firstneigh[i] = neighptr;
ILP_numneigh[i] = n;
- if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
+ if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration");
+ if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index be0e81d48d..93a2376c33 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -249,11 +249,9 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
f[i][0] += fkcx - fprod1[0]*Tap;
f[i][1] += fkcy - fprod1[1]*Tap;
f[i][2] += fkcz - fprod1[2]*Tap;
- if (newton_pair || j < nlocal) {
- f[j][0] -= fkcx + fprod2[0]*Tap;
- f[j][1] -= fkcy + fprod2[1]*Tap;
- f[j][2] -= fkcz + fprod2[2]*Tap;
- }
+ f[j][0] -= fkcx + fprod2[0]*Tap;
+ f[j][1] -= fkcy + fprod2[1]*Tap;
+ f[j][2] -= fkcz + fprod2[2]*Tap;
// calculate the forces acted on the neighbors of atom i from atom j
KC_neighs_i = KC_firstneigh[i];
@@ -274,15 +272,13 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag)
for (ll = 0; ll < KC_numneigh[j]; ll++) {
l = KC_neighs_j[ll];
if (l == j) continue;
- if (newton_pair || l < nlocal) {
- // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
- dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
- dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
- dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
- f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
- f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
- f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
- }
+ // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j
+ dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz;
+ dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz;
+ dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz;
+ f[l][0] += (-prodnorm2*dprodnorm2[0]*fpair2)*Tap;
+ f[l][1] += (-prodnorm2*dprodnorm2[1]*fpair2)*Tap;
+ f[l][2] += (-prodnorm2*dprodnorm2[2]*fpair2)*Tap;
}
if (eflag) {
@@ -734,7 +730,8 @@ void PairKolmogorovCrespiFull::KC_neigh()
KC_firstneigh[i] = neighptr;
KC_numneigh[i] = n;
- if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
+ if (n == 0) error->all(FLERR,"Could not build neighbor list to calculate normals, please check your configuration");
+ if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please check your configuration");
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
--
GitLab
From 01beaf38a1162c0d81ad9591b490782b73997179 Mon Sep 17 00:00:00 2001
From: oywg11 <w.g.ouyang@gmail.com>
Date: Wed, 12 Sep 2018 21:51:57 +0300
Subject: [PATCH 263/332] small modifications for potential #839
---
doc/src/pair_coul_shield.txt | 10 +++++-----
doc/src/pair_ilp_graphene_hbn.txt | 10 +++++-----
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 517cb47740..c6eb7bf7a1 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -38,7 +38,7 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
-"(Leven1)"_#Leven2, "(Leven2)"_#Leven3 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
+"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
@@ -82,11 +82,11 @@ LAMMPS"_Section_start.html#start_2_3 section for more info.
:line
-:link(Leven2)
-[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
-
:link(Leven3)
-[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+:link(Leven4)
+[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi1)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index dd175b3b4f..d5d8a29fbe 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -31,7 +31,7 @@ pair_coeff 2 2 coul/shield 0.69 :pre
[Description:]
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
-potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven and
+potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven2 and
"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
in "(Kolmogorov)"_#Kolmogorov2.
@@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2.
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
-equation can be found in "(Leven)"_#Leven1 and "(Maaravi)"_#Maaravi2.
+equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
@@ -112,10 +112,10 @@ units, if your simulation does not use {metal} units.
:line
:link(Leven1)
-[(Leven)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
-:link(Leven)
-[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+:link(Leven2)
+[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
:link(Maaravi2)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
--
GitLab
From e14db00d522bbc7802a648c1844c44ded1417fa1 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 14 Sep 2018 17:31:33 -0600
Subject: [PATCH 264/332] doc link adjustments
---
doc/src/Howto_nemd.txt | 10 +++++-----
doc/src/Howto_thermostat.txt | 10 +++++-----
doc/src/Howto_viscosity.txt | 10 +++++-----
doc/src/fix_nvt_sllod.txt | 10 +++++-----
4 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
index 0a76859dcf..3387611d4e 100644
--- a/doc/src/Howto_nemd.txt
+++ b/doc/src/Howto_nemd.txt
@@ -24,10 +24,10 @@ by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/chunk"_fix_ave_chunk.html command.
-NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
-use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
-generally, for both simple and complex fluids, e.g. molecular systems.
-The latter can be tricky to do correctly.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermosttating generally, for both simple and complex fluids,
+e.g. molecular systems. The latter can be tricky to do correctly.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
@@ -54,6 +54,6 @@ using the "fix flow/gauss"_fix_flow_gauss.html command.
:line
-:link(Daivis2)
+:link(Daivis-nemd)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
index 6a0095e741..ccc9674641 100644
--- a/doc/src/Howto_thermostat.txt
+++ b/doc/src/Howto_thermostat.txt
@@ -43,10 +43,10 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
-NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
-use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
-generally, for both simple and complex fluids, e.g. molecular systems.
-The latter can be tricky to do correctly.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermosttating generally, for both simple and complex fluids,
+e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of "fix
@@ -95,6 +95,6 @@ temperature compute is used for default thermodynamic output.
:line
-:link(Daivis2)
+:link(Daivis-thermostat)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
index adfabf8279..0b3892c1ad 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/src/Howto_viscosity.txt
@@ -37,10 +37,10 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
-NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
-use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
-generally, for both simple and complex fluids, e.g. molecular systems.
-The latter can be tricky to do correctly.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermosttating generally, for both simple and complex fluids,
+e.g. molecular systems. The latter can be tricky to do correctly.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html
@@ -139,6 +139,6 @@ with time at sufficiently long times.
:line
-:link(Daivis2)
+:link(Daivis-viscosity)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 67c4d76417..fbc3143af3 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -63,10 +63,10 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the "fix nvt"_fix_nh.html command.
-NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis2 discusses
-use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating
-generally, for both simple and complex fluids, e.g. molecular systems.
-The latter can be tricky to do correctly.
+NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod
+discusses use of the SLLOD method and non-equilibrium MD (NEMD)
+thermosttating generally, for both simple and complex fluids,
+e.g. molecular systems. The latter can be tricky to do correctly.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
@@ -183,6 +183,6 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.
:link(Daivis)
[(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006).
-:link(Daivis2)
+:link(Daivis-sllod)
[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
--
GitLab
From 8fa80081df3513dfd20fb6ab92471b6a451bc55a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Sep 2018 05:08:22 -0400
Subject: [PATCH 265/332] fix typo
---
doc/src/Howto_nemd.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
index 3387611d4e..10139d907c 100644
--- a/doc/src/Howto_nemd.txt
+++ b/doc/src/Howto_nemd.txt
@@ -26,7 +26,7 @@ the "fix ave/chunk"_fix_ave_chunk.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
-thermosttating generally, for both simple and complex fluids,
+thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
As discussed in the previous section on non-orthogonal simulation
--
GitLab
From 39ee7876c48dcdf1367b05f7f184f2f88048618a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Sep 2018 05:09:23 -0400
Subject: [PATCH 266/332] fix typo
---
doc/src/Howto_thermostat.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
index ccc9674641..9f7e2f3000 100644
--- a/doc/src/Howto_thermostat.txt
+++ b/doc/src/Howto_thermostat.txt
@@ -45,7 +45,7 @@ particles.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
-thermosttating generally, for both simple and complex fluids,
+thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
--
GitLab
From 494b1492720bf34c7dee6b9ade18c570c38dcf48 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Sep 2018 05:10:56 -0400
Subject: [PATCH 267/332] fix typo
---
doc/src/Howto_viscosity.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
index 0b3892c1ad..b4e441557d 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/src/Howto_viscosity.txt
@@ -39,7 +39,7 @@ velocity to prevent the fluid from heating up.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
-thermosttating generally, for both simple and complex fluids,
+thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
In both cases, the velocity profile setup in the fluid by this
--
GitLab
From 5f6b5c5400019d1b4e09f0138eb0aac4b789d5fe Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 17 Sep 2018 05:11:59 -0400
Subject: [PATCH 268/332] fix typo
---
doc/src/fix_nvt_sllod.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index fbc3143af3..7a350e48b5 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -65,7 +65,7 @@ implementation used for the "fix nvt"_fix_nh.html command.
NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
-thermosttating generally, for both simple and complex fluids,
+thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
Additional parameters affecting the thermostat are specified by
--
GitLab
From d753c51c450064c5a4ac8a7157fac6ddadb4a0dc Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Mon, 17 Sep 2018 19:44:32 -0600
Subject: [PATCH 269/332] The sna*/atom computes were not destroying SNA
objects. Fixed.
---
src/SNAP/compute_sna_atom.cpp | 5 ++++-
src/SNAP/compute_sna_atom.h | 1 +
src/SNAP/compute_snad_atom.cpp | 2 ++
src/SNAP/compute_snad_atom.h | 1 +
src/SNAP/compute_snav_atom.cpp | 3 +++
src/SNAP/compute_snav_atom.h | 1 +
6 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index a2c1f55788..5ca63a7e85 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -115,7 +115,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal compute sna/atom command");
}
- snaptr = new SNA*[comm->nthreads];
+ nthreads = comm->nthreads;
+ snaptr = new SNA*[nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
@@ -146,6 +147,8 @@ ComputeSNAAtom::~ComputeSNAAtom()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
+ for (int tid = 0; tid<nthreads; tid++)
+ delete snaptr[tid];
delete [] snaptr;
}
diff --git a/src/SNAP/compute_sna_atom.h b/src/SNAP/compute_sna_atom.h
index b22eea71b5..2f6fb18996 100644
--- a/src/SNAP/compute_sna_atom.h
+++ b/src/SNAP/compute_sna_atom.h
@@ -45,6 +45,7 @@ class ComputeSNAAtom : public Compute {
class SNA** snaptr;
double cutmax;
int quadraticflag;
+ int nthreads;
};
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 800d1942e3..da56555055 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -148,6 +148,8 @@ ComputeSNADAtom::~ComputeSNADAtom()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
+ for (int tid = 0; tid<nthreads; tid++)
+ delete snaptr[tid];
delete [] snaptr;
}
diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h
index a33e6047c2..92003a9bc5 100644
--- a/src/SNAP/compute_snad_atom.h
+++ b/src/SNAP/compute_snad_atom.h
@@ -47,6 +47,7 @@ class ComputeSNADAtom : public Compute {
class SNA** snaptr;
double cutmax;
int quadraticflag;
+ int nthreads;
};
}
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 2b823f7b8b..27bfc1bef0 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -142,6 +142,9 @@ ComputeSNAVAtom::~ComputeSNAVAtom()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
+
+ for (int tid = 0; tid<nthreads; tid++)
+ delete snaptr[tid];
delete [] snaptr;
}
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 7d39786ef9..9be5e1d389 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -46,6 +46,7 @@ class ComputeSNAVAtom : public Compute {
double *wjelem;
class SNA** snaptr;
int quadraticflag;
+ int nthreads;
};
}
--
GitLab
From 8dff5fd5d7bed558b28d6bb7e1d620cbad0deaf9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Sep 2018 17:24:10 -0400
Subject: [PATCH 270/332] patch 18Sep18
---
doc/src/Manual.txt | 4 ++--
src/version.h | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 5af157d8ea..ecee17269a 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="5 Sep 2018 version">
+<META NAME="docnumber" CONTENT="18 Sep 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-5 Sep 2018 version :c,h2
+18 Sep 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/src/version.h b/src/version.h
index 0b8c1e8736..469d74fed7 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "5 Sep 2018"
+#define LAMMPS_VERSION "18 Sep 2018"
--
GitLab
From 4bfac61b1a72aa254d0a4831881661457806a97a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Sep 2018 17:41:02 -0400
Subject: [PATCH 271/332] fix typo in gzip support for fix reax/bonds
---
src/REAX/fix_reax_bonds.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index 5273cd1faa..c6c1d309ee 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -53,7 +53,7 @@ FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
if (suffix && strcmp(suffix,".gz") == 0) {
#ifdef LAMMPS_GZIP
char gzip[128];
- snprintf(gzip128,,"gzip -6 > %s",arg[4]);
+ snprintf(gzip,128,"gzip -6 > %s",arg[4]);
#ifdef _WIN32
fp = _popen(gzip,"wb");
#else
--
GitLab
From cda89283aa3c3d5221305515ab5a914feec626ff Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 18 Sep 2018 22:13:17 -0400
Subject: [PATCH 272/332] warn more loudly about REAX and MEAM going away soon
---
src/MEAM/pair_meam.cpp | 4 ++--
src/REAX/pair_reax.cpp | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index b8f5291338..38e8e97810 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -48,8 +48,8 @@ static const char *keywords[] = {
PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp)
{
if (comm->me == 0)
- error->warning(FLERR,"The pair_style meam command is unsupported. "
- "Please use pair_style meam/c instead");
+ error->warning(FLERR,"THE pair_style meam COMMAND IS OBSOLETE AND "
+ "WILL BE REMOVED VERY SOON. PLEASE USE meam/c");
single_enable = 0;
restartinfo = 0;
diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp
index 24083a288a..a430380711 100644
--- a/src/REAX/pair_reax.cpp
+++ b/src/REAX/pair_reax.cpp
@@ -46,8 +46,8 @@ using namespace LAMMPS_NS;
PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp)
{
if (comm->me == 0)
- error->warning(FLERR,"The pair_style reax command is unsupported. "
- "Please switch to pair_style reax/c instead");
+ error->warning(FLERR,"THE pair_style reax COMMAND IS OBSOLETE AND "
+ "WILL BE REMOVED VERY SOON. PLEASE USE reax/c");
single_enable = 0;
restartinfo = 0;
--
GitLab
From c705e8d0e6a3b1a739f2ddf6cd1ee40a3241d40a Mon Sep 17 00:00:00 2001
From: pmla <pete.mahler.larsen@gmail.com>
Date: Wed, 19 Sep 2018 20:46:48 -0400
Subject: [PATCH 273/332] renamed files for LAMMPS build system compatibility
---
src/PTM/compute_ptm_atom.cpp | 307 ++++
src/PTM/compute_ptm_atom.h | 48 +
src/PTM/ptm_alloy_types.cpp | 101 ++
src/PTM/ptm_alloy_types.h | 9 +
src/PTM/ptm_canonical_coloured.cpp | 167 ++
src/PTM/ptm_canonical_coloured.h | 9 +
src/PTM/ptm_constants.h | 174 ++
src/PTM/ptm_convex_hull_incremental.cpp | 363 ++++
src/PTM/ptm_convex_hull_incremental.h | 27 +
src/PTM/ptm_deformation_gradient.cpp | 37 +
src/PTM/ptm_deformation_gradient.h | 142 ++
src/PTM/ptm_functions.h | 27 +
src/PTM/ptm_fundamental_mappings.h | 180 ++
src/PTM/ptm_graph_data.cpp | 2059 +++++++++++++++++++++++
src/PTM/ptm_graph_data.h | 37 +
src/PTM/ptm_graph_tools.cpp | 52 +
src/PTM/ptm_graph_tools.h | 11 +
src/PTM/ptm_index.cpp | 218 +++
src/PTM/ptm_initialize_data.cpp | 71 +
src/PTM/ptm_initialize_data.h | 61 +
src/PTM/ptm_neighbour_ordering.cpp | 203 +++
src/PTM/ptm_neighbour_ordering.h | 13 +
src/PTM/ptm_normalize_vertices.cpp | 55 +
src/PTM/ptm_normalize_vertices.h | 8 +
src/PTM/ptm_polar.cpp | 337 ++++
src/PTM/ptm_polar.h | 12 +
src/PTM/ptm_quat.cpp | 396 +++++
src/PTM/ptm_quat.h | 32 +
src/PTM/ptm_structure_matcher.cpp | 294 ++++
src/PTM/ptm_structure_matcher.h | 21 +
src/PTM/ptm_voronoi_cell.cpp | 1368 +++++++++++++++
src/PTM/ptm_voronoi_cell.h | 324 ++++
src/PTM/ptm_voronoi_config.h | 129 ++
33 files changed, 7292 insertions(+)
create mode 100644 src/PTM/compute_ptm_atom.cpp
create mode 100644 src/PTM/compute_ptm_atom.h
create mode 100644 src/PTM/ptm_alloy_types.cpp
create mode 100644 src/PTM/ptm_alloy_types.h
create mode 100644 src/PTM/ptm_canonical_coloured.cpp
create mode 100644 src/PTM/ptm_canonical_coloured.h
create mode 100644 src/PTM/ptm_constants.h
create mode 100644 src/PTM/ptm_convex_hull_incremental.cpp
create mode 100644 src/PTM/ptm_convex_hull_incremental.h
create mode 100644 src/PTM/ptm_deformation_gradient.cpp
create mode 100644 src/PTM/ptm_deformation_gradient.h
create mode 100644 src/PTM/ptm_functions.h
create mode 100644 src/PTM/ptm_fundamental_mappings.h
create mode 100644 src/PTM/ptm_graph_data.cpp
create mode 100644 src/PTM/ptm_graph_data.h
create mode 100644 src/PTM/ptm_graph_tools.cpp
create mode 100644 src/PTM/ptm_graph_tools.h
create mode 100644 src/PTM/ptm_index.cpp
create mode 100644 src/PTM/ptm_initialize_data.cpp
create mode 100644 src/PTM/ptm_initialize_data.h
create mode 100644 src/PTM/ptm_neighbour_ordering.cpp
create mode 100644 src/PTM/ptm_neighbour_ordering.h
create mode 100644 src/PTM/ptm_normalize_vertices.cpp
create mode 100644 src/PTM/ptm_normalize_vertices.h
create mode 100644 src/PTM/ptm_polar.cpp
create mode 100644 src/PTM/ptm_polar.h
create mode 100644 src/PTM/ptm_quat.cpp
create mode 100644 src/PTM/ptm_quat.h
create mode 100644 src/PTM/ptm_structure_matcher.cpp
create mode 100644 src/PTM/ptm_structure_matcher.h
create mode 100644 src/PTM/ptm_voronoi_cell.cpp
create mode 100644 src/PTM/ptm_voronoi_cell.h
create mode 100644 src/PTM/ptm_voronoi_config.h
diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp
new file mode 100644
index 0000000000..b6b4a9786c
--- /dev/null
+++ b/src/PTM/compute_ptm_atom.cpp
@@ -0,0 +1,307 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed
+under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: PM Larsen (MIT)
+------------------------------------------------------------------------- */
+
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include "atom.h"
+#include "comm.h"
+#include "compute_ptm_atom.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include "ptm_functions.h"
+
+#define MAX_NEIGHBORS 30
+#define NUM_COLUMNS 7
+#define UNKNOWN 0
+#define OTHER 8
+
+using namespace LAMMPS_NS;
+
+static const char cite_user_ptm_package[] =
+ "USER-PTM package:\n\n"
+ "@Article{larsen2016ptm,\n"
+ " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, "
+ "Jakob},\n"
+ " title={Robust structural identification via polyhedral template "
+ "matching},\n"
+ " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n"
+ " year={2016},\n"
+ " number={5},\n"
+ " volume={24},\n"
+ " pages={055007},\n"
+ " DOI = {10.1088/0965-0393/24/5/055007}"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
+ : Compute(lmp, narg, arg), list(NULL), output(NULL) {
+ if (narg != 5)
+ error->all(FLERR, "Illegal compute ptm/atom command");
+
+ char *structures = arg[3];
+ char *ptr = structures;
+
+ const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc",
+ "dcub", "dhex", "all", "default"};
+ int32_t flags[] = {
+ PTM_CHECK_FCC,
+ PTM_CHECK_HCP,
+ PTM_CHECK_BCC,
+ PTM_CHECK_ICO,
+ PTM_CHECK_SC,
+ PTM_CHECK_DCUB,
+ PTM_CHECK_DHEX,
+ PTM_CHECK_ALL,
+ PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
+
+ input_flags = 0;
+ while (*ptr != '\0') {
+
+ bool found = false;
+ for (int i = 0; i < 9; i++) {
+ int len = strlen(strings[i]);
+ if (strncmp(ptr, strings[i], len) == 0) {
+ input_flags |= flags[i];
+ ptr += len;
+ found = true;
+ break;
+ }
+ }
+
+ if (!found)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ if (*ptr == '\0')
+ break;
+
+ if (*ptr != '-')
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (invalid structure type)");
+
+ ptr++;
+ }
+
+ double threshold = force->numeric(FLERR, arg[4]);
+ if (threshold < 0.0)
+ error->all(FLERR,
+ "Illegal compute ptm/atom command (threshold is negative)");
+ rmsd_threshold = threshold;
+ if (rmsd_threshold == 0)
+ rmsd_threshold = INFINITY;
+
+ peratom_flag = 1;
+ size_peratom_cols = NUM_COLUMNS;
+ create_attribute = 1;
+ nmax = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); }
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init() {
+ if (force->pair == NULL)
+ error->all(FLERR, "Compute ptm/atom requires a pair style be defined");
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "ptm/atom") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute ptm/atom defined");
+
+ // need an occasional full neighbor list
+
+ int irequest = neighbor->request(this, instance_me);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; }
+
+/* ---------------------------------------------------------------------- */
+
+typedef struct {
+ int index;
+ double d;
+} ptmnbr_t;
+
+static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
+ return a.d < b.d;
+}
+
+static int get_neighbors(double *pos, int jnum, int *jlist, double **x,
+ double (*nbr)[3]) {
+
+ ptmnbr_t *nbr_order = new ptmnbr_t[jnum];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ int j = jlist[jj];
+ j &= NEIGHMASK;
+
+ double dx = pos[0] - x[j][0];
+ double dy = pos[1] - x[j][1];
+ double dz = pos[2] - x[j][2];
+ double rsq = dx * dx + dy * dy + dz * dz;
+
+ nbr_order[jj].index = j;
+ nbr_order[jj].d = rsq;
+ }
+
+ std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare);
+ int num_nbrs = std::min(MAX_NEIGHBORS, jnum);
+
+ nbr[0][0] = nbr[0][1] = nbr[0][2] = 0;
+ for (int jj = 0; jj < num_nbrs; jj++) {
+
+ int j = nbr_order[jj].index;
+ nbr[jj + 1][0] = x[j][0] - pos[0];
+ nbr[jj + 1][1] = x[j][1] - pos[1];
+ nbr[jj + 1][2] = x[j][2] - pos[2];
+ }
+
+ delete[] nbr_order;
+ return num_nbrs;
+}
+
+void ComputePTMAtom::compute_peratom() {
+ // PTM global initialization. If already initialized this function does
+ // nothing.
+ ptm_initialize_global();
+
+ // initialize PTM local storage
+ ptm_local_handle_t local_handle = ptm_initialize_local();
+
+ invoked_peratom = update->ntimestep;
+
+ // grow arrays if necessary
+ if (atom->nmax > nmax) {
+ memory->destroy(output);
+ nmax = atom->nmax;
+
+ memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output");
+ array_atom = output;
+ }
+
+ // invoke full neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ int inum = list->inum;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int ii = 0; ii < inum; ii++) {
+
+ int i = ilist[ii];
+ output[i][0] = UNKNOWN;
+ if (!(mask[i] & groupbit))
+ continue;
+
+ double *pos = x[i];
+
+ int *jlist = firstneigh[i];
+ int jnum = numneigh[i];
+ if (jnum <= 0)
+ continue;
+
+ // get neighbours ordered by increasing distance
+ double nbr[MAX_NEIGHBORS + 1][3];
+ int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr);
+
+ // check that we have enough neighbours for the desired structure types
+ int32_t flags = 0;
+ if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC))
+ flags |= PTM_CHECK_SC;
+ if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC))
+ flags |= PTM_CHECK_FCC;
+ if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP))
+ flags |= PTM_CHECK_HCP;
+ if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO))
+ flags |= PTM_CHECK_ICO;
+ if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC))
+ flags |= PTM_CHECK_BCC;
+ if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB))
+ flags |= PTM_CHECK_DCUB;
+ if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX))
+ flags |= PTM_CHECK_DHEX;
+
+ // now run PTM
+ int8_t mapping[MAX_NEIGHBORS + 1];
+ int32_t type, alloy_type;
+ double scale, rmsd, interatomic_distance, lattice_constant;
+ double q[4], F[9], F_res[3], U[9], P[9];
+ ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type,
+ &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping,
+ &interatomic_distance, &lattice_constant);
+
+ if (rmsd > rmsd_threshold) {
+ type = PTM_MATCH_NONE;
+ }
+
+ // printf("%d type=%d rmsd=%f\n", i, type, rmsd);
+
+ if (type == PTM_MATCH_NONE)
+ type = OTHER;
+
+ output[i][0] = type;
+ output[i][1] = rmsd;
+ output[i][2] = interatomic_distance;
+ output[i][3] = q[0];
+ output[i][4] = q[1];
+ output[i][5] = q[2];
+ output[i][6] = q[3];
+ }
+
+ // printf("finished ptm analysis\n");
+ ptm_uninitialize_local(local_handle);
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputePTMAtom::memory_usage() {
+ double bytes = nmax * NUM_COLUMNS * sizeof(double);
+ bytes += nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h
new file mode 100644
index 0000000000..5c10e0c443
--- /dev/null
+++ b/src/PTM/compute_ptm_atom.h
@@ -0,0 +1,48 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(ptm/atom,ComputePTMAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_PTM_ATOM_H
+#define LMP_COMPUTE_PTM_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePTMAtom : public Compute {
+ public:
+ ComputePTMAtom(class LAMMPS *, int, char **);
+ ~ComputePTMAtom();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_peratom();
+ double memory_usage();
+
+ private:
+ int nmax;
+ int32_t input_flags;
+ double rmsd_threshold;
+ class NeighList *list;
+ double **output;
+};
+
+}
+
+#endif
+#endif
+
diff --git a/src/PTM/ptm_alloy_types.cpp b/src/PTM/ptm_alloy_types.cpp
new file mode 100644
index 0000000000..e14d06db99
--- /dev/null
+++ b/src/PTM/ptm_alloy_types.cpp
@@ -0,0 +1,101 @@
+#include <algorithm>
+#include "ptm_constants.h"
+#include "ptm_initialize_data.h"
+
+
+#define NUM_ALLOY_TYPES 3
+static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
+ {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e},
+ {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe},
+};
+
+static bool test_pure(int num_nbrs, int32_t* numbers)
+{
+ for (int i=1;i<num_nbrs + 1;i++)
+ if (numbers[i] != numbers[0])
+ return false;
+ return true;
+}
+
+static bool test_binary(int num_nbrs, int32_t* numbers)
+{
+ int a = numbers[0], b = -1;
+ for (int i=1;i<num_nbrs + 1;i++)
+ {
+ if (numbers[i] != a)
+ {
+ if (b == -1)
+ b = numbers[i];
+ else if (numbers[i] != b)
+ return false;
+ }
+ }
+
+ return true;
+}
+
+static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ for (int i=1;i<num_inner + 1;i++)
+ if (binary[i] == binary[0])
+ return false;
+
+ for (int i=num_inner+1;i<ref->num_nbrs+1;i++)
+ if (binary[i] != binary[0])
+ return false;
+
+ return true;
+}
+
+static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ int8_t binary[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
+
+ int8_t temp[PTM_MAX_POINTS];
+ uint32_t best = 0xFFFFFFFF;
+ for (int j=0;j<ref->num_mappings;j++)
+ {
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[j][i]] = binary[i];
+
+ uint32_t code = 0;
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ code |= (temp[i] << i);
+
+ best = std::min(best, code);
+ }
+
+ return best;
+}
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
+{
+ if (test_pure(ref->num_nbrs, numbers))
+ return PTM_ALLOY_PURE;
+
+ if (!test_binary(ref->num_nbrs, numbers))
+ return PTM_ALLOY_NONE;
+
+ uint32_t code = canonical_alloy_representation(ref, mapping, numbers);
+ for (int i=0;i<NUM_ALLOY_TYPES;i++)
+ if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
+ return typedata[i][1];
+
+ if (ref->type == PTM_MATCH_BCC)
+ if (test_shell_structure(ref, mapping, numbers, 8))
+ return PTM_ALLOY_B2;
+
+ if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)
+ if (test_shell_structure(ref, mapping, numbers, 4))
+ return PTM_ALLOY_SIC;
+
+ return PTM_ALLOY_NONE;
+}
+
diff --git a/src/PTM/ptm_alloy_types.h b/src/PTM/ptm_alloy_types.h
new file mode 100644
index 0000000000..6ea6ed1b8a
--- /dev/null
+++ b/src/PTM/ptm_alloy_types.h
@@ -0,0 +1,9 @@
+#ifndef PTM_ALLOY_TYPES_H
+#define PTM_ALLOY_TYPES_H
+
+#include "ptm_initialize_data.h"
+
+int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+
+#endif
+
diff --git a/src/PTM/ptm_canonical_coloured.cpp b/src/PTM/ptm_canonical_coloured.cpp
new file mode 100644
index 0000000000..551f52d7e4
--- /dev/null
+++ b/src/PTM/ptm_canonical_coloured.cpp
@@ -0,0 +1,167 @@
+#include <string.h>
+#include <climits>
+#include <algorithm>
+#include "ptm_graph_tools.h"
+#include "ptm_constants.h"
+
+
+static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
+{
+ bool m[PTM_MAX_NBRS][PTM_MAX_NBRS];
+ memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ int8_t index[PTM_MAX_NBRS];
+ memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS);
+
+
+ int n = 0;
+ index[a] = colours[a] * num_nodes + n++;
+ if (index[a] > best_code[0])
+ return false;
+
+ bool winning = false;
+ if (index[a] < best_code[0])
+ {
+ best_code[0] = index[a];
+ winning = true;
+ }
+
+ int c = -1;
+ for (int it=1;it<2*num_edges;it++)
+ {
+ bool newvertex = index[b] == -1;
+
+ if (newvertex)
+ index[b] = colours[b] * num_nodes + n++;
+
+ if (!winning && index[b] > best_code[it])
+ return false;
+
+ if (winning || index[b] < best_code[it])
+ {
+ winning = true;
+ best_code[it] = index[b];
+ }
+
+ if (newvertex)
+ {
+ //When a new vertex is reached, take the right-most edge
+ //relative to the edge on which the vertex is reached.
+
+ c = common[a][b];
+ }
+ else if (m[b][a] == false)
+ {
+ //When an old vertex is reached on a new path, go back
+ //in the opposite direction.
+
+ c = a;
+ }
+ else
+ {
+ //When an old vertex is reached on an old path, leave the
+ //vertex on the right-most edge that has not previously
+ //been traversed in that direction.
+
+ c = common[a][b];
+ while (m[b][c] == true)
+ c = common[c][b];
+ }
+
+ m[a][b] = true;
+ a = b;
+ b = c;
+ }
+
+ if (winning)
+ {
+ memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes);
+ return true;
+ }
+
+ return false;
+}
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash)
+{
+ int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}};
+ int num_edges = 3 * num_facets / 2;
+ if (!build_facet_map(num_facets, facets, common))
+ return -1;
+
+ memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES);
+
+ bool equal = true;
+ for (int i = 1;i<num_nodes;i++)
+ if (degree[i] != degree[0] || colours[i] != colours[0])
+ equal = false;
+
+ if (equal)
+ {
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]);
+ }
+ else
+ {
+ uint32_t best_degree = 0;
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ best_degree = std::max(best_degree, ((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0));
+ best_degree = std::max(best_degree, ((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8));
+ best_degree = std::max(best_degree, ((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16));
+ }
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //int da = colours[a] * num_nodes + degree[a];
+ //int db = colours[b] * num_nodes + degree[b];
+ //int dc = colours[c] * num_nodes + degree[c];
+
+ int da = degree[a];
+ int db = degree[b];
+ int dc = degree[c];
+
+ if (best_degree == (((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, a, b);
+
+ if (best_degree == (((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, b, c);
+
+ if (best_degree == (((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16)))
+ weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, c, a);
+ }
+ }
+
+ for (int i = num_nodes-1;i>=0;i--)
+ canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1;
+ canonical_labelling[0] = 0;
+
+ uint64_t hash = 0;
+ for (int i = 0;i<2 * num_edges;i++)
+ {
+ uint64_t e = best_code[i];
+ e += i % 8;
+ e &= 0xF;
+ e <<= (4 * i) % 64;
+ hash ^= e;
+ }
+
+ *p_hash = hash;
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_canonical_coloured.h b/src/PTM/ptm_canonical_coloured.h
new file mode 100644
index 0000000000..e71bb08bfc
--- /dev/null
+++ b/src/PTM/ptm_canonical_coloured.h
@@ -0,0 +1,9 @@
+#ifndef PTM_CANONICAL_COLOURED_H
+#define PTM_CANONICAL_COLOURED_H
+
+#include <stdint.h>
+
+int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
+
+#endif
+
diff --git a/src/PTM/ptm_constants.h b/src/PTM/ptm_constants.h
new file mode 100644
index 0000000000..f868f51e84
--- /dev/null
+++ b/src/PTM/ptm_constants.h
@@ -0,0 +1,174 @@
+#ifndef PTM_CONSTANTS_H
+#define PTM_CONSTANTS_H
+
+//------------------------------------
+// definitions
+//------------------------------------
+#define PTM_NO_ERROR 0
+
+
+#define PTM_CHECK_FCC (1 << 0)
+#define PTM_CHECK_HCP (1 << 1)
+#define PTM_CHECK_BCC (1 << 2)
+#define PTM_CHECK_ICO (1 << 3)
+#define PTM_CHECK_SC (1 << 4)
+#define PTM_CHECK_DCUB (1 << 5)
+#define PTM_CHECK_DHEX (1 << 6)
+#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)
+#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX)
+
+#define PTM_MATCH_NONE 0
+#define PTM_MATCH_FCC 1
+#define PTM_MATCH_HCP 2
+#define PTM_MATCH_BCC 3
+#define PTM_MATCH_ICO 4
+#define PTM_MATCH_SC 5
+#define PTM_MATCH_DCUB 6
+#define PTM_MATCH_DHEX 7
+
+#define PTM_ALLOY_NONE 0
+#define PTM_ALLOY_PURE 1
+#define PTM_ALLOY_L10 2
+#define PTM_ALLOY_L12_CU 3
+#define PTM_ALLOY_L12_AU 4
+#define PTM_ALLOY_B2 5
+#define PTM_ALLOY_SIC 6
+
+
+#define PTM_MAX_INPUT_POINTS 35
+#define PTM_MAX_NBRS 16
+#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1)
+#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4
+#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6
+
+
+//------------------------------------
+// number of neighbours
+//------------------------------------
+#define PTM_NUM_NBRS_FCC 12
+#define PTM_NUM_NBRS_HCP 12
+#define PTM_NUM_NBRS_BCC 14
+#define PTM_NUM_NBRS_ICO 12
+#define PTM_NUM_NBRS_SC 6
+#define PTM_NUM_NBRS_DCUB 16
+#define PTM_NUM_NBRS_DHEX 16
+
+#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1)
+#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1)
+#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1)
+#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1)
+#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1)
+#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1)
+#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1)
+
+const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX};
+
+//------------------------------------
+// template structures
+//------------------------------------
+
+//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1
+
+const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. },
+ { 0. , 0.707106781187, 0.707106781187 },
+ { 0. , -0.707106781187, -0.707106781187 },
+ { 0. , 0.707106781187, -0.707106781187 },
+ { 0. , -0.707106781187, 0.707106781187 },
+ { 0.707106781187, 0. , 0.707106781187 },
+ { -0.707106781187, 0. , -0.707106781187 },
+ { 0.707106781187, 0. , -0.707106781187 },
+ { -0.707106781187, 0. , 0.707106781187 },
+ { 0.707106781187, 0.707106781187, 0. },
+ { -0.707106781187, -0.707106781187, 0. },
+ { 0.707106781187, -0.707106781187, 0. },
+ { -0.707106781187, 0.707106781187, 0. } };
+
+const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. },
+ { 0.707106781186, 0. , 0.707106781186 },
+ { -0.235702260395, -0.942809041583, -0.235702260395 },
+ { 0.707106781186, 0.707106781186, 0. },
+ { -0.235702260395, -0.235702260395, -0.942809041583 },
+ { 0. , 0.707106781186, 0.707106781186 },
+ { -0.942809041583, -0.235702260395, -0.235702260395 },
+ { -0.707106781186, 0.707106781186, 0. },
+ { 0. , 0.707106781186, -0.707106781186 },
+ { 0.707106781186, 0. , -0.707106781186 },
+ { 0.707106781186, -0.707106781186, 0. },
+ { -0.707106781186, 0. , 0.707106781186 },
+ { 0. , -0.707106781186, 0.707106781186 } };
+
+const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. },
+ { -0.541451884327, -0.541451884327, -0.541451884327 },
+ { 0.541451884327, 0.541451884327, 0.541451884327 },
+ { 0.541451884327, -0.541451884327, -0.541451884327 },
+ { -0.541451884327, 0.541451884327, 0.541451884327 },
+ { -0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0.541451884327, -0.541451884327, 0.541451884327 },
+ { -0.541451884327, -0.541451884327, 0.541451884327 },
+ { 0.541451884327, 0.541451884327, -0.541451884327 },
+ { 0. , 0. , -1.082903768655 },
+ { 0. , 0. , 1.082903768655 },
+ { 0. , -1.082903768655, 0. },
+ { 0. , 1.082903768655, 0. },
+ { -1.082903768655, 0. , 0. },
+ { 1.082903768655, 0. , 0. } };
+
+const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. },
+ { 0. , 0.525731112119, 0.850650808352 },
+ { 0. , -0.525731112119, -0.850650808352 },
+ { 0. , 0.525731112119, -0.850650808352 },
+ { 0. , -0.525731112119, 0.850650808352 },
+ { -0.525731112119, -0.850650808352, 0. },
+ { 0.525731112119, 0.850650808352, 0. },
+ { 0.525731112119, -0.850650808352, 0. },
+ { -0.525731112119, 0.850650808352, 0. },
+ { -0.850650808352, 0. , -0.525731112119 },
+ { 0.850650808352, 0. , 0.525731112119 },
+ { 0.850650808352, 0. , -0.525731112119 },
+ { -0.850650808352, 0. , 0.525731112119 } };
+
+const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. },
+ { 0. , 0. , -1. },
+ { 0. , 0. , 1. },
+ { 0. , -1. , 0. },
+ { 0. , 1. , 0. },
+ { -1. , 0. , 0. },
+ { 1. , 0. , 0. } };
+
+const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, -0.782983254107, 0. },
+ { -0.782983254107, 0. , -0.782983254107 },
+ { 0. , -0.782983254107, -0.782983254107 },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. } };
+
+const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. },
+ { -0.391491627053, -0.391491627053, -0.391491627053 },
+ { 0.391491627053, -0.391491627053, 0.391491627053 },
+ { -0.391491627053, 0.391491627053, 0.391491627053 },
+ { 0.391491627053, 0.391491627053, -0.391491627053 },
+ { -0.260994418036, -1.043977672142, -0.260994418036 },
+ { -1.043977672142, -0.260994418036, -0.260994418036 },
+ { -0.260994418036, -0.260994418036, -1.043977672142 },
+ { 0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, -0.782983254107, 0. },
+ { 0. , -0.782983254107, 0.782983254107 },
+ { 0. , 0.782983254107, 0.782983254107 },
+ { -0.782983254107, 0.782983254107, 0. },
+ { -0.782983254107, 0. , 0.782983254107 },
+ { 0.782983254107, 0.782983254107, 0. },
+ { 0. , 0.782983254107, -0.782983254107 },
+ { 0.782983254107, 0. , -0.782983254107 } };
+#endif
+
diff --git a/src/PTM/ptm_convex_hull_incremental.cpp b/src/PTM/ptm_convex_hull_incremental.cpp
new file mode 100644
index 0000000000..c996b17b58
--- /dev/null
+++ b/src/PTM/ptm_convex_hull_incremental.cpp
@@ -0,0 +1,363 @@
+#include <cmath>
+#include <cfloat>
+#include <string.h>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_constants.h"
+
+
+#define VISIBLE 1
+#define INVISIBLE 2
+#define BOTH 3
+#define TOLERANCE 1E-8
+
+static double norm_squared(double* p)
+{
+ double x = p[0];
+ double y = p[1];
+ double z = p[2];
+
+ return x*x + y*y + z*z;
+}
+
+static double dot_product(const double* a, const double* b)
+{
+ return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
+}
+
+static void cross_product(double* a, double* b, double* c)
+{
+ c[0] = a[1] * b[2] - a[2] * b[1];
+ c[1] = a[2] * b[0] - a[0] * b[2];
+ c[2] = a[0] * b[1] - a[1] * b[0];
+}
+
+static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal)
+{
+ double u[3] = { points[b][0] - points[a][0],
+ points[b][1] - points[a][1],
+ points[b][2] - points[a][2] };
+
+ double v[3] = { points[c][0] - points[a][0],
+ points[c][1] - points[a][1],
+ points[c][2] - points[a][2] };
+
+ cross_product(u, v, plane_normal);
+ double norm = sqrt(norm_squared(plane_normal));
+ plane_normal[0] /= norm;
+ plane_normal[1] /= norm;
+ plane_normal[2] /= norm;
+}
+
+static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross)
+{
+ return plane_cross[0] * (plane_point[0] - w[0])
+ + plane_cross[1] * (plane_point[1] - w[1])
+ + plane_cross[2] * (plane_point[2] - w[2]);
+}
+
+static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index)
+{
+ for (int j=0;j<3;j++)
+ {
+ double dmin = DBL_MAX, dmax = -DBL_MAX;
+ int imin = 0, imax = 0;
+
+ for (int i = 0;i<num_points;i++)
+ {
+ double d = points[i][j];
+ if (d < dmin)
+ {
+ dmin = d;
+ imin = i;
+ }
+ if (d > dmax)
+ {
+ dmax = d;
+ imax = i;
+ }
+ }
+
+ if (imin == imax)
+ return false; //degenerate point set
+
+ min_index[j] = imin;
+ max_index[j] = imax;
+ }
+
+ return true;
+}
+
+static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c)
+{
+ const double* x1 = points[a];
+ const double* x2 = points[b];
+
+ double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]};
+ double ns_x2x1 = norm_squared(x2x1);
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b)
+ continue;
+
+ const double* x0 = points[i];
+
+ double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]};
+ double dot = dot_product(x1x0, x2x1);
+ double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1;
+
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_c = bi;
+ return max_dist > TOLERANCE;
+}
+
+static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d)
+{
+ double plane_normal[3];
+ calculate_plane_normal(points, a, b, c, plane_normal);
+
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<num_points;i++)
+ {
+ if (i == a || i == b || i == c)
+ continue;
+
+ const double* x0 = points[i];
+ double dist = fabs(point_plane_distance(x0, points[a], plane_normal));
+ if (dist > max_dist)
+ {
+ max_dist = dist;
+ bi = i;
+ }
+ }
+
+ *p_d = bi;
+ return max_dist > TOLERANCE;
+}
+
+static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices)
+{
+ int min_index[3] = {0};
+ int max_index[3] = {0};
+ if (!calc_max_extent(num_points, points, min_index, max_index))
+ return -1;
+
+ int bi = -1;
+ double max_dist = 0.0;
+ for (int i = 0;i<3;i++)
+ {
+ int a = min_index[i], b = max_index[i];
+ double delta[3] = { points[a][0] - points[b][0],
+ points[a][1] - points[b][1],
+ points[a][2] - points[b][2] };
+ double dist = norm_squared(delta);
+ if (dist > max_dist)
+ {
+ bi = i;
+ max_dist = dist;
+ }
+ }
+
+ //first two points are (a, b)
+ int a = min_index[bi], b = max_index[bi], c = -1, d = -1;
+
+ if (!find_third_point(num_points, points, a, b, &c))
+ return -2;
+
+ if (!find_fourth_point(num_points, points, a, b, c, &d))
+ return -3;
+
+ initial_vertices[0] = a;
+ initial_vertices[1] = b;
+ initial_vertices[2] = c;
+ initial_vertices[3] = d;
+ return 0;
+}
+
+static bool visible(const double* w, const double* plane_point, const double* plane_normal)
+{
+ return point_plane_distance(w, plane_point, plane_normal) > 0;
+}
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre)
+{
+ calculate_plane_normal(points, a, b, c, plane_normal);
+ if (visible(barycentre, points[a], plane_normal))
+ {
+ plane_normal[0] = -plane_normal[0];
+ plane_normal[1] = -plane_normal[1];
+ plane_normal[2] = -plane_normal[2];
+
+ facet[0] = b;
+ facet[1] = a;
+ facet[2] = c;
+ }
+ else
+ {
+ facet[0] = a;
+ facet[1] = b;
+ facet[2] = c;
+ }
+}
+
+static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre)
+{
+ memset(processed, 0, PTM_MAX_POINTS * sizeof(bool));
+ memset(barycentre, 0, 3 * sizeof(double));
+ int ret = initial_simplex(num_points, points, initial_vertices);
+ if (ret != 0)
+ return ret;
+
+ for (int i = 0;i<4;i++)
+ {
+ int a = initial_vertices[i];
+ processed[a] = true;
+
+ barycentre[0] += points[a][0];
+ barycentre[1] += points[a][1];
+ barycentre[2] += points[a][2];
+ }
+ barycentre[0] /= 4;
+ barycentre[1] /= 4;
+ barycentre[2] /= 4;
+
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre);
+ add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre);
+ add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre);
+ return 0;
+}
+
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3])
+{
+ assert( num_points == PTM_NUM_POINTS_FCC
+ || num_points == PTM_NUM_POINTS_HCP
+ || num_points == PTM_NUM_POINTS_BCC
+ || num_points == PTM_NUM_POINTS_ICO
+ || num_points == PTM_NUM_POINTS_SC
+ || num_points == PTM_NUM_POINTS_DCUB
+ || num_points == PTM_NUM_POINTS_DHEX);
+
+ int ret = 0;
+ int num_prev = ch->num_prev;
+ ch->num_prev = num_points;
+ if (!ch->ok || 0)
+ {
+ ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre);
+ if (ret != 0)
+ return ret;
+
+ ch->num_facets = 4;
+ num_prev = 0;
+ }
+
+ for (int i = num_prev;i<num_points;i++)
+ {
+ if (ch->processed[i])
+ continue;
+ ch->processed[i] = true;
+
+ int num_to_add = 0;
+ int8_t to_add[PTM_MAX_FACETS][3];
+ int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS];
+ memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS);
+ for (int j = 0;j<ch->num_facets;j++)
+ {
+ int a = ch->facets[j][0];
+ int b = ch->facets[j][1];
+ int c = ch->facets[j][2];
+
+ int u = 0, v = 0, w = 0;
+
+ double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]);
+ bool vis = distance > TOLERANCE;
+ if (vis)
+ {
+ u = edge_visible[a][b] |= VISIBLE;
+ edge_visible[b][a] |= VISIBLE;
+
+ v = edge_visible[b][c] |= VISIBLE;
+ edge_visible[c][b] |= VISIBLE;
+
+ w = edge_visible[c][a] |= VISIBLE;
+ edge_visible[a][c] |= VISIBLE;
+
+ memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t));
+ memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double));
+ ch->num_facets--;
+ j--;
+ }
+ else
+ {
+ u = edge_visible[a][b] |= INVISIBLE;
+ edge_visible[b][a] |= INVISIBLE;
+
+ v = edge_visible[b][c] |= INVISIBLE;
+ edge_visible[c][b] |= INVISIBLE;
+
+ w = edge_visible[c][a] |= INVISIBLE;
+ edge_visible[a][c] |= INVISIBLE;
+ }
+
+ if (u == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = a;
+ to_add[num_to_add][2] = b;
+ num_to_add++;
+ }
+
+ if (v == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = b;
+ to_add[num_to_add][2] = c;
+ num_to_add++;
+ }
+
+ if (w == BOTH)
+ {
+ to_add[num_to_add][0] = i;
+ to_add[num_to_add][1] = c;
+ to_add[num_to_add][2] = a;
+ num_to_add++;
+ }
+ }
+
+ for (int j = 0;j<num_to_add;j++)
+ {
+ if (ch->num_facets >= PTM_MAX_FACETS)
+ return -4;
+
+ add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++;
+ }
+ }
+
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = ch->facets[i][0];
+ int b = ch->facets[i][1];
+ int c = ch->facets[i][2];
+ if (a == 0 || b == 0 || c == 0)
+ return 1; //central atom contained in convex hull
+
+ simplex[i][0] = a - 1;
+ simplex[i][1] = b - 1;
+ simplex[i][2] = c - 1;
+ }
+
+ return ret;
+}
+
diff --git a/src/PTM/ptm_convex_hull_incremental.h b/src/PTM/ptm_convex_hull_incremental.h
new file mode 100644
index 0000000000..563a0c436a
--- /dev/null
+++ b/src/PTM/ptm_convex_hull_incremental.h
@@ -0,0 +1,27 @@
+#ifndef PTM_CONVEX_HULL_INCREMENTAL_H
+#define PTM_CONVEX_HULL_INCREMENTAL_H
+
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int8_t facets[PTM_MAX_FACETS][3];
+ double plane_normal[PTM_MAX_FACETS][3];
+ bool processed[PTM_MAX_POINTS];
+ int initial_vertices[4];
+ double barycentre[3];
+ int num_facets;
+ int num_prev;
+ bool ok;
+
+} convexhull_t;
+
+void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
+int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
+
+#endif
+
diff --git a/src/PTM/ptm_deformation_gradient.cpp b/src/PTM/ptm_deformation_gradient.cpp
new file mode 100644
index 0000000000..d566d5ca11
--- /dev/null
+++ b/src/PTM/ptm_deformation_gradient.cpp
@@ -0,0 +1,37 @@
+#include "ptm_deformation_gradient.h"
+
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
+{
+ for (int i = 0;i<3;i++)
+ {
+ for (int j = 0;j<3;j++)
+ {
+ double acc = 0.0;
+ for (int k = 0;k<num_points;k++)
+ acc += penrose[k][j] * normalized[mapping[k]][i];
+
+ F[i*3 + j] = acc;
+ }
+ }
+
+ res[0] = 0;
+ res[1] = 0;
+ res[2] = 0;
+
+ for (int k = 0;k<num_points;k++)
+ {
+ for (int i = 0;i<3;i++)
+ {
+ double acc = 0.0;
+ for (int j = 0;j<3;j++)
+ {
+ acc += F[i*3 + j] * ideal_points[k][j];
+ }
+
+ double delta = acc - normalized[mapping[k]][i];
+ res[i] += delta * delta;
+ }
+ }
+}
+
diff --git a/src/PTM/ptm_deformation_gradient.h b/src/PTM/ptm_deformation_gradient.h
new file mode 100644
index 0000000000..7decab4b76
--- /dev/null
+++ b/src/PTM/ptm_deformation_gradient.h
@@ -0,0 +1,142 @@
+#ifndef PTM_DEFORMATION_GRADIENT_H
+#define PTM_DEFORMATION_GRADIENT_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
+
+//sc
+#define k_sc 0.5
+const double penrose_sc[PTM_NUM_POINTS_SC][3] = {
+ {0, 0, 0},
+ {0, 0, -k_sc},
+ {0, 0, k_sc},
+ {0, -k_sc, 0},
+ {0, k_sc, 0},
+ {-k_sc, 0, 0},
+ {k_sc, 0, 0},
+ };
+
+//fcc
+#define k_fcc 0.17677669529663678216
+const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = {
+ {0, 0, 0},
+ {0, k_fcc, k_fcc},
+ {0, -k_fcc, -k_fcc},
+ {0, k_fcc, -k_fcc},
+ {0, -k_fcc, k_fcc},
+ {k_fcc, 0, k_fcc},
+ {-k_fcc, 0, -k_fcc},
+ {k_fcc, 0, -k_fcc},
+ {-k_fcc, 0, k_fcc},
+ {k_fcc, k_fcc, -0},
+ {-k_fcc, -k_fcc, 0},
+ {k_fcc, -k_fcc, 0},
+ {-k_fcc, k_fcc, -0},
+ };
+
+//hcp
+#define k_hcp 0.17677669529663678216
+const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = {
+ {0, 0, 0},
+ {k_hcp, 0, k_hcp},
+ {-k_hcp/3, -4*k_hcp/3, -k_hcp/3},
+ {k_hcp, k_hcp, 0},
+ {-k_hcp/3, -k_hcp/3, -4*k_hcp/3},
+ {0, k_hcp, k_hcp},
+ {-4*k_hcp/3, -k_hcp/3, -k_hcp/3},
+ {-k_hcp, k_hcp, -0},
+ {0, k_hcp, -k_hcp},
+ {k_hcp, 0, -k_hcp},
+ {k_hcp, -k_hcp, 0},
+ {-k_hcp, 0, k_hcp},
+ {0, -k_hcp, k_hcp},
+ };
+
+//ico
+#define k_ico 0.13143277802974323576
+#define phi 1.61803398874989490253
+//((1.0 + sqrt(5)) / 2)
+const double penrose_ico[PTM_NUM_POINTS_ICO][3] = {
+ {0, 0, 0},
+ {0, k_ico, phi*k_ico},
+ {0, -k_ico, -phi*k_ico},
+ {0, k_ico, -phi*k_ico},
+ {0, -k_ico, phi*k_ico},
+ {-k_ico, -phi*k_ico, -0},
+ {k_ico, phi*k_ico, 0},
+ {k_ico, -phi*k_ico, 0},
+ {-k_ico, phi*k_ico, -0},
+ {-phi*k_ico, 0, -k_ico},
+ {phi*k_ico, 0, k_ico},
+ {phi*k_ico, 0, -k_ico},
+ {-phi*k_ico, 0, k_ico},
+ };
+
+//bcc
+#define k_bcc 0.11543038598460284017
+const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = {
+ {0, 0, 0},
+ {-k_bcc, -k_bcc, -k_bcc},
+ {k_bcc, k_bcc, k_bcc},
+ {k_bcc, -k_bcc, -k_bcc},
+ {-k_bcc, k_bcc, k_bcc},
+ {-k_bcc, k_bcc, -k_bcc},
+ {k_bcc, -k_bcc, k_bcc},
+ {-k_bcc, -k_bcc, k_bcc},
+ {k_bcc, k_bcc, -k_bcc},
+ {0, 0, -2*k_bcc},
+ {0, 0, 2*k_bcc},
+ {0, -2*k_bcc, 0},
+ {0, 2*k_bcc, 0},
+ {-2*k_bcc, 0, 0},
+ {2*k_bcc, 0, -0},
+ };
+
+//dcub
+#define kdcub 0.07095369570691034689
+const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = {
+ { 0, 0, 0 },
+ { -kdcub, kdcub, kdcub },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, -2 * kdcub, 0 },
+ { -2 * kdcub, 0, -2 * kdcub },
+ { 0, -2 * kdcub, -2 * kdcub },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ };
+
+
+#define kdhex 0.04730246380471011397
+const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
+ { 0, 0, 0 },
+ { -kdcub, -kdcub, -kdcub },
+ { kdcub, -kdcub, kdcub },
+ { -kdcub, kdcub, kdcub },
+ { kdcub, kdcub, -kdcub },
+ { -kdhex, -4 * kdhex, -kdhex },
+ { -4 * kdhex, -kdhex, -kdhex },
+ { -kdhex, -kdhex, -4 * kdhex },
+ { 2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, -2 * kdcub, 0 },
+ { 0, -2 * kdcub, 2 * kdcub },
+ { 0, 2 * kdcub, 2 * kdcub },
+ { -2 * kdcub, 2 * kdcub, 0 },
+ { -2 * kdcub, 0, 2 * kdcub },
+ { 2 * kdcub, 2 * kdcub, 0 },
+ { 0, 2 * kdcub, -2 * kdcub },
+ { 2 * kdcub, 0, -2 * kdcub },
+ };
+#endif
+
+
diff --git a/src/PTM/ptm_functions.h b/src/PTM/ptm_functions.h
new file mode 100644
index 0000000000..cd67d4940d
--- /dev/null
+++ b/src/PTM/ptm_functions.h
@@ -0,0 +1,27 @@
+#ifndef PTM_FUNCTIONS_H
+#define PTM_FUNCTIONS_H
+
+#include <stdint.h>
+#include <stdbool.h>
+#include "ptm_initialize_data.h"
+#include "ptm_constants.h"
+
+
+//------------------------------------
+// function declarations
+//------------------------------------
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
diff --git a/src/PTM/ptm_fundamental_mappings.h b/src/PTM/ptm_fundamental_mappings.h
new file mode 100644
index 0000000000..3dd7c39cbb
--- /dev/null
+++ b/src/PTM/ptm_fundamental_mappings.h
@@ -0,0 +1,180 @@
+#ifndef PTM_FUNDAMENTAL_MAPPINGS_H
+#define PTM_FUNDAMENTAL_MAPPINGS_H
+
+#include <stdint.h>
+
+#define NUM_CUBIC_MAPPINGS 24
+#define NUM_ICO_MAPPINGS 60
+#define NUM_HEX_MAPPINGS 6
+#define NUM_DCUB_MAPPINGS 12
+#define NUM_DHEX_MAPPINGS 3
+
+const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6},
+ {0, 2, 1, 4, 3, 5, 6},
+ {0, 2, 1, 3, 4, 6, 5},
+ {0, 1, 2, 4, 3, 6, 5},
+ {0, 3, 4, 5, 6, 1, 2},
+ {0, 5, 6, 2, 1, 4, 3},
+ {0, 6, 5, 1, 2, 4, 3},
+ {0, 4, 3, 5, 6, 2, 1},
+ {0, 5, 6, 1, 2, 3, 4},
+ {0, 4, 3, 6, 5, 1, 2},
+ {0, 3, 4, 6, 5, 2, 1},
+ {0, 6, 5, 2, 1, 3, 4},
+ {0, 3, 4, 2, 1, 5, 6},
+ {0, 6, 5, 3, 4, 1, 2},
+ {0, 1, 2, 5, 6, 4, 3},
+ {0, 4, 3, 1, 2, 5, 6},
+ {0, 5, 6, 3, 4, 2, 1},
+ {0, 1, 2, 6, 5, 3, 4},
+ {0, 2, 1, 5, 6, 3, 4},
+ {0, 5, 6, 4, 3, 1, 2},
+ {0, 3, 4, 1, 2, 6, 5},
+ {0, 2, 1, 6, 5, 4, 3},
+ {0, 6, 5, 4, 3, 2, 1},
+ {0, 4, 3, 2, 1, 6, 5} };
+
+const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9},
+ {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11},
+ {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7},
+ {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5},
+ {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2},
+ {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6},
+ {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3},
+ {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9},
+ {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8},
+ {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1},
+ {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10},
+ {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11},
+ {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2},
+ {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5},
+ {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12},
+ {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4},
+ {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} };
+
+const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14},
+ {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14},
+ {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13},
+ {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13},
+ {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10},
+ {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11},
+ {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11},
+ {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9},
+ {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12},
+ {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10},
+ {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9},
+ {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12},
+ {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14},
+ {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10},
+ {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11},
+ {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14},
+ {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9},
+ {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12},
+ {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12},
+ {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10},
+ {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11},
+ {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} };
+
+const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4},
+ {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4},
+ {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5},
+ {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1},
+ {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5},
+ {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12},
+ {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12},
+ {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1},
+ {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9},
+ {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8},
+ {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9},
+ {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8},
+ {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8},
+ {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9},
+ {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3},
+ {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5},
+ {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6},
+ {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
+ {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6},
+ {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4},
+ {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2},
+ {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3},
+ {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10},
+ {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10},
+ {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1},
+ {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7},
+ {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
+ {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2},
+ {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4},
+ {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7},
+ {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5},
+ {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9},
+ {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2},
+ {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10},
+ {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7},
+ {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7},
+ {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12},
+ {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6},
+ {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12},
+ {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3},
+ {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10},
+ {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3},
+ {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6},
+ {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2},
+ {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9},
+ {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3},
+ {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8},
+ {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2},
+ {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5},
+ {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4},
+ {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11},
+ {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1},
+ {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11},
+ {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11},
+ {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6},
+ {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11},
+ {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7},
+ {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11},
+ {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} };
+
+const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
+ {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7},
+ {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9},
+ {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8},
+ {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10},
+ {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} };
+
+const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12},
+ {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6},
+ {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8},
+ {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13},
+ {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10},
+ {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11},
+ {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15},
+ {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7},
+ {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5},
+ {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9},
+ {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} };
+
+const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
+ {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
+ {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
+
+#endif
+
diff --git a/src/PTM/ptm_graph_data.cpp b/src/PTM/ptm_graph_data.cpp
new file mode 100644
index 0000000000..a591dbf993
--- /dev/null
+++ b/src/PTM/ptm_graph_data.cpp
@@ -0,0 +1,2059 @@
+#include "ptm_graph_data.h"
+
+
+int8_t automorphisms[65][17] = {
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1},
+ { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1},
+ { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1},
+ { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1},
+ { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1},
+ { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1},
+ { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1},
+ { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1},
+ { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1},
+ { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
+ { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1},
+ { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1},
+ { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1},
+ { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1},
+ { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1},
+ { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1},
+ { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1},
+ { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1},
+ { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1},
+ { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1},
+ { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1},
+ { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
+ { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8},
+ { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
+ { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9},
+ { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11},
+ { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
+};
+
+graph_t graphs_sc[NUM_SC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}},
+
+};
+
+graph_t graphs_ico[NUM_ICO_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}},
+
+};
+
+graph_t graphs_fcc[NUM_FCC_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
+
+{7,
+0,
+1,
+5,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
+
+};
+
+graph_t graphs_hcp[NUM_HCP_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{6,
+0,
+6,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
+
+{7,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
+
+{9,
+0,
+8,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
+
+{12,
+0,
+0,
+1,
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+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}},
+
+};
+
+graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
+
+{0,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}},
+
+{1,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{2,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{3,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{4,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{5,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{6,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{7,
+0,
+53,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{8,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{9,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{10,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{11,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{12,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{13,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{14,
+0,
+55,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
+
+{15,
+0,
+59,
+2,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{16,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{17,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{18,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{19,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{20,
+0,
+61,
+4,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
+
+{21,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{22,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+{23,
+0,
+0,
+1,
+{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
+
+};
+
diff --git a/src/PTM/ptm_graph_data.h b/src/PTM/ptm_graph_data.h
new file mode 100644
index 0000000000..11f46a471f
--- /dev/null
+++ b/src/PTM/ptm_graph_data.h
@@ -0,0 +1,37 @@
+#ifndef PTM_GRAPH_DATA_H
+#define PTM_GRAPH_DATA_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+
+typedef struct
+{
+ int id;
+ uint64_t hash;
+ int automorphism_index;
+ int num_automorphisms;
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ int8_t facets[PTM_MAX_FACETS][3];
+} graph_t;
+
+#define NUM_SC_GRAPHS 1
+#define NUM_ICO_GRAPHS 1
+#define NUM_FCC_GRAPHS 8
+#define NUM_HCP_GRAPHS 16
+#define NUM_BCC_GRAPHS 218
+#define NUM_DCUB_GRAPHS 12
+#define NUM_DHEX_GRAPHS 24
+
+extern int8_t automorphisms[][PTM_MAX_POINTS];
+
+extern graph_t graphs_sc[NUM_SC_GRAPHS];
+extern graph_t graphs_fcc[NUM_FCC_GRAPHS];
+extern graph_t graphs_hcp[NUM_HCP_GRAPHS];
+extern graph_t graphs_ico[NUM_ICO_GRAPHS];
+extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
+extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
+extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
+
+#endif
+
diff --git a/src/PTM/ptm_graph_tools.cpp b/src/PTM/ptm_graph_tools.cpp
new file mode 100644
index 0000000000..89d07fc87a
--- /dev/null
+++ b/src/PTM/ptm_graph_tools.cpp
@@ -0,0 +1,52 @@
+#include <string.h>
+#include <algorithm>
+#include "ptm_graph_tools.h"
+#include "ptm_constants.h"
+
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
+{
+ memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ //assert(common[a][b] == -1);
+ //assert(common[b][c] == -1);
+ //assert(common[c][a] == -1);
+ if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1)
+ return false;
+
+ common[a][b] = c;
+ common[b][c] = a;
+ common[c][a] = b;
+ }
+
+ return true;
+}
+
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree)
+{
+ memset(degree, 0, sizeof(int8_t) * num_nodes);
+
+ for (int i = 0;i<num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+
+ degree[a]++;
+ degree[b]++;
+ degree[c]++;
+ }
+
+ int8_t max_degree = 0;
+ for (int i = 0;i<num_nodes;i++)
+ max_degree = std::max(max_degree, degree[i]);
+
+ return max_degree;
+}
+
diff --git a/src/PTM/ptm_graph_tools.h b/src/PTM/ptm_graph_tools.h
new file mode 100644
index 0000000000..78934e87c1
--- /dev/null
+++ b/src/PTM/ptm_graph_tools.h
@@ -0,0 +1,11 @@
+#ifndef PTM_GRAPH_TOOLS_H
+#define PTM_GRAPH_TOOLS_H
+
+#include <stdint.h>
+#include "ptm_constants.h"
+
+bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
+int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
+
+#endif
+
diff --git a/src/PTM/ptm_index.cpp b/src/PTM/ptm_index.cpp
new file mode 100644
index 0000000000..7b6618848e
--- /dev/null
+++ b/src/PTM/ptm_index.cpp
@@ -0,0 +1,218 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_graph_data.h"
+#include "ptm_deformation_gradient.h"
+#include "ptm_alloy_types.h"
+#include "ptm_neighbour_ordering.h"
+#include "ptm_normalize_vertices.h"
+#include "ptm_quat.h"
+#include "ptm_polar.h"
+#include "ptm_initialize_data.h"
+#include "ptm_structure_matcher.h"
+#include "ptm_functions.h"
+#include "ptm_constants.h"
+
+
+//todo: verify that c == norm(template[1])
+static double calculate_interatomic_distance(int type, double scale)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))};
+ return c[type] / scale;
+}
+
+static double calculate_lattice_constant(int type, double interatomic_distance)
+{
+ assert(type >= 1 && type <= 7);
+ double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)};
+ return c[type] * interatomic_distance;
+}
+
+static int rotate_into_fundamental_zone(int type, double* q)
+{
+ if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
+ if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
+ if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
+ return -1;
+}
+
+static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ if (topological_ordering)
+ {
+ double normalized_points[PTM_MAX_INPUT_POINTS][3];
+ normalize_vertices(num_points, unpermuted_points, normalized_points);
+ int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
+ if (ret != 0)
+ topological_ordering = false;
+ }
+
+ if (!topological_ordering)
+ for (int i=0;i<num_points;i++)
+ ordering[i] = i;
+
+ for (int i=0;i<num_points;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+}
+
+static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ *p_type = PTM_MATCH_NONE;
+ if (p_alloy_type != NULL)
+ *p_alloy_type = PTM_ALLOY_NONE;
+
+ if (mapping != NULL)
+ memset(mapping, -1, num_points * sizeof(int8_t));
+
+ const refdata_t* ref = res->ref_struct;
+ if (ref == NULL)
+ return;
+
+ *p_type = ref->type;
+ if (p_alloy_type != NULL && unpermuted_numbers != NULL)
+ *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
+
+ int bi = rotate_into_fundamental_zone(ref->type, res->q);
+ int8_t temp[PTM_MAX_POINTS];
+ for (int i=0;i<ref->num_nbrs+1;i++)
+ temp[ref->mapping[bi][i]] = res->mapping[i];
+
+ memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t));
+
+ if (F != NULL && F_res != NULL)
+ {
+ double scaled_points[PTM_MAX_INPUT_POINTS][3];
+
+ subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
+ for (int i = 0;i<ref->num_nbrs + 1;i++)
+ {
+ scaled_points[i][0] *= res->scale;
+ scaled_points[i][1] *= res->scale;
+ scaled_points[i][2] *= res->scale;
+ }
+ calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
+
+ if (P != NULL && U != NULL)
+ polar_decomposition_3x3(F, false, U, P);
+ }
+
+ if (mapping != NULL)
+ for (int i=0;i<ref->num_nbrs + 1;i++)
+ mapping[i] = ordering[res->mapping[i]];
+
+ double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale);
+ double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance);
+
+ if (p_interatomic_distance != NULL)
+ *p_interatomic_distance = interatomic_distance;
+
+ if (p_lattice_constant != NULL)
+ *p_lattice_constant = lattice_constant;
+
+ *p_rmsd = res->rmsd;
+ *p_scale = res->scale;
+ memcpy(q, res->q, 4 * sizeof(double));
+}
+
+
+extern bool ptm_initialized;
+
+int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
+ int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
+ int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
+ double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
+{
+ assert(ptm_initialized);
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ if (flags & PTM_CHECK_SC)
+ assert(num_points >= PTM_NUM_POINTS_SC);
+
+ if (flags & PTM_CHECK_BCC)
+ assert(num_points >= PTM_NUM_POINTS_BCC);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ assert(num_points >= PTM_NUM_POINTS_FCC);
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ assert(num_points >= PTM_NUM_POINTS_DCUB);
+
+ int ret = 0;
+ result_t res;
+ res.ref_struct = NULL;
+ res.rmsd = INFINITY;
+
+ int8_t ordering[PTM_MAX_INPUT_POINTS];
+ double points[PTM_MAX_POINTS][3];
+ int32_t numbers[PTM_MAX_POINTS];
+
+ int8_t dordering[PTM_MAX_INPUT_POINTS];
+ double dpoints[PTM_MAX_POINTS][3];
+ int32_t dnumbers[PTM_MAX_POINTS];
+
+ convexhull_t ch;
+ double ch_points[PTM_MAX_INPUT_POINTS][3];
+
+ if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
+ {
+ int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
+ order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
+ normalize_vertices(num_lpoints, points, ch_points);
+ ch.ok = false;
+
+ if (flags & PTM_CHECK_SC)
+ ret = match_general(&structure_sc, ch_points, points, &ch, &res);
+
+ if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
+ ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
+
+ if (flags & PTM_CHECK_BCC)
+ ret = match_general(&structure_bcc, ch_points, points, &ch, &res);
+ }
+
+ if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
+ {
+ ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
+ if (ret == 0)
+ {
+ normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
+ ch.ok = false;
+
+ ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
+ }
+ }
+
+ if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX))
+ {
+ output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+ else
+ {
+ output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering,
+ p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
+ U, P, mapping, p_interatomic_distance, p_lattice_constant);
+ }
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_initialize_data.cpp b/src/PTM/ptm_initialize_data.cpp
new file mode 100644
index 0000000000..6157ff862f
--- /dev/null
+++ b/src/PTM/ptm_initialize_data.cpp
@@ -0,0 +1,71 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_initialize_data.h"
+
+
+static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
+{
+ double plane_normal[3];
+ double origin[3] = {0, 0, 0};
+
+ for (int i = 0;i<num_facets;i++)
+ add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
+}
+
+static int initialize_graphs(const refdata_t* s, int8_t* colours)
+{
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
+ assert(_max_degree <= s->max_degree);
+
+ make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
+ int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
+ if (ret != 0)
+ return ret;
+ }
+
+ return PTM_NO_ERROR;
+}
+
+bool ptm_initialized = false;
+int ptm_initialize_global()
+{
+ if (ptm_initialized)
+ return PTM_NO_ERROR;
+
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+
+ int ret = initialize_graphs(&structure_sc, colours);
+ ret |= initialize_graphs(&structure_fcc, colours);
+ ret |= initialize_graphs(&structure_hcp, colours);
+ ret |= initialize_graphs(&structure_ico, colours);
+ ret |= initialize_graphs(&structure_bcc, colours);
+ ret |= initialize_graphs(&structure_dcub, dcolours);
+ ret |= initialize_graphs(&structure_dhex, dcolours);
+
+ if (ret == PTM_NO_ERROR)
+ ptm_initialized = true;
+
+ return ret;
+}
+
+ptm_local_handle_t ptm_initialize_local()
+{
+ assert(ptm_initialized);
+ return (ptm_local_handle_t)voronoi_initialize_local();
+}
+
+void ptm_uninitialize_local(ptm_local_handle_t ptr)
+{
+ voronoi_uninitialize_local(ptr);
+}
+
diff --git a/src/PTM/ptm_initialize_data.h b/src/PTM/ptm_initialize_data.h
new file mode 100644
index 0000000000..f381dd864b
--- /dev/null
+++ b/src/PTM/ptm_initialize_data.h
@@ -0,0 +1,61 @@
+#ifndef PTM_INITIALIZE_DATA_H
+#define PTM_INITIALIZE_DATA_H
+
+
+#include "ptm_graph_data.h"
+#include "ptm_graph_tools.h"
+#include "ptm_deformation_gradient.h"
+#include "ptm_fundamental_mappings.h"
+#include "ptm_neighbour_ordering.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_convex_hull_incremental.h"
+
+
+typedef struct
+{
+ int type;
+ int num_nbrs;
+ int num_facets;
+ int max_degree;
+ int num_graphs;
+ int num_mappings;
+ graph_t* graphs;
+ const double (*points)[3];
+ const double (*penrose)[3];
+ const int8_t (*mapping)[PTM_MAX_POINTS];
+} refdata_t;
+
+
+//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc };
+const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc };
+const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc };
+const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp };
+const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico };
+const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc };
+const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
+const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct ptm_local_handle* ptm_local_handle_t;
+ptm_local_handle_t ptm_initialize_local();
+void ptm_uninitialize_local(ptm_local_handle_t ptr);
+
+int ptm_initialize_global();
+
+//------------------------------------
+// global initialization switch
+//------------------------------------
+extern bool ptm_initialized;
+
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#endif
+
diff --git a/src/PTM/ptm_neighbour_ordering.cpp b/src/PTM/ptm_neighbour_ordering.cpp
new file mode 100644
index 0000000000..6b5ac9601a
--- /dev/null
+++ b/src/PTM/ptm_neighbour_ordering.cpp
@@ -0,0 +1,203 @@
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
+#include <cassert>
+#include <algorithm>
+#include "ptm_constants.h"
+#include "ptm_voronoi_cell.h"
+using namespace voro;
+
+
+
+typedef struct
+{
+ double area;
+ double dist;
+ int index;
+} sorthelper_t;
+
+static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
+{
+ if (a.area > b.area)
+ return true;
+
+ if (a.area < b.area)
+ return false;
+
+ if (a.dist < b.dist)
+ return true;
+
+ return false;
+}
+
+//todo: change voronoi code to return errors rather than exiting
+static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
+{
+ const double k = 1000 * max_norm; //todo: reduce this constant
+ v->init(-k,k,-k,k,-k,k);
+
+ for (int i=1;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ v->nplane(x,y,z,normsq[i],i);
+ }
+
+ v->neighbors(nbr_indices);
+ v->face_areas(face_areas);
+ return 0;
+}
+
+int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
+
+ double max_norm = 0;
+ double points[PTM_MAX_INPUT_POINTS][3];
+ double normsq[PTM_MAX_INPUT_POINTS];
+ for (int i = 0;i<num_points;i++)
+ {
+ double x = _points[i][0] - _points[0][0];
+ double y = _points[i][1] - _points[0][1];
+ double z = _points[i][2] - _points[0][2];
+ points[i][0] = x;
+ points[i][1] = y;
+ points[i][2] = z;
+
+ normsq[i] = x*x + y*y + z*z;
+ max_norm = std::max(max_norm, normsq[i]);
+#ifdef DEBUG
+ printf("point %d: %f\t%f\t%f\t%f\n", i, x, y, z, x*x + y*y + z*z);
+#endif
+ }
+
+ max_norm = sqrt(max_norm);
+
+ std::vector<int> nbr_indices(num_points + 6);
+ std::vector<double> face_areas(num_points + 6);
+ int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas);
+ if (ret != 0)
+ return ret;
+
+ double areas[PTM_MAX_INPUT_POINTS];
+ memset(areas, 0, num_points * sizeof(double));
+ areas[0] = INFINITY;
+ for (size_t i=0;i<nbr_indices.size();i++)
+ {
+ int index = nbr_indices[i];
+ if (index > 0)
+ areas[index] = face_areas[i];
+ }
+
+ sorthelper_t data[PTM_MAX_INPUT_POINTS];
+ for (int i=0;i<num_points;i++)
+ {
+ assert(areas[i] == areas[i]);
+ data[i].area = areas[i];
+ data[i].dist = normsq[i];
+ data[i].index = i;
+ }
+
+ std::sort(data, data + num_points, &sorthelper_compare);
+
+#ifdef DEBUG
+ for (int i=0;i<num_points;i++)
+ printf("%d %f\n", data[i].index, data[i].area);
+#endif
+
+ for (int i=0;i<num_points;i++)
+ ordering[i] = data[i].index;
+
+ return ret;
+}
+
+void* voronoi_initialize_local()
+{
+ voronoicell_neighbor* ptr = new voronoicell_neighbor;
+ return (void*)ptr;
+}
+
+void voronoi_uninitialize_local(void* _ptr)
+{
+ voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
+ delete ptr;
+}
+
+
+typedef struct
+{
+ double dist;
+ int p;
+ int index;
+} diamond_t;
+
+static bool diamond_compare(diamond_t const& a, diamond_t const& b)
+{
+ return a.dist < b.dist;
+}
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers)
+{
+ assert(num_points <= PTM_MAX_INPUT_POINTS);
+
+ diamond_t data[4 * (PTM_MAX_INPUT_POINTS - 5)];
+ int index = 0;
+ for (int i=5;i<num_points;i++)
+ {
+ for (int j=1;j<5;j++)
+ {
+ double dx = unpermuted_points[i][0] - unpermuted_points[j][0];
+ double dy = unpermuted_points[i][1] - unpermuted_points[j][1];
+ double dz = unpermuted_points[i][2] - unpermuted_points[j][2];
+
+ double d = dx*dx + dy*dy + dz*dz;
+
+ data[index].p = j - 1;
+ data[index].index = i;
+ data[index].dist = d;
+ index++;
+ }
+ }
+ int n = index;
+
+ std::sort(data, data + n, &diamond_compare);
+
+ for (index=0;index<5;index++)
+ ordering[index] = index;
+
+ int num_found = 0;
+ bool hit[PTM_MAX_INPUT_POINTS] = {0};
+ int counts[4] = {0};
+ for (int i=0;i<n;i++)
+ {
+ int p = data[i].p;
+ int q = data[i].index;
+ if (hit[q] || counts[p] >= 3)
+ continue;
+
+ ordering[1 + 4 + 3 * p + counts[p]] = q;
+ counts[p]++;
+ index++;
+ num_found++;
+ if (num_found >= 12)
+ break;
+ }
+
+ if (num_found != 12)
+ return -1;
+
+ for (int i=0;i<PTM_NUM_NBRS_DCUB+1;i++)
+ {
+ memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
+
+ if (unpermuted_numbers != NULL)
+ numbers[i] = unpermuted_numbers[ordering[i]];
+ }
+
+ return 0;
+}
+
diff --git a/src/PTM/ptm_neighbour_ordering.h b/src/PTM/ptm_neighbour_ordering.h
new file mode 100644
index 0000000000..ce4dfca2c0
--- /dev/null
+++ b/src/PTM/ptm_neighbour_ordering.h
@@ -0,0 +1,13 @@
+#ifndef PTM_NEIGHBOUR_ORDERING_H
+#define PTM_NEIGHBOUR_ORDERING_H
+
+int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
+
+int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
+ int8_t* ordering, double (*points)[3], int32_t* numbers);
+
+void* voronoi_initialize_local();
+void voronoi_uninitialize_local(void* ptr);
+
+#endif
+
diff --git a/src/PTM/ptm_normalize_vertices.cpp b/src/PTM/ptm_normalize_vertices.cpp
new file mode 100644
index 0000000000..61dca5006f
--- /dev/null
+++ b/src/PTM/ptm_normalize_vertices.cpp
@@ -0,0 +1,55 @@
+#include <cmath>
+
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
+{
+ //calculate barycentre
+ double sum[3] = {0, 0, 0};
+ for (int i=0;i<num;i++)
+ {
+ sum[0] += points[i][0];
+ sum[1] += points[i][1];
+ sum[2] += points[i][2];
+ }
+
+ sum[0] /= num;
+ sum[1] /= num;
+ sum[2] /= num;
+
+ //subtract barycentre
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] = points[i][0] - sum[0];
+ normalized[i][1] = points[i][1] - sum[1];
+ normalized[i][2] = points[i][2] - sum[2];
+ }
+}
+
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
+{
+ subtract_barycentre(num, points, normalized);
+
+ //calculate mean length
+ double scale = 0.0;
+ for (int i=1;i<num;i++)
+ {
+ double x = normalized[i][0];
+ double y = normalized[i][1];
+ double z = normalized[i][2];
+
+ double norm = sqrt(x*x + y*y + z*z);
+ scale += norm;
+ }
+ scale /= num;
+
+ //scale vertices such that mean length is 1
+ for (int i=0;i<num;i++)
+ {
+ normalized[i][0] /= scale;
+ normalized[i][1] /= scale;
+ normalized[i][2] /= scale;
+ }
+
+ return scale;
+}
+
diff --git a/src/PTM/ptm_normalize_vertices.h b/src/PTM/ptm_normalize_vertices.h
new file mode 100644
index 0000000000..2c7b722752
--- /dev/null
+++ b/src/PTM/ptm_normalize_vertices.h
@@ -0,0 +1,8 @@
+#ifndef PTM_NORMALIZE_VERTICES_H
+#define PTM_NORMALIZE_VERTICES_H
+
+void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
+double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
+
+#endif
+
diff --git a/src/PTM/ptm_polar.cpp b/src/PTM/ptm_polar.cpp
new file mode 100644
index 0000000000..9089b327b9
--- /dev/null
+++ b/src/PTM/ptm_polar.cpp
@@ -0,0 +1,337 @@
+/*******************************************************************************
+ * -/_|:|_|_\-
+ *
+ * This code is a modification of D.L. Theobald's QCP rotation code.
+ * It has been adapted to calculate the polar decomposition of a 3x3 matrix
+ * Adaption by P.M. Larsen
+ *
+ * Original Author(s): Douglas L. Theobald
+ * Department of Biochemistry
+ * MS 009
+ * Brandeis University
+ * 415 South St
+ * Waltham, MA 02453
+ * USA
+ *
+ * dtheobald@brandeis.edu
+ *
+ * Pu Liu
+ * Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
+ * 665 Stockton Drive
+ * Exton, PA 19341
+ * USA
+ *
+ * pliu24@its.jnj.com
+ *
+ *
+ * If you use this QCP rotation calculation method in a publication, please
+ * reference:
+ *
+ * Douglas L. Theobald (2005)
+ * "Rapid calculation of RMSD using a quaternion-based characteristic
+ * polynomial."
+ * Acta Crystallographica A 61(4):478-480.
+ *
+ * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
+ * "Fast determination of the optimal rotational matrix for macromolecular
+ * superpositions."
+ * Journal of Computational Chemistry 31(7):1561-1563.
+ *
+ *
+ * Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without modification, are permitted
+ * provided that the following conditions are met:
+ *
+ * * Redistributions of source code must retain the above copyright notice, this list of
+ * conditions and the following disclaimer.
+ * * Redistributions in binary form must reproduce the above copyright notice, this list
+ * of conditions and the following disclaimer in the documentation and/or other materials
+ * provided with the distribution.
+ * * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to
+ * endorse or promote products derived from this software without specific prior written
+ * permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Source: started anew.
+ *
+ * Change History:
+ * 2009/04/13 Started source
+ * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr
+ * If trying all rows of the adjoint still gives too small
+ * qsqr, then just return identity matrix. (DLT)
+ * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct()
+ * invalid mem access
+ * 2011/02/21 Made CenterCoords use weights
+ * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h
+ * Also changed some functions to static
+ * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error
+ * 2012/07/26 minor changes to comments and main.c, more info (v.1.4)
+ *
+ * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
+ * for use in Polyhedral Template Matching.
+ *
+ ******************************************************************************/
+
+#include <cmath>
+#include <algorithm>
+#include <string.h>
+#include "ptm_quat.h"
+
+
+static void matmul_3x3(double* A, double* x, double* b)
+{
+ b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
+ b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6];
+ b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6];
+
+ b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7];
+ b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7];
+ b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7];
+
+ b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8];
+ b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8];
+ b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8];
+}
+
+static double matrix_determinant_3x3(double* A)
+{
+ return A[0] * (A[4]*A[8] - A[5]*A[7])
+ - A[1] * (A[3]*A[8] - A[5]*A[6])
+ + A[2] * (A[3]*A[7] - A[4]*A[6]);
+}
+
+static void flip_matrix(double* A)
+{
+ for (int i=0;i<9;i++)
+ A[i] = -A[i];
+}
+
+static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt)
+{
+ const double evecprec = 1e-6;
+ const double evalprec = 1e-11;
+
+ double Sxx = A[0], Sxy = A[1], Sxz = A[2],
+ Syx = A[3], Syy = A[4], Syz = A[5],
+ Szx = A[6], Szy = A[7], Szz = A[8];
+
+ double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz,
+ Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz,
+ Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx;
+
+ double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2;
+
+ double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
+ double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
+ double SxzpSzx = Sxz + Szx;
+ double SyzpSzy = Syz + Szy;
+ double SxypSyx = Sxy + Syx;
+ double SyzmSzy = Syz - Szy;
+ double SxzmSzx = Sxz - Szx;
+ double SxymSyx = Sxy - Syx;
+ double SxxpSyy = Sxx + Syy;
+ double SxxmSyy = Sxx - Syy;
+ double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
+
+ double C[3];
+ C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
+ + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
+ + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz))
+ + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz))
+ + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz));
+
+ C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz);
+ C[2] = -2.0 * fnorm_squared;
+
+ //Newton-Raphson
+ double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0;
+ if (mxEigenV > evalprec)
+ {
+ for (int i=0;i<50;i++)
+ {
+ double oldg = mxEigenV;
+ double x2 = mxEigenV*mxEigenV;
+ double b = (x2 + C[2])*mxEigenV;
+ double a = b + C[1];
+ double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a));
+ mxEigenV -= delta;
+ if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
+ break;
+ }
+ }
+ else
+ {
+ mxEigenV = 0.0;
+ }
+
+ (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV));
+
+ double a11 = SxxpSyy + Szz - mxEigenV;
+ double a12 = SyzmSzy;
+ double a13 = -SxzmSzx;
+ double a14 = SxymSyx;
+
+ double a21 = SyzmSzy;
+ double a22 = SxxmSyy - Szz -mxEigenV;
+ double a23 = SxypSyx;
+ double a24 = SxzpSzx;
+
+ double a31 = a13;
+ double a32 = a23;
+ double a33 = Syy - Sxx - Szz - mxEigenV;
+ double a34 = SyzpSzy;
+
+ double a41 = a14;
+ double a42 = a24;
+ double a43 = a34;
+ double a44 = Szz - SxxpSyy - mxEigenV;
+
+ double a3344_4334 = a33 * a44 - a43 * a34;
+ double a3244_4234 = a32 * a44 - a42 * a34;
+ double a3243_4233 = a32 * a43 - a42 * a33;
+ double a3143_4133 = a31 * a43 - a41 * a33;
+ double a3144_4134 = a31 * a44 - a41 * a34;
+ double a3142_4132 = a31 * a42 - a41 * a32;
+ double a1324_1423 = a13 * a24 - a14 * a23;
+ double a1224_1422 = a12 * a24 - a14 * a22;
+ double a1223_1322 = a12 * a23 - a13 * a22;
+ double a1124_1421 = a11 * a24 - a14 * a21;
+ double a1123_1321 = a11 * a23 - a13 * a21;
+ double a1122_1221 = a11 * a22 - a12 * a21;
+
+ double q[4][4];
+ q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233;
+ q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
+ q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132;
+ q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132;
+
+ q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
+ q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133;
+ q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
+ q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132;
+
+ q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
+ q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321;
+ q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
+ q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221;
+
+ q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
+ q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321;
+ q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
+ q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
+
+ double qsqr[4];
+ for (int i=0;i<4;i++)
+ qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3];
+
+ int bi = 0;
+ double max = 0;
+ for (int i=0;i<4;i++)
+ {
+ if (qsqr[i] > max)
+ {
+ bi = i;
+ max = qsqr[i];
+ }
+ }
+
+ bool too_small = false;
+ if (qsqr[bi] < evecprec)
+ {
+ //if qsqr is still too small, return the identity rotation.
+ q[bi][0] = 1;
+ q[bi][1] = 0;
+ q[bi][2] = 0;
+ q[bi][3] = 0;
+ too_small = true;
+ }
+ else
+ {
+ double normq = sqrt(qsqr[bi]);
+ q[bi][0] /= normq;
+ q[bi][1] /= normq;
+ q[bi][2] /= normq;
+ q[bi][3] /= normq;
+ }
+
+ memcpy(qopt, q[bi], 4 * sizeof(double));
+ return !too_small;
+}
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P)
+{
+ double A[9];
+ memcpy(A, _A, 9 * sizeof(double));
+
+ double det = matrix_determinant_3x3(A);
+ if (det < 0)
+ flip_matrix(A);
+
+ double q[4];
+ double nrmsdsq = 0;
+ optimal_quaternion(A, true, -1, &nrmsdsq, q);
+ q[0] = -q[0];
+ quaternion_to_rotation_matrix(q, U);
+
+ if (det < 0)
+ flip_matrix(U);
+
+ double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]};
+
+ if (right_sided)
+ matmul_3x3(UT, _A, P);
+ else
+ matmul_3x3(_A, UT, P);
+
+ return 0;
+}
+
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation)
+{
+ A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0;
+
+ for (int i = 0; i < num; ++i)
+ {
+ double x1 = coords1[i][0];
+ double y1 = coords1[i][1];
+ double z1 = coords1[i][2];
+
+ double x2 = coords2[permutation[i]][0];
+ double y2 = coords2[permutation[i]][1];
+ double z2 = coords2[permutation[i]][2];
+
+ A[0] += x1 * x2;
+ A[1] += x1 * y2;
+ A[2] += x1 * z2;
+
+ A[3] += y1 * x2;
+ A[4] += y1 * y2;
+ A[5] += y1 * z2;
+
+ A[6] += z1 * x2;
+ A[7] += z1 * y2;
+ A[8] += z1 * z2;
+ }
+}
+
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U)
+{
+ optimal_quaternion(A, false, E0, p_nrmsdsq, q);
+ quaternion_to_rotation_matrix(q, U);
+ return 0;
+}
+
diff --git a/src/PTM/ptm_polar.h b/src/PTM/ptm_polar.h
new file mode 100644
index 0000000000..d5aa3d9540
--- /dev/null
+++ b/src/PTM/ptm_polar.h
@@ -0,0 +1,12 @@
+#ifndef PTM_POLAR_H
+#define PTM_POLAR_H
+
+#include <stdint.h>
+#include <stdbool.h>
+
+int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
+void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
+int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
+
+#endif
+
diff --git a/src/PTM/ptm_quat.cpp b/src/PTM/ptm_quat.cpp
new file mode 100644
index 0000000000..f55aff3d2b
--- /dev/null
+++ b/src/PTM/ptm_quat.cpp
@@ -0,0 +1,396 @@
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+
+
+#define SIGN(x) (x >= 0 ? 1 : -1)
+#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
+#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
+
+
+#define SQRT_2 1.4142135623730951454746218587388284504414
+#define HALF_SQRT_2 0.7071067811865474617150084668537601828575
+
+#define PHI 1.6180339887498949025257388711906969547272
+#define HALF_PHI 0.8090169943749474512628694355953484773636
+
+#define INV_PHI 0.6180339887498947915034364086750429123640
+#define HALF_INV_PHI 0.3090169943749473957517182043375214561820
+
+#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089
+#define SQRT_2_3 0.8164965809277260344600790631375275552273
+#define SQRT_1_6 0.4082482904638630172300395315687637776136
+
+
+double generator_cubic[24][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 },
+ {HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
+ {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
+ {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
+ {0, HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, HALF_SQRT_2, HALF_SQRT_2 },
+ {0, -HALF_SQRT_2, HALF_SQRT_2, 0 },
+ {0, -HALF_SQRT_2, 0, HALF_SQRT_2 },
+ {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } };
+
+double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 },
+ {0, 1, 0, 0 },
+ {0, 0, 1, 0 },
+ {0, 0, 0, 1 },
+ {0.5, 0.5, 0.5, 0.5 },
+ {0.5, 0.5, -0.5, 0.5 },
+ {0.5, -0.5, 0.5, 0.5 },
+ {0.5, -0.5, -0.5, 0.5 },
+ {-0.5, 0.5, 0.5, 0.5 },
+ {-0.5, 0.5, -0.5, 0.5 },
+ {-0.5, -0.5, 0.5, 0.5 },
+ {-0.5, -0.5, -0.5, 0.5 } };
+
+double generator_hcp[6][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6},
+ {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6},
+ {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} };
+
+double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5} };
+
+double generator_icosahedral[60][4] = { {1, 0, 0, 0},
+ {HALF_PHI, -HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, -HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, HALF_INV_PHI, -0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, -0.5},
+ {HALF_PHI, -0.5, 0, HALF_INV_PHI},
+ {HALF_PHI, 0.5, 0, -HALF_INV_PHI},
+ {HALF_PHI, 0, -HALF_INV_PHI, 0.5},
+ {HALF_PHI, -HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0, HALF_INV_PHI, 0.5},
+ {HALF_PHI, HALF_INV_PHI, 0.5, 0},
+ {HALF_PHI, 0.5, 0, HALF_INV_PHI},
+ {0.5, HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, HALF_PHI, HALF_INV_PHI, 0},
+ {0.5, 0.5, 0.5, 0.5},
+ {0.5, 0.5, 0.5, -0.5},
+ {0.5, 0.5, -0.5, 0.5},
+ {0.5, 0.5, -0.5, -0.5},
+ {0.5, HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, 0, HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, HALF_PHI, HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, -HALF_INV_PHI},
+ {0.5, 0, -HALF_PHI, HALF_INV_PHI},
+ {0.5, -HALF_INV_PHI, 0, HALF_PHI},
+ {0.5, -HALF_INV_PHI, 0, -HALF_PHI},
+ {0.5, -0.5, 0.5, 0.5},
+ {0.5, -0.5, 0.5, -0.5},
+ {0.5, -0.5, -0.5, 0.5},
+ {0.5, -0.5, -0.5, -0.5},
+ {0.5, -HALF_PHI, -HALF_INV_PHI, 0},
+ {0.5, -HALF_PHI, HALF_INV_PHI, 0},
+ {HALF_INV_PHI, -HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, 0, -0.5, -HALF_PHI},
+ {HALF_INV_PHI, -0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, 0, 0.5, -HALF_PHI},
+ {HALF_INV_PHI, -HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0.5, -HALF_PHI, 0},
+ {HALF_INV_PHI, HALF_PHI, 0, -0.5},
+ {HALF_INV_PHI, -0.5, HALF_PHI, 0},
+ {HALF_INV_PHI, 0, -0.5, HALF_PHI},
+ {HALF_INV_PHI, HALF_PHI, 0, 0.5},
+ {HALF_INV_PHI, 0, 0.5, HALF_PHI},
+ {HALF_INV_PHI, 0.5, HALF_PHI, 0},
+ {0, 1, 0, 0},
+ {0, HALF_PHI, -0.5, HALF_INV_PHI},
+ {0, HALF_PHI, -0.5, -HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, HALF_INV_PHI},
+ {0, HALF_PHI, 0.5, -HALF_INV_PHI},
+ {0, 0.5, HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, HALF_INV_PHI, HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, -HALF_PHI},
+ {0, 0.5, -HALF_INV_PHI, HALF_PHI},
+ {0, HALF_INV_PHI, -HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, -HALF_PHI, -0.5},
+ {0, HALF_INV_PHI, HALF_PHI, 0.5},
+ {0, HALF_INV_PHI, HALF_PHI, -0.5},
+ {0, 0, 1, 0},
+ {0, 0, 0, 1} };
+
+static void quat_rot(double* r, double* a, double* b)
+{
+ b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]);
+ b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]);
+ b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]);
+ b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]);
+}
+
+static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q)
+{
+ double max = 0.0;
+ int i = 0, bi = -1;
+ for (i=0;i<num_generators;i++)
+ {
+ double* g = generator[i];
+ double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]);
+ if (t > max)
+ {
+ max = t;
+ bi = i;
+ }
+ }
+
+ double f[4];
+ quat_rot(q, generator[bi], f);
+ memcpy(q, &f, 4 * sizeof(double));
+ if (q[0] < 0)
+ {
+ q[0] = -q[0];
+ q[1] = -q[1];
+ q[2] = -q[2];
+ q[3] = -q[3];
+ }
+
+ return bi;
+}
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q);
+}
+
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q);
+}
+
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q);
+}
+
+int rotate_quaternion_into_hcp_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q);
+}
+
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q)
+{
+ return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q);
+}
+
+double quat_dot(double* a, double* b)
+{
+ return a[0] * b[0]
+ + a[1] * b[1]
+ + a[2] * b[2]
+ + a[3] * b[3];
+}
+
+double quat_size(double* q)
+{
+ return sqrt(quat_dot(q, q));
+}
+
+void normalize_quaternion(double* q)
+{
+ double size = quat_size(q);
+
+ q[0] /= size;
+ q[1] /= size;
+ q[2] /= size;
+ q[3] /= size;
+}
+
+void rotation_matrix_to_quaternion(double* u, double* q)
+{
+ double r11 = u[0];
+ double r12 = u[1];
+ double r13 = u[2];
+ double r21 = u[3];
+ double r22 = u[4];
+ double r23 = u[5];
+ double r31 = u[6];
+ double r32 = u[7];
+ double r33 = u[8];
+
+ q[0] = (1.0 + r11 + r22 + r33) / 4.0;
+ q[1] = (1.0 + r11 - r22 - r33) / 4.0;
+ q[2] = (1.0 - r11 + r22 - r33) / 4.0;
+ q[3] = (1.0 - r11 - r22 + r33) / 4.0;
+
+ q[0] = sqrt(MAX(0, q[0]));
+ q[1] = sqrt(MAX(0, q[1]));
+ q[2] = sqrt(MAX(0, q[2]));
+ q[3] = sqrt(MAX(0, q[3]));
+
+ double m0 = MAX(q[0], q[1]);
+ double m1 = MAX(q[2], q[3]);
+ double max = MAX(m0, m1);
+
+ int i = 0;
+ for (i=0;i<4;i++)
+ if (q[i] == max)
+ break;
+
+ if (i == 0)
+ {
+ q[1] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r13 - r31);
+ q[3] *= SIGN(r21 - r12);
+ }
+ else if (i == 1)
+ {
+ q[0] *= SIGN(r32 - r23);
+ q[2] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r13 + r31);
+ }
+ else if (i == 2)
+ {
+ q[0] *= SIGN(r13 - r31);
+ q[1] *= SIGN(r21 + r12);
+ q[3] *= SIGN(r32 + r23);
+ }
+ else if (i == 3)
+ {
+ q[0] *= SIGN(r21 - r12);
+ q[1] *= SIGN(r31 + r13);
+ q[2] *= SIGN(r32 + r23);
+ }
+
+ normalize_quaternion(q);
+}
+
+void quaternion_to_rotation_matrix(double* q, double* u)
+{
+ double a = q[0];
+ double b = q[1];
+ double c = q[2];
+ double d = q[3];
+
+ u[0] = a*a + b*b - c*c - d*d;
+ u[1] = 2*b*c - 2*a*d;
+ u[2] = 2*b*d + 2*a*c;
+
+ u[3] = 2*b*c + 2*a*d;
+ u[4] = a*a - b*b + c*c - d*d;
+ u[5] = 2*c*d - 2*a*b;
+
+ u[6] = 2*b*d - 2*a*c;
+ u[7] = 2*c*d + 2*a*b;
+ u[8] = a*a - b*b - c*c + d*d;
+}
+
+double quat_quick_misorientation(double* q1, double* q2)
+{
+ double t = quat_dot(q1, q2);
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_misorientation(double* q1, double* q2)
+{
+ return acos(quat_quick_misorientation(q1, q2));
+}
+
+
+double quat_quick_disorientation_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_cubic(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_cubic(q0, q1));
+}
+
+double quat_quick_disorientation_hcp(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_hcp_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_hcp(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_hcp(q0, q1));
+}
+
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1));
+}
+
+double quat_quick_disorientation_icosahedral(double* q0, double* q1)
+{
+ double qrot[4];
+ double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
+ quat_rot(qinv, q1, qrot);
+
+ rotate_quaternion_into_icosahedral_fundamental_zone(qrot);
+ double t = qrot[0];
+ t = MIN(1, MAX(-1, t));
+ return 2 * t * t - 1;
+}
+
+double quat_disorientation_icosahedral(double* q0, double* q1)
+{
+ return acos(quat_quick_disorientation_icosahedral(q0, q1));
+}
+
diff --git a/src/PTM/ptm_quat.h b/src/PTM/ptm_quat.h
new file mode 100644
index 0000000000..381c3ce876
--- /dev/null
+++ b/src/PTM/ptm_quat.h
@@ -0,0 +1,32 @@
+#ifndef PTM_QUAT_H
+#define PTM_QUAT_H
+
+int rotate_quaternion_into_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
+int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
+int rotate_quaternion_into_hcp_fundamental_zone(double* q);
+int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q);
+
+void normalize_quaternion(double* q);
+void quaternion_to_rotation_matrix(double* q, double* U);
+void rotation_matrix_to_quaternion(double* u, double* q);
+double quat_dot(double* a, double* b);
+double quat_quick_misorientation(double* q1, double* q2);
+double quat_misorientation(double* q1, double* q2);
+
+double quat_quick_disorientation_cubic(double* q0, double* q1);
+double quat_disorientation_cubic(double* q0, double* q1);
+double quat_quick_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_disorientation_diamond_cubic(double* q0, double* q1);
+double quat_quick_disorientation_hcp(double* q0, double* q1);
+double quat_disorientation_hcp(double* q0, double* q1);
+double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
+double quat_quick_disorientation_icosahedral(double* q0, double* q1);
+double quat_disorientation_icosahedral(double* q0, double* q1);
+
+#endif
+
+
+
+
diff --git a/src/PTM/ptm_structure_matcher.cpp b/src/PTM/ptm_structure_matcher.cpp
new file mode 100644
index 0000000000..7eb0a44143
--- /dev/null
+++ b/src/PTM/ptm_structure_matcher.cpp
@@ -0,0 +1,294 @@
+#include <cstdio>
+#include <cstdlib>
+#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cassert>
+#include <algorithm>
+#include "ptm_convex_hull_incremental.h"
+#include "ptm_canonical_coloured.h"
+#include "ptm_graph_data.h"
+#include "ptm_graph_tools.h"
+#include "ptm_normalize_vertices.h"
+#include "ptm_polar.h"
+#include "ptm_structure_matcher.h"
+#include "ptm_constants.h"
+
+
+static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
+ double G1, double G2, double E0, double* q, double* p_scale)
+{
+ double A0[9];
+ InnerProduct(A0, num_points, ideal_points, normalized, mapping);
+
+ double nrmsdsq, rot[9];
+ FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot);
+
+ double k0 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ for (int j=0;j<3;j++)
+ {
+ double v = 0.0;
+ for (int k=0;k<3;k++)
+ v += rot[j*3+k] * ideal_points[i][k];
+
+ k0 += v * normalized[mapping[i]][j];
+ }
+ }
+
+ double scale = k0 / G2;
+ *p_scale = scale;
+ return sqrt(fabs(G1 - scale*k0) / num_points);
+}
+
+static void check_graphs( const refdata_t* s,
+ uint64_t hash,
+ int8_t* canonical_labelling,
+ double (*normalized)[3],
+ result_t* res)
+{
+ int num_points = s->num_nbrs + 1;
+ const double (*ideal_points)[3] = s->points;
+ int8_t inverse_labelling[PTM_MAX_POINTS];
+ int8_t mapping[PTM_MAX_POINTS];
+
+ for (int i=0; i<num_points; i++)
+ inverse_labelling[ canonical_labelling[i] ] = i;
+
+ double G1 = 0, G2 = 0;
+ for (int i=0;i<num_points;i++)
+ {
+ double x1 = ideal_points[i][0];
+ double y1 = ideal_points[i][1];
+ double z1 = ideal_points[i][2];
+
+ double x2 = normalized[i][0];
+ double y2 = normalized[i][1];
+ double z2 = normalized[i][2];
+
+ G1 += x1 * x1 + y1 * y1 + z1 * z1;
+ G2 += x2 * x2 + y2 * y2 + z2 * z2;
+ }
+ double E0 = (G1 + G2) / 2;
+
+ for (int i = 0;i<s->num_graphs;i++)
+ {
+ if (hash != s->graphs[i].hash)
+ continue;
+
+ graph_t* gref = &s->graphs[i];
+ for (int j = 0;j<gref->num_automorphisms;j++)
+ {
+ for (int k=0;k<num_points;k++)
+ mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ];
+
+ double q[4], scale = 0;
+ double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale);
+ if (rmsd < res->rmsd)
+ {
+ res->rmsd = rmsd;
+ res->scale = scale;
+ res->ref_struct = s;
+ memcpy(res->q, q, 4 * sizeof(double));
+ memcpy(res->mapping, mapping, sizeof(int8_t) * num_points);
+ }
+ }
+ }
+}
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res)
+{
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != s->num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree);
+ if (max_degree > s->max_degree)
+ return PTM_NO_ERROR;
+
+ if (s->type == PTM_MATCH_SC)
+ for (int i = 0;i<s->num_nbrs;i++)
+ if (degree[i] != 4)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(s->num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ check_graphs(s, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_fcc.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_fcc.max_degree;
+
+ int8_t degree[PTM_MAX_NBRS];
+ int8_t facets[PTM_MAX_FACETS][3];
+
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ if (ch->num_facets != num_facets)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res);
+ return PTM_NO_ERROR;
+}
+
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
+{
+ int num_nbrs = structure_dcub.num_nbrs;
+ int num_facets = structure_fcc.num_facets;
+ int max_degree = structure_dcub.max_degree;
+
+
+ int8_t facets[PTM_MAX_FACETS][3];
+ int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
+ ch->ok = ret >= 0;
+ if (ret != 0)
+ return PTM_NO_ERROR;
+
+ //check for facets with multiple inner atoms
+ bool inverted[4] = {false, false, false, false};
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int n = 0;
+ for (int j=0;j<3;j++)
+ {
+ if (facets[i][j] <= 3)
+ {
+ inverted[facets[i][j]] = true;
+ n++;
+ }
+ }
+ if (n > 1)
+ return PTM_NO_ERROR;
+ }
+
+ int num_inverted = 0;
+ for (int i=0;i<4;i++)
+ num_inverted += inverted[i] ? 1 : 0;
+
+ if (ch->num_facets != num_facets + 2 * num_inverted)
+ return PTM_NO_ERROR; //incorrect number of facets in convex hull
+
+ int8_t degree[PTM_MAX_NBRS];
+ int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ int num_found = 0;
+ int8_t toadd[4][3];
+ for (int i=0;i<ch->num_facets;i++)
+ {
+ int a = facets[i][0];
+ int b = facets[i][1];
+ int c = facets[i][2];
+ if (a <= 3 || b <= 3 || c <= 3)
+ continue;
+
+ int i0 = (a - 4) / 3;
+ int i1 = (b - 4) / 3;
+ int i2 = (c - 4) / 3;
+
+ if (i0 == i1 && i0 == i2)
+ {
+ if (num_found + num_inverted >= 4)
+ return PTM_NO_ERROR;
+
+ toadd[num_found][0] = a;
+ toadd[num_found][1] = b;
+ toadd[num_found][2] = c;
+ num_found++;
+
+ memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t));
+ ch->num_facets--;
+ i--;
+ }
+ }
+
+ if (num_found + num_inverted != 4)
+ return PTM_NO_ERROR;
+
+ for (int i=0;i<num_found;i++)
+ {
+ int a = toadd[i][0];
+ int b = toadd[i][1];
+ int c = toadd[i][2];
+
+ int i0 = (a - 4) / 3;
+
+ facets[ch->num_facets][0] = i0;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = i0;
+ facets[ch->num_facets][2] = c;
+ ch->num_facets++;
+
+ facets[ch->num_facets][0] = a;
+ facets[ch->num_facets][1] = b;
+ facets[ch->num_facets][2] = i0;
+ ch->num_facets++;
+ }
+
+ _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree);
+ if (_max_degree > max_degree)
+ return PTM_NO_ERROR;
+
+ double normalized[PTM_MAX_POINTS][3];
+ subtract_barycentre(num_nbrs + 1, points, normalized);
+
+ int8_t code[2 * PTM_MAX_EDGES];
+ int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+ int8_t canonical_labelling[PTM_MAX_POINTS];
+ uint64_t hash = 0;
+ ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
+ if (ret != PTM_NO_ERROR)
+ return ret;
+
+ if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res);
+ if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res);
+
+ return PTM_NO_ERROR;
+}
+
diff --git a/src/PTM/ptm_structure_matcher.h b/src/PTM/ptm_structure_matcher.h
new file mode 100644
index 0000000000..4b6f969597
--- /dev/null
+++ b/src/PTM/ptm_structure_matcher.h
@@ -0,0 +1,21 @@
+#ifndef PTM_STRUCTURE_MATCHER_H
+#define PTM_STRUCTURE_MATCHER_H
+
+#include "ptm_initialize_data.h"
+#include "ptm_constants.h"
+
+typedef struct
+{
+ double rmsd;
+ double scale;
+ double q[4]; //rotation in quaternion form (rigid body transformation)
+ int8_t mapping[PTM_MAX_POINTS];
+ const refdata_t* ref_struct;
+} result_t;
+
+int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res);
+int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+
+#endif
+
diff --git a/src/PTM/ptm_voronoi_cell.cpp b/src/PTM/ptm_voronoi_cell.cpp
new file mode 100644
index 0000000000..6503ea16c6
--- /dev/null
+++ b/src/PTM/ptm_voronoi_cell.cpp
@@ -0,0 +1,1368 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file cell.cc
+ * \brief Function implementations for the voronoicell and related classes. */
+
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include "ptm_voronoi_config.h"
+#include "ptm_voronoi_cell.h"
+
+namespace voro {
+
+inline void voro_fatal_error(const char *p,int status) {
+ fprintf(stderr,"voro++: %s\n",p);
+ exit(status);
+ //return -1;//status;
+}
+
+/** Constructs a Voronoi cell and sets up the initial memory. */
+voronoicell_base::voronoicell_base() :
+ current_vertices(init_vertices), current_vertex_order(init_vertex_order),
+ current_delete_size(init_delete_size), current_delete2_size(init_delete2_size),
+ ed(new int*[current_vertices]), nu(new int[current_vertices]),
+ pts(new double[3*current_vertices]), mem(new int[current_vertex_order]),
+ mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]),
+ ds(new int[current_delete_size]), stacke(ds+current_delete_size),
+ ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size),
+ current_marginal(init_marginal), marg(new int[current_marginal]) {
+ int i;
+ for(i=0;i<3;i++) {
+ mem[i]=init_n_vertices;mec[i]=0;
+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
+ }
+ mem[3]=init_3_vertices;mec[3]=0;
+ mep[3]=new int[init_3_vertices*7];
+ for(i=4;i<current_vertex_order;i++) {
+ mem[i]=init_n_vertices;mec[i]=0;
+ mep[i]=new int[init_n_vertices*((i<<1)+1)];
+ }
+}
+
+/** The voronoicell destructor deallocates all the dynamic memory. */
+voronoicell_base::~voronoicell_base() {
+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mep[i];
+ delete [] marg;
+ delete [] ds2;delete [] ds;
+ delete [] mep;delete [] mec;
+ delete [] mem;delete [] pts;
+ delete [] nu;delete [] ed;
+}
+
+/** Ensures that enough memory is allocated prior to carrying out a copy.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] vb a pointered to the class to be copied. */
+template<class vc_class>
+void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) {
+ while(current_vertex_order<vb->current_vertex_order) add_memory_vorder(vc);
+ for(int i=0;i<current_vertex_order;i++) while(mem[i]<vb->mec[i]) add_memory(vc,i,ds2);
+ while(current_vertices<vb->p) add_memory_vertices(vc);
+}
+
+/** Increases the memory storage for a particular vertex order, by increasing
+ * the size of the of the corresponding mep array. If the arrays already exist,
+ * their size is doubled; if they don't exist, then new ones of size
+ * init_n_vertices are allocated. The routine also ensures that the pointers in
+ * the ed array are updated, by making use of the back pointers. For the cases
+ * where the back pointer has been temporarily overwritten in the marginal
+ * vertex code, the auxiliary delete stack is scanned to find out how to update
+ * the ed value. If the template has been instantiated with the neighbor
+ * tracking turned on, then the routine also reallocates the corresponding mne
+ * array.
+ * \param[in] i the order of the vertex memory to be increased. */
+template<class vc_class>
+void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) {
+ int s=(i<<1)+1;
+ if(mem[i]==0) {
+ vc.n_allocate(i,init_n_vertices);
+ mep[i]=new int[init_n_vertices*s];
+ mem[i]=init_n_vertices;
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Order %d vertex memory created\n",i);
+#endif
+ } else {
+ int j=0,k,*l;
+ mem[i]<<=1;
+ if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]);
+#endif
+ l=new int[s*mem[i]];
+ int m=0;
+ vc.n_allocate_aux1(i);
+ while(j<s*mec[i]) {
+ k=mep[i][j+(i<<1)];
+ if(k>=0) {
+ ed[k]=l+j;
+ vc.n_set_to_aux1_offset(k,m);
+ } else {
+ int *dsp;
+ for(dsp=ds2;dsp<stackp2;dsp++) {
+ if(ed[*dsp]==mep[i]+j) {
+ ed[*dsp]=l+j;
+ vc.n_set_to_aux1_offset(*dsp,m);
+ break;
+ }
+ }
+ if(dsp==stackp2) voro_fatal_error("Couldn't relocate dangling pointer",VOROPP_INTERNAL_ERROR);
+#if VOROPP_VERBOSE >=3
+ fputs("Relocated dangling pointer",stderr);
+#endif
+ }
+ for(k=0;k<s;k++,j++) l[j]=mep[i][j];
+ for(k=0;k<i;k++,m++) vc.n_copy_to_aux1(i,m);
+ }
+ delete [] mep[i];
+ mep[i]=l;
+ vc.n_switch_to_aux1(i);
+ }
+}
+
+/** Doubles the maximum number of vertices allowed, by reallocating the ed, nu,
+ * and pts arrays. If the allocation exceeds the absolute maximum set in
+ * max_vertices, then the routine exits with a fatal error. If the template has
+ * been instantiated with the neighbor tracking turned on, then the routine
+ * also reallocates the ne array. */
+template<class vc_class>
+void voronoicell_base::add_memory_vertices(vc_class &vc) {
+
+printf("nope: %d\n", current_vertices);
+exit(3);
+
+ int i=(current_vertices<<1),j,**pp,*pnu;
+ if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Vertex memory scaled up to %d\n",i);
+#endif
+ double *ppts;
+ pp=new int*[i];
+ for(j=0;j<current_vertices;j++) pp[j]=ed[j];
+ delete [] ed;ed=pp;
+ vc.n_add_memory_vertices(i);
+ pnu=new int[i];
+ for(j=0;j<current_vertices;j++) pnu[j]=nu[j];
+ delete [] nu;nu=pnu;
+ ppts=new double[3*i];
+ for(j=0;j<3*current_vertices;j++) ppts[j]=pts[j];
+ delete [] pts;pts=ppts;
+ current_vertices=i;
+}
+
+/** Doubles the maximum allowed vertex order, by reallocating mem, mep, and mec
+ * arrays. If the allocation exceeds the absolute maximum set in
+ * max_vertex_order, then the routine causes a fatal error. If the template has
+ * been instantiated with the neighbor tracking turned on, then the routine
+ * also reallocates the mne array. */
+template<class vc_class>
+void voronoicell_base::add_memory_vorder(vc_class &vc) {
+ int i=(current_vertex_order<<1),j,*p1,**p2;
+ if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
+#endif
+ p1=new int[i];
+ for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];while(j<i) p1[j++]=0;
+ delete [] mem;mem=p1;
+ p2=new int*[i];
+ for(j=0;j<current_vertex_order;j++) p2[j]=mep[j];
+ delete [] mep;mep=p2;
+ p1=new int[i];
+ for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];while(j<i) p1[j++]=0;
+ delete [] mec;mec=p1;
+ vc.n_add_memory_vorder(i);
+ current_vertex_order=i;
+}
+
+/** Doubles the size allocation of the main delete stack. If the allocation
+ * exceeds the absolute maximum set in max_delete_size, then routine causes a
+ * fatal error. */
+void voronoicell_base::add_memory_ds(int *&stackp) {
+ current_delete_size<<=1;
+ if(current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size);
+#endif
+ int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds;
+ while(dsp<stackp) *(dsnp++)=*(dsp++);
+ delete [] ds;ds=dsn;stackp=dsnp;
+ stacke=ds+current_delete_size;
+}
+
+/** Doubles the size allocation of the auxiliary delete stack. If the
+ * allocation exceeds the absolute maximum set in max_delete2_size, then the
+ * routine causes a fatal error. */
+void voronoicell_base::add_memory_ds2(int *&stackp2) {
+ current_delete2_size<<=1;
+ if(current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size);
+#endif
+ int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2;
+ while(dsp<stackp2) *(dsnp++)=*(dsp++);
+ delete [] ds2;ds2=dsn;stackp2=dsnp;
+ stacke2=ds2+current_delete2_size;
+}
+
+/** Initializes a Voronoi cell as a rectangular box with the given dimensions.
+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
+void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
+ for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
+ mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
+ *pts=xmin;pts[1]=ymin;pts[2]=zmin;
+ pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
+ pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
+ pts[9]=xmax;pts[10]=ymax;pts[11]=zmin;
+ pts[12]=xmin;pts[13]=ymin;pts[14]=zmax;
+ pts[15]=xmax;pts[16]=ymin;pts[17]=zmax;
+ pts[18]=xmin;pts[19]=ymax;pts[20]=zmax;
+ pts[21]=xmax;pts[22]=ymax;pts[23]=zmax;
+ int *q=mep[3];
+ *q=1;q[1]=4;q[2]=2;q[3]=2;q[4]=1;q[5]=0;q[6]=0;
+ q[7]=3;q[8]=5;q[9]=0;q[10]=2;q[11]=1;q[12]=0;q[13]=1;
+ q[14]=0;q[15]=6;q[16]=3;q[17]=2;q[18]=1;q[19]=0;q[20]=2;
+ q[21]=2;q[22]=7;q[23]=1;q[24]=2;q[25]=1;q[26]=0;q[27]=3;
+ q[28]=6;q[29]=0;q[30]=5;q[31]=2;q[32]=1;q[33]=0;q[34]=4;
+ q[35]=4;q[36]=1;q[37]=7;q[38]=2;q[39]=1;q[40]=0;q[41]=5;
+ q[42]=7;q[43]=2;q[44]=4;q[45]=2;q[46]=1;q[47]=0;q[48]=6;
+ q[49]=5;q[50]=3;q[51]=6;q[52]=2;q[53]=1;q[54]=0;q[55]=7;
+ *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
+ ed[4]=q+28;ed[5]=q+35;ed[6]=q+42;ed[7]=q+49;
+ *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=nu[6]=nu[7]=3;
+}
+
+/** Starting from a point within the current cutting plane, this routine attempts
+ * to find an edge to a point outside the cutting plane. This prevents the plane
+ * routine from .
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in,out] up */
+template<class vc_class>
+inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) {
+ int i,lp,lw,*j(ds2),*stackp2(ds2);
+ double l;
+ *(stackp2++)=up;
+ while(j<stackp2) {
+ up=*(j++);
+ for(i=0;i<nu[up];i++) {
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ if(lw==-1) return true;
+ else if(lw==0) add_to_stack(vc,lp,stackp2);
+ }
+ }
+ return false;
+}
+
+/** Adds a point to the auxiliary delete stack if it is not already there.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] lp the index of the point to add.
+ * \param[in,out] stackp2 a pointer to the end of the stack entries. */
+template<class vc_class>
+inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) {
+ for(int *k(ds2);k<stackp2;k++) if(*k==lp) return;
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=lp;
+}
+
+/** Cuts the Voronoi cell by a particle whose center is at a separation of
+ * (x,y,z) from the cell center. The value of rsq should be initially set to
+ * \f$x^2+y^2+z^2\f$.
+ * \param[in] vc a reference to the specialized version of the calling class.
+ * \param[in] (x,y,z) the normal vector to the plane.
+ * \param[in] rsq the distance along this vector of the plane.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely, true otherwise. */
+template<class vc_class>
+bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) {
+ int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp;
+ int us=0,ls=0,qs,iqs,cs,uw,qw,lw;
+ int *edp,*edd;
+ double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false;
+
+ // Initialize the safe testing routine
+ n_marg=0;px=x;py=y;pz=z;prsq=rsq;
+
+ // Test approximately sqrt(n)/4 points for their proximity to the plane
+ // and keep the one which is closest
+ uw=m_test(up,u);
+
+ // Starting from an initial guess, we now move from vertex to vertex,
+ // to try and find an edge which intersects the cutting plane,
+ // or a vertex which is on the plane
+ try {
+ if(uw==1) {
+
+ // The test point is inside the cutting plane.
+ us=0;
+ do {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ us++;
+ } while (us<nu[up]);
+
+ if(us==nu[up]) {
+ return false;
+ }
+
+ ls=ed[up][nu[up]+us];
+ while(lw==1) {
+ if(++count>=p) throw true;
+ u=l;up=lp;
+ for(us=0;us<ls;us++) {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ }
+ if(us==ls) {
+ us++;
+ while(us<nu[up]) {
+ lp=ed[up][us];
+ lw=m_test(lp,l);
+ if(l<u) break;
+ us++;
+ }
+ if(us==nu[up]) {
+ return false;
+ }
+ }
+ ls=ed[up][nu[up]+us];
+ }
+
+ // If the last point in the iteration is within the
+ // plane, we need to do the complicated setup
+ // routine. Otherwise, we use the regular iteration.
+ if(lw==0) {
+ up=lp;
+ complicated_setup=true;
+ } else complicated_setup=false;
+ } else if(uw==-1) {
+ us=0;
+ do {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ us++;
+ } while (us<nu[up]);
+ if(us==nu[up]) return true;
+
+ while(qw==-1) {
+ qs=ed[up][nu[up]+us];
+ if(++count>=p) throw true;
+ u=q;up=qp;
+ for(us=0;us<qs;us++) {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ }
+ if(us==qs) {
+ us++;
+ while(us<nu[up]) {
+ qp=ed[up][us];
+ qw=m_test(qp,q);
+ if(u<q) break;
+ us++;
+ }
+ if(us==nu[up]) return true;
+ }
+ }
+ if(qw==1) {
+ lp=up;ls=us;l=u;
+ up=qp;us=ed[lp][nu[lp]+ls];u=q;
+ complicated_setup=false;
+ } else {
+ up=qp;
+ complicated_setup=true;
+ }
+ } else {
+
+ // Our original test point was on the plane, so we
+ // automatically head for the complicated setup
+ // routine
+ complicated_setup=true;
+ }
+ }
+ catch(bool except) {
+ // This routine is a fall-back, in case floating point errors
+ // cause the usual search routine to fail. In the fall-back
+ // routine, we just test every edge to find one straddling
+ // the plane.
+#if VOROPP_VERBOSE >=1
+ fputs("Bailed out of convex calculation\n",stderr);
+#endif
+ qw=1;lw=0;
+ for(qp=0;qp<p;qp++) {
+ qw=m_test(qp,q);
+ if(qw==1) {
+
+ // The point is inside the cutting space. Now
+ // see if we can find a neighbor which isn't.
+ for(us=0;us<nu[qp];us++) {
+ lp=ed[qp][us];
+ if(lp<qp) {
+ lw=m_test(lp,l);
+ if(lw!=1) break;
+ }
+ }
+ if(us<nu[qp]) {
+ up=qp;
+ if(lw==0) {
+ complicated_setup=true;
+ } else {
+ complicated_setup=false;
+ u=q;
+ ls=ed[up][nu[up]+us];
+ }
+ break;
+ }
+ } else if(qw==-1) {
+
+ // The point is outside the cutting space. See
+ // if we can find a neighbor which isn't.
+ for(ls=0;ls<nu[qp];ls++) {
+ up=ed[qp][ls];
+ if(up<qp) {
+ uw=m_test(up,u);
+ if(uw!=-1) break;
+ }
+ }
+ if(ls<nu[qp]) {
+ if(uw==0) {
+ up=qp;
+ complicated_setup=true;
+ } else {
+ complicated_setup=false;
+ lp=qp;l=q;
+ us=ed[lp][nu[lp]+ls];
+ }
+ break;
+ }
+ } else {
+
+ // The point is in the plane, so we just
+ // proceed with the complicated setup routine
+ up=qp;
+ complicated_setup=true;
+ break;
+ }
+ }
+ if(qp==p) return qw==-1?true:false;
+ }
+
+ // We're about to add the first point of the new facet. In either
+ // routine, we have to add a point, so first check there's space for
+ // it.
+ if(p==current_vertices) add_memory_vertices(vc);
+
+ if(complicated_setup) {
+
+ // We want to be strict about reaching the conclusion that the
+ // cell is entirely within the cutting plane. It's not enough
+ // to find a vertex that has edges which are all inside or on
+ // the plane. If the vertex has neighbors that are also on the
+ // plane, we should check those too.
+ if(!search_for_outside_edge(vc,up)) return false;
+
+ // The search algorithm found a point which is on the cutting
+ // plane. We leave that point in place, and create a new one at
+ // the same location.
+ pts[3*p]=pts[3*up];
+ pts[3*p+1]=pts[3*up+1];
+ pts[3*p+2]=pts[3*up+2];
+
+ // Search for a collection of edges of the test vertex which
+ // are outside of the cutting space. Begin by testing the
+ // zeroth edge.
+ i=0;
+ lp=*ed[up];
+ lw=m_test(lp,l);
+ if(lw!=-1) {
+
+ // The first edge is either inside the cutting space,
+ // or lies within the cutting plane. Test the edges
+ // sequentially until we find one that is outside.
+ rp=lw;
+ do {
+ i++;
+
+ // If we reached the last edge with no luck
+ // then all of the vertices are inside
+ // or on the plane, so the cell is completely
+ // deleted
+ if(i==nu[up]) return false;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ } while (lw!=-1);
+ j=i+1;
+
+ // We found an edge outside the cutting space. Keep
+ // moving through these edges until we find one that's
+ // inside or on the plane.
+ while(j<nu[up]) {
+ lp=ed[up][j];
+ lw=m_test(lp,l);
+ if(lw!=-1) break;
+ j++;
+ }
+
+ // Compute the number of edges for the new vertex. In
+ // general it will be the number of outside edges
+ // found, plus two. But we need to recognize the
+ // special case when all but one edge is outside, and
+ // the remaining one is on the plane. For that case we
+ // have to reduce the edge count by one to prevent
+ // doubling up.
+ if(j==nu[up]&&i==1&&rp==0) {
+ nu[p]=nu[up];
+ double_edge=true;
+ } else nu[p]=j-i+2;
+ k=1;
+
+ // Add memory for the new vertex if needed, and
+ // initialize
+ while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
+ vc.n_set_pointer(p,nu[p]);
+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
+ ed[p][nu[p]<<1]=p;
+
+ // Copy the edges of the original vertex into the new
+ // one. Delete the edges of the original vertex, and
+ // update the relational table.
+ us=cycle_down(i,up);
+ while(i<j) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ qs=i==nu[up]?0:i;
+ } else {
+
+ // In this case, the zeroth edge is outside the cutting
+ // plane. Begin by searching backwards from the last
+ // edge until we find an edge which isn't outside.
+ i=nu[up]-1;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ while(lw==-1) {
+ i--;
+
+ // If i reaches zero, then we have a point in
+ // the plane all of whose edges are outside
+ // the cutting space, so we just exit
+ if(i==0) return true;
+ lp=ed[up][i];
+ lw=m_test(lp,l);
+ }
+
+ // Now search forwards from zero
+ j=1;
+ qp=ed[up][j];
+ qw=m_test(qp,q);
+ while(qw==-1) {
+ j++;
+ qp=ed[up][j];
+ qw=m_test(qp,l);
+ }
+
+ // Compute the number of edges for the new vertex. In
+ // general it will be the number of outside edges
+ // found, plus two. But we need to recognize the
+ // special case when all but one edge is outside, and
+ // the remaining one is on the plane. For that case we
+ // have to reduce the edge count by one to prevent
+ // doubling up.
+ if(i==j&&qw==0) {
+ double_edge=true;
+ nu[p]=nu[up];
+ } else {
+ nu[p]=nu[up]-i+j+1;
+ }
+
+ // Add memory to store the vertex if it doesn't exist
+ // already
+ k=1;
+ while(nu[p]>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
+
+ // Copy the edges of the original vertex into the new
+ // one. Delete the edges of the original vertex, and
+ // update the relational table.
+ vc.n_set_pointer(p,nu[p]);
+ ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
+ ed[p][nu[p]<<1]=p;
+ us=i++;
+ while(i<nu[up]) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ i=0;
+ while(i<j) {
+ qp=ed[up][i];
+ qs=ed[up][nu[up]+i];
+ vc.n_copy(p,k,up,i);
+ ed[p][k]=qp;
+ ed[p][nu[p]+k]=qs;
+ ed[qp][qs]=p;
+ ed[qp][nu[qp]+qs]=k;
+ ed[up][i]=-1;
+ i++;k++;
+ }
+ qs=j;
+ }
+ if(!double_edge) {
+ vc.n_copy(p,k,up,qs);
+ vc.n_set(p,0,p_id);
+ } else vc.n_copy(p,0,up,qs);
+
+ // Add this point to the auxiliary delete stack
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=up;
+
+ // Look at the edges on either side of the group that was
+ // detected. We're going to commence facet computation by
+ // moving along one of them. We are going to end up coming back
+ // along the other one.
+ cs=k;
+ qp=up;q=u;
+ i=ed[up][us];
+ us=ed[up][nu[up]+us];
+ up=i;
+ ed[qp][nu[qp]<<1]=-p;
+
+ } else {
+
+ // The search algorithm found an intersected edge between the
+ // points lp and up. Create a new vertex between them which
+ // lies on the cutting plane. Since u and l differ by at least
+ // the tolerance, this division should never screw up.
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=up;
+ r=u/(u-l);l=1-r;
+ pts[3*p]=pts[3*lp]*r+pts[3*up]*l;
+ pts[3*p+1]=pts[3*lp+1]*r+pts[3*up+1]*l;
+ pts[3*p+2]=pts[3*lp+2]*r+pts[3*up+2]*l;
+
+ // This point will always have three edges. Connect one of them
+ // to lp.
+ nu[p]=3;
+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
+ vc.n_set_pointer(p,3);
+ vc.n_set(p,0,p_id);
+ vc.n_copy(p,1,up,us);
+ vc.n_copy(p,2,lp,ls);
+ ed[p]=mep[3]+7*mec[3]++;
+ ed[p][6]=p;
+ ed[up][us]=-1;
+ ed[lp][ls]=p;
+ ed[lp][nu[lp]+ls]=1;
+ ed[p][1]=lp;
+ ed[p][nu[p]+1]=ls;
+ cs=2;
+
+ // Set the direction to move in
+ qs=cycle_up(us,up);
+ qp=up;q=u;
+ }
+
+ // When the code reaches here, we have initialized the first point, and
+ // we have a direction for moving it to construct the rest of the facet
+ cp=p;rp=p;p++;
+ while(qp!=up||qs!=us) {
+
+ // We're currently tracing round an intersected facet. Keep
+ // moving around it until we find a point or edge which
+ // intersects the plane.
+ lp=ed[qp][qs];
+ lw=m_test(lp,l);
+
+ if(lw==1) {
+
+ // The point is still in the cutting space. Just add it
+ // to the delete stack and keep moving.
+ qs=cycle_up(ed[qp][nu[qp]+qs],lp);
+ qp=lp;
+ q=l;
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=qp;
+
+ } else if(lw==-1) {
+
+ // The point is outside of the cutting space, so we've
+ // found an intersected edge. Introduce a regular point
+ // at the point of intersection. Connect it to the
+ // point we just tested. Also connect it to the previous
+ // new point in the facet we're constructing.
+ if(p==current_vertices) add_memory_vertices(vc);
+ r=q/(q-l);l=1-r;
+ pts[3*p]=pts[3*lp]*r+pts[3*qp]*l;
+ pts[3*p+1]=pts[3*lp+1]*r+pts[3*qp+1]*l;
+ pts[3*p+2]=pts[3*lp+2]*r+pts[3*qp+2]*l;
+ nu[p]=3;
+ if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
+ ls=ed[qp][qs+nu[qp]];
+ vc.n_set_pointer(p,3);
+ vc.n_set(p,0,p_id);
+ vc.n_copy(p,1,qp,qs);
+ vc.n_copy(p,2,lp,ls);
+ ed[p]=mep[3]+7*mec[3]++;
+ *ed[p]=cp;
+ ed[p][1]=lp;
+ ed[p][3]=cs;
+ ed[p][4]=ls;
+ ed[p][6]=p;
+ ed[lp][ls]=p;
+ ed[lp][nu[lp]+ls]=1;
+ ed[cp][cs]=p;
+ ed[cp][nu[cp]+cs]=0;
+ ed[qp][qs]=-1;
+ qs=cycle_up(qs,qp);
+ cp=p++;
+ cs=2;
+ } else {
+
+ // We've found a point which is on the cutting plane.
+ // We're going to introduce a new point right here, but
+ // first we need to figure out the number of edges it
+ // has.
+ if(p==current_vertices) add_memory_vertices(vc);
+
+ // If the previous vertex detected a double edge, our
+ // new vertex will have one less edge.
+ k=double_edge?0:1;
+ qs=ed[qp][nu[qp]+qs];
+ qp=lp;
+ iqs=qs;
+
+ // Start testing the edges of the current point until
+ // we find one which isn't outside the cutting space
+ do {
+ k++;
+ qs=cycle_up(qs,qp);
+ lp=ed[qp][qs];
+ lw=m_test(lp,l);
+ } while (lw==-1);
+
+ // Now we need to find out whether this marginal vertex
+ // we are on has been visited before, because if that's
+ // the case, we need to add vertices to the existing
+ // new vertex, rather than creating a fresh one. We also
+ // need to figure out whether we're in a case where we
+ // might be creating a duplicate edge.
+ j=-ed[qp][nu[qp]<<1];
+ if(qp==up&&qs==us) {
+
+ // If we're heading into the final part of the
+ // new facet, then we never worry about the
+ // duplicate edge calculation.
+ new_double_edge=false;
+ if(j>0) k+=nu[j];
+ } else {
+ if(j>0) {
+
+ // This vertex was visited before, so
+ // count those vertices to the ones we
+ // already have.
+ k+=nu[j];
+
+ // The only time when we might make a
+ // duplicate edge is if the point we're
+ // going to move to next is also a
+ // marginal point, so test for that
+ // first.
+ if(lw==0) {
+
+ // Now see whether this marginal point
+ // has been visited before.
+ i=-ed[lp][nu[lp]<<1];
+ if(i>0) {
+
+ // Now see if the last edge of that other
+ // marginal point actually ends up here.
+ if(ed[i][nu[i]-1]==j) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ } else {
+
+ // That marginal point hasn't been visited
+ // before, so we probably don't have to worry
+ // about duplicate edges, except in the
+ // case when that's the way into the end
+ // of the facet, because that way always creates
+ // an edge.
+ if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ }
+ } else new_double_edge=false;
+ } else {
+
+ // The vertex hasn't been visited
+ // before, but let's see if it's
+ // marginal
+ if(lw==0) {
+
+ // If it is, we need to check
+ // for the case that it's a
+ // small branch, and that we're
+ // heading right back to where
+ // we came from
+ i=-ed[lp][nu[lp]<<1];
+ if(i==cp) {
+ new_double_edge=true;
+ k-=1;
+ } else new_double_edge=false;
+ } else new_double_edge=false;
+ }
+ }
+
+ // k now holds the number of edges of the new vertex
+ // we are forming. Add memory for it if it doesn't exist
+ // already.
+ while(k>=current_vertex_order) add_memory_vorder(vc);
+ if(mec[k]==mem[k]) add_memory(vc,k,stackp2);
+
+ // Now create a new vertex with order k, or augment
+ // the existing one
+ if(j>0) {
+
+ // If we're augmenting a vertex but we don't
+ // actually need any more edges, just skip this
+ // routine to avoid memory confusion
+ if(nu[j]!=k) {
+ // Allocate memory and copy the edges
+ // of the previous instance into it
+ vc.n_set_aux1(k);
+ edp=mep[k]+((k<<1)+1)*mec[k]++;
+ i=0;
+ while(i<nu[j]) {
+ vc.n_copy_aux1(j,i);
+ edp[i]=ed[j][i];
+ edp[k+i]=ed[j][nu[j]+i];
+ i++;
+ }
+ edp[k<<1]=j;
+
+ // Remove the previous instance with
+ // fewer vertices from the memory
+ // structure
+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
+ if(edd!=ed[j]) {
+ for(lw=0;lw<=(nu[j]<<1);lw++) ed[j][lw]=edd[lw];
+ vc.n_set_aux2_copy(j,nu[j]);
+ vc.n_copy_pointer(edd[nu[j]<<1],j);
+ ed[edd[nu[j]<<1]]=ed[j];
+ }
+ vc.n_set_to_aux1(j);
+ ed[j]=edp;
+ } else i=nu[j];
+ } else {
+
+ // Allocate a new vertex of order k
+ vc.n_set_pointer(p,k);
+ ed[p]=mep[k]+((k<<1)+1)*mec[k]++;
+ ed[p][k<<1]=p;
+ if(stackp2==stacke2) add_memory_ds2(stackp2);
+ *(stackp2++)=qp;
+ pts[3*p]=pts[3*qp];
+ pts[3*p+1]=pts[3*qp+1];
+ pts[3*p+2]=pts[3*qp+2];
+ ed[qp][nu[qp]<<1]=-p;
+ j=p++;
+ i=0;
+ }
+ nu[j]=k;
+
+ // Unless the previous case was a double edge, connect
+ // the first available edge of the new vertex to the
+ // last one in the facet
+ if(!double_edge) {
+ ed[j][i]=cp;
+ ed[j][nu[j]+i]=cs;
+ vc.n_set(j,i,p_id);
+ ed[cp][cs]=j;
+ ed[cp][nu[cp]+cs]=i;
+ i++;
+ }
+
+ // Copy in the edges of the underlying vertex,
+ // and do one less if this was a double edge
+ qs=iqs;
+ while(i<(new_double_edge?k:k-1)) {
+ qs=cycle_up(qs,qp);
+ lp=ed[qp][qs];ls=ed[qp][nu[qp]+qs];
+ vc.n_copy(j,i,qp,qs);
+ ed[j][i]=lp;
+ ed[j][nu[j]+i]=ls;
+ ed[lp][ls]=j;
+ ed[lp][nu[lp]+ls]=i;
+ ed[qp][qs]=-1;
+ i++;
+ }
+ qs=cycle_up(qs,qp);
+ cs=i;
+ cp=j;
+ vc.n_copy(j,new_double_edge?0:cs,qp,qs);
+
+ // Update the double_edge flag, to pass it
+ // to the next instance of this routine
+ double_edge=new_double_edge;
+ }
+ }
+
+ // Connect the final created vertex to the initial one
+ ed[cp][cs]=rp;
+ *ed[rp]=cp;
+ ed[cp][nu[cp]+cs]=0;
+ ed[rp][nu[rp]]=cs;
+
+ // Delete points: first, remove any duplicates
+ dsp=ds;
+ while(dsp<stackp) {
+ j=*dsp;
+ if(ed[j][nu[j]]!=-1) {
+ ed[j][nu[j]]=-1;
+ dsp++;
+ } else *dsp=*(--stackp);
+ }
+
+ // Add the points in the auxiliary delete stack,
+ // and reset their back pointers
+ for(dsp=ds2;dsp<stackp2;dsp++) {
+ j=*dsp;
+ ed[j][nu[j]<<1]=j;
+ if(ed[j][nu[j]]!=-1) {
+ ed[j][nu[j]]=-1;
+ if(stackp==stacke) add_memory_ds(stackp);
+ *(stackp++)=j;
+ }
+ }
+
+ // Scan connections and add in extras
+ for(dsp=ds;dsp<stackp;dsp++) {
+ cp=*dsp;
+ for(edp=ed[cp];edp<ed[cp]+nu[cp];edp++) {
+ qp=*edp;
+ if(qp!=-1&&ed[qp][nu[qp]]!=-1) {
+ if(stackp==stacke) {
+ int dis=stackp-dsp;
+ add_memory_ds(stackp);
+ dsp=ds+dis;
+ }
+ *(stackp++)=qp;
+ ed[qp][nu[qp]]=-1;
+ }
+ }
+ }
+ up=0;
+
+ // Delete them from the array structure
+ while(stackp>ds) {
+ --p;
+ while(ed[p][nu[p]]==-1) {
+ j=nu[p];
+ edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]);
+ while(edp<ed[p]+(j<<1)+1) *(edp++)=*(edd++);
+ vc.n_set_aux2_copy(p,j);
+ vc.n_copy_pointer(ed[p][(j<<1)],p);
+ ed[ed[p][(j<<1)]]=ed[p];
+ --p;
+ }
+ up=*(--stackp);
+ if(up<p) {
+
+ // Vertex management
+ pts[3*up]=pts[3*p];
+ pts[3*up+1]=pts[3*p+1];
+ pts[3*up+2]=pts[3*p+2];
+
+ // Memory management
+ j=nu[up];
+ edp=ed[up];edd=(mep[j]+((j<<1)+1)*--mec[j]);
+ while(edp<ed[up]+(j<<1)+1) *(edp++)=*(edd++);
+ vc.n_set_aux2_copy(up,j);
+ vc.n_copy_pointer(ed[up][j<<1],up);
+ vc.n_copy_pointer(up,p);
+ ed[ed[up][j<<1]]=ed[up];
+
+ // Edge management
+ ed[up]=ed[p];
+ nu[up]=nu[p];
+ for(i=0;i<nu[up];i++) ed[ed[up][i]][ed[up][nu[up]+i]]=up;
+ ed[up][nu[up]<<1]=up;
+ } else up=p++;
+ }
+
+ // Check for any vertices of zero order
+ if(*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR);
+
+ // Collapse any order 2 vertices and exit
+ return collapse_order2(vc);
+}
+
+/** During the creation of a new facet in the plane routine, it is possible
+ * that some order two vertices may arise. This routine removes them.
+ * Suppose an order two vertex joins c and d. If there's a edge between
+ * c and d already, then the order two vertex is just removed; otherwise,
+ * the order two vertex is removed and c and d are joined together directly.
+ * It is possible this process will create order two or order one vertices,
+ * and the routine is continually run until all of them are removed.
+ * \return False if the vertex removal was unsuccessful, indicative of the cell
+ * reducing to zero volume and disappearing; true if the vertex removal
+ * was successful. */
+template<class vc_class>
+inline bool voronoicell_base::collapse_order2(vc_class &vc) {
+ if(!collapse_order1(vc)) return false;
+ int a,b,i,j,k,l;
+ while(mec[2]>0) {
+
+ // Pick a order 2 vertex and read in its edges
+ i=--mec[2];
+ j=mep[2][5*i];k=mep[2][5*i+1];
+ if(j==k) {
+#if VOROPP_VERBOSE >=1
+ fputs("Order two vertex joins itself",stderr);
+#endif
+ return false;
+ }
+
+ // Scan the edges of j to see if joins k
+ for(l=0;l<nu[j];l++) {
+ if(ed[j][l]==k) break;
+ }
+
+ // If j doesn't already join k, join them together.
+ // Otherwise delete the connection to the current
+ // vertex from j and k.
+ a=mep[2][5*i+2];b=mep[2][5*i+3];i=mep[2][5*i+4];
+ if(l==nu[j]) {
+ ed[j][a]=k;
+ ed[k][b]=j;
+ ed[j][nu[j]+a]=b;
+ ed[k][nu[k]+b]=a;
+ } else {
+ if(!delete_connection(vc,j,a,false)) return false;
+ if(!delete_connection(vc,k,b,true)) return false;
+ }
+
+ // Compact the memory
+ --p;
+ if(up==i) up=0;
+ if(p!=i) {
+ if(up==p) up=i;
+ pts[3*i]=pts[3*p];
+ pts[3*i+1]=pts[3*p+1];
+ pts[3*i+2]=pts[3*p+2];
+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
+ vc.n_copy_pointer(i,p);
+ ed[i]=ed[p];
+ nu[i]=nu[p];
+ ed[i][nu[i]<<1]=i;
+ }
+
+ // Collapse any order 1 vertices if they were created
+ if(!collapse_order1(vc)) return false;
+ }
+ return true;
+}
+
+/** Order one vertices can potentially be created during the order two collapse
+ * routine. This routine keeps removing them until there are none left.
+ * \return False if the vertex removal was unsuccessful, indicative of the cell
+ * having zero volume and disappearing; true if the vertex removal was
+ * successful. */
+template<class vc_class>
+inline bool voronoicell_base::collapse_order1(vc_class &vc) {
+ int i,j,k;
+ while(mec[1]>0) {
+ up=0;
+#if VOROPP_VERBOSE >=1
+ fputs("Order one collapse\n",stderr);
+#endif
+ i=--mec[1];
+ j=mep[1][3*i];k=mep[1][3*i+1];
+ i=mep[1][3*i+2];
+ if(!delete_connection(vc,j,k,false)) return false;
+ --p;
+ if(up==i) up=0;
+ if(p!=i) {
+ if(up==p) up=i;
+ pts[3*i]=pts[3*p];
+ pts[3*i+1]=pts[3*p+1];
+ pts[3*i+2]=pts[3*p+2];
+ for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
+ vc.n_copy_pointer(i,p);
+ ed[i]=ed[p];
+ nu[i]=nu[p];
+ ed[i][nu[i]<<1]=i;
+ }
+ }
+ return true;
+}
+
+/** This routine deletes the kth edge of vertex j and reorganizes the memory.
+ * If the neighbor computation is enabled, we also have to supply an handedness
+ * flag to decide whether to preserve the plane on the left or right of the
+ * connection.
+ * \return False if a zero order vertex was formed, indicative of the cell
+ * disappearing; true if the vertex removal was successful. */
+template<class vc_class>
+inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) {
+ int q=hand?k:cycle_up(k,j);
+ int i=nu[j]-1,l,*edp,*edd,m;
+#if VOROPP_VERBOSE >=1
+ if(i<1) {
+ fputs("Zero order vertex formed\n",stderr);
+ return false;
+ }
+#endif
+ if(mec[i]==mem[i]) add_memory(vc,i,ds2);
+ vc.n_set_aux1(i);
+ for(l=0;l<q;l++) vc.n_copy_aux1(j,l);
+ while(l<i) {
+ vc.n_copy_aux1_shift(j,l);
+ l++;
+ }
+ edp=mep[i]+((i<<1)+1)*mec[i]++;
+ edp[i<<1]=j;
+ for(l=0;l<k;l++) {
+ edp[l]=ed[j][l];
+ edp[l+i]=ed[j][l+nu[j]];
+ }
+ while(l<i) {
+ m=ed[j][l+1];
+ edp[l]=m;
+ k=ed[j][l+nu[j]+1];
+ edp[l+i]=k;
+ ed[m][nu[m]+k]--;
+ l++;
+ }
+
+ edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
+ for(l=0;l<=(nu[j]<<1);l++) ed[j][l]=edd[l];
+ vc.n_set_aux2_copy(j,nu[j]);
+ vc.n_set_to_aux2(edd[nu[j]<<1]);
+ vc.n_set_to_aux1(j);
+ ed[edd[nu[j]<<1]]=edd;
+ ed[j]=edp;
+ nu[j]=i;
+ return true;
+}
+
+/** Calculates the areas of each face of the Voronoi cell and prints the
+ * results to an output stream.
+ * \param[out] v the vector to store the results in. */
+void voronoicell_base::face_areas(std::vector<double> &v) {
+ double area;
+ v.clear();
+ int i,j,k,l,m,n;
+ double ux,uy,uz,vx,vy,vz,wx,wy,wz;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ area=0;
+ ed[i][j]=-1-k;
+ l=cycle_up(ed[i][nu[i]+j],k);
+ m=ed[k][l];ed[k][l]=-1-m;
+ while(m!=i) {
+ n=cycle_up(ed[k][nu[k]+l],m);
+ ux=pts[3*k]-pts[3*i];
+ uy=pts[3*k+1]-pts[3*i+1];
+ uz=pts[3*k+2]-pts[3*i+2];
+ vx=pts[3*m]-pts[3*i];
+ vy=pts[3*m+1]-pts[3*i+1];
+ vz=pts[3*m+2]-pts[3*i+2];
+ wx=uy*vz-uz*vy;
+ wy=uz*vx-ux*vz;
+ wz=ux*vy-uy*vx;
+ area+=sqrt(wx*wx+wy*wy+wz*wz);
+ k=m;l=n;
+ m=ed[k][l];ed[k][l]=-1-m;
+ }
+ v.push_back(0.125*area);
+ }
+ }
+ reset_edges();
+}
+
+/** Several routines in the class that gather cell-based statistics internally
+ * track their progress by flipping edges to negative so that they know what
+ * parts of the cell have already been tested. This function resets them back
+ * to positive. When it is called, it assumes that every edge in the routine
+ * should have already been flipped to negative, and it bails out with an
+ * internal error if it encounters a positive edge. */
+inline void voronoicell_base::reset_edges() {
+ int i,j;
+ for(i=0;i<p;i++) for(j=0;j<nu[i];j++) {
+ if(ed[i][j]>=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR);
+ ed[i][j]=-1-ed[i][j];
+ }
+}
+
+/** Checks to see if a given vertex is inside, outside or within the test
+ * plane. If the point is far away from the test plane, the routine immediately
+ * returns whether it is inside or outside. If the routine is close the the
+ * plane and within the specified tolerance, then the special check_marginal()
+ * routine is called.
+ * \param[in] n the vertex to test.
+ * \param[out] ans the result of the scalar product used in evaluating the
+ * location of the point.
+ * \return -1 if the point is inside the plane, 1 if the point is outside the
+ * plane, or 0 if the point is within the plane. */
+inline int voronoicell_base::m_test(int n,double &ans) {
+ double *pp=pts+n+(n<<1);
+ ans=*(pp++)*px;
+ ans+=*(pp++)*py;
+ ans+=*pp*pz-prsq;
+ if(ans<-tolerance2) {
+ return -1;
+ } else if(ans>tolerance2) {
+ return 1;
+ }
+ return check_marginal(n,ans);
+}
+
+/** Checks to see if a given vertex is inside, outside or within the test
+ * plane, for the case when the point has been detected to be very close to the
+ * plane. The routine ensures that the returned results are always consistent
+ * with previous tests, by keeping a table of any marginal results. The routine
+ * first sees if the vertex is in the table, and if it finds a previously
+ * computed result it uses that. Otherwise, it computes a result for this
+ * vertex and adds it the table.
+ * \param[in] n the vertex to test.
+ * \param[in] ans the result of the scalar product used in evaluating
+ * the location of the point.
+ * \return -1 if the point is inside the plane, 1 if the point is outside the
+ * plane, or 0 if the point is within the plane. */
+int voronoicell_base::check_marginal(int n,double &ans) {
+ int i;
+ for(i=0;i<n_marg;i+=2) if(marg[i]==n) return marg[i+1];
+ if(n_marg==current_marginal) {
+ current_marginal<<=1;
+ if(current_marginal>max_marginal)
+ voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
+#if VOROPP_VERBOSE >=2
+ fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i);
+#endif
+ int *pmarg=new int[current_marginal];
+ for(int j=0;j<n_marg;j++) pmarg[j]=marg[j];
+ delete [] marg;
+ marg=pmarg;
+ }
+ marg[n_marg++]=n;
+ marg[n_marg++]=ans>tolerance?1:(ans<-tolerance?-1:0);
+ return marg[n_marg-1];
+}
+
+/** This initializes the class to be a rectangular box. It calls the base class
+ * initialization routine to set up the edge and vertex information, and then
+ * sets up the neighbor information, with initial faces being assigned ID
+ * numbers from -1 to -6.
+ * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
+ * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
+ * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
+void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
+ init_base(xmin,xmax,ymin,ymax,zmin,zmax);
+ int *q=mne[3];
+ *q=-5;q[1]=-3;q[2]=-1;
+ q[3]=-5;q[4]=-2;q[5]=-3;
+ q[6]=-5;q[7]=-1;q[8]=-4;
+ q[9]=-5;q[10]=-4;q[11]=-2;
+ q[12]=-6;q[13]=-1;q[14]=-3;
+ q[15]=-6;q[16]=-3;q[17]=-2;
+ q[18]=-6;q[19]=-4;q[20]=-1;
+ q[21]=-6;q[22]=-2;q[23]=-4;
+ *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
+ ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21;
+}
+
+/** This routine checks to make sure the neighbor information of each face is
+ * consistent. */
+void voronoicell_neighbor::check_facets() {
+ int i,j,k,l,m,q;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ ed[i][j]=-1-k;
+ q=ne[i][j];
+ l=cycle_up(ed[i][nu[i]+j],k);
+ do {
+ m=ed[k][l];
+ ed[k][l]=-1-m;
+ if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q);
+ l=cycle_up(ed[k][nu[k]+l],m);
+ k=m;
+ } while (k!=i);
+ }
+ }
+ reset_edges();
+}
+
+/** The class constructor allocates memory for storing neighbor information. */
+voronoicell_neighbor::voronoicell_neighbor() {
+ int i;
+ mne=new int*[current_vertex_order];
+ ne=new int*[current_vertices];
+ for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i];
+ mne[3]=new int[init_3_vertices*3];
+ for(i=4;i<current_vertex_order;i++) mne[i]=new int[init_n_vertices*i];
+}
+
+/** The class destructor frees the dynamically allocated memory for storing
+ * neighbor information. */
+voronoicell_neighbor::~voronoicell_neighbor() {
+ for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mne[i];
+ delete [] mne;
+ delete [] ne;
+}
+
+/** Computes a vector list of neighbors. */
+void voronoicell_neighbor::neighbors(std::vector<int> &v) {
+ v.clear();
+ int i,j,k,l,m;
+ for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
+ k=ed[i][j];
+ if(k>=0) {
+ v.push_back(ne[i][j]);
+ ed[i][j]=-1-k;
+ l=cycle_up(ed[i][nu[i]+j],k);
+ do {
+ m=ed[k][l];
+ ed[k][l]=-1-m;
+ l=cycle_up(ed[k][nu[k]+l],m);
+ k=m;
+ } while (k!=i);
+ }
+ }
+ reset_edges();
+}
+
+// Explicit instantiation
+template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int);
+template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*);
+
+}
+
diff --git a/src/PTM/ptm_voronoi_cell.h b/src/PTM/ptm_voronoi_cell.h
new file mode 100644
index 0000000000..80a0501b3c
--- /dev/null
+++ b/src/PTM/ptm_voronoi_cell.h
@@ -0,0 +1,324 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file cell.hh
+ * \brief Header file for the voronoicell and related classes. */
+
+#ifndef PTM_VOROPP_CELL_HH
+#define PTM_VOROPP_CELL_HH
+
+#include <vector>
+#include <cstdio>
+
+#include "ptm_voronoi_config.h"
+
+namespace voro {
+
+/** \brief A class representing a single Voronoi cell.
+ *
+ * This class represents a single Voronoi cell, as a collection of vertices
+ * that are connected by edges. The class contains routines for initializing
+ * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
+ * It the contains routines for recomputing the cell based on cutting it
+ * by a plane, which forms the key routine for the Voronoi cell computation.
+ * It contains numerous routine for computing statistics about the Voronoi cell,
+ * and it can output the cell in several formats.
+ *
+ * This class is not intended for direct use, but forms the base of the
+ * voronoicell and voronoicell_neighbor classes, which extend it based on
+ * whether neighboring particle ID information needs to be tracked. */
+class voronoicell_base {
+ public:
+ /** This holds the current size of the arrays ed and nu, which
+ * hold the vertex information. If more vertices are created
+ * than can fit in this array, then it is dynamically extended
+ * using the add_memory_vertices routine. */
+ int current_vertices;
+ /** This holds the current maximum allowed order of a vertex,
+ * which sets the size of the mem, mep, and mec arrays. If a
+ * vertex is created with more vertices than this, the arrays
+ * are dynamically extended using the add_memory_vorder routine.
+ */
+ int current_vertex_order;
+ /** This sets the size of the main delete stack. */
+ int current_delete_size;
+ /** This sets the size of the auxiliary delete stack. */
+ int current_delete2_size;
+ /** This sets the total number of vertices in the current cell.
+ */
+ int p;
+ /** This is the index of particular point in the cell, which is
+ * used to start the tracing routines for plane intersection
+ * and cutting. These routines will work starting from any
+ * point, but it's often most efficient to start from the last
+ * point considered, since in many cases, the cell construction
+ * algorithm may consider many planes with similar vectors
+ * concurrently. */
+ int up;
+ /** This is a two dimensional array that holds information
+ * about the edge connections of the vertices that make up the
+ * cell. The two dimensional array is not allocated in the
+ * usual method. To account for the fact the different vertices
+ * have different orders, and thus require different amounts of
+ * storage, the elements of ed[i] point to one-dimensional
+ * arrays in the mep[] array of different sizes.
+ *
+ * More specifically, if vertex i has order m, then ed[i]
+ * points to a one-dimensional array in mep[m] that has 2*m+1
+ * entries. The first m elements hold the neighboring edges, so
+ * that the jth edge of vertex i is held in ed[i][j]. The next
+ * m elements hold a table of relations which is redundant but
+ * helps speed up the computation. It satisfies the relation
+ * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
+ * pointer, so that ed[i+2*m]=i. The back pointers are used
+ * when rearranging the memory. */
+ int **ed;
+ /** This array holds the order of the vertices in the Voronoi
+ * cell. This array is dynamically allocated, with its current
+ * size held by current_vertices. */
+ int *nu;
+ /** This in an array with size 3*current_vertices for holding
+ * the positions of the vertices. */
+ double *pts;
+ voronoicell_base();
+ virtual ~voronoicell_base();
+ void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void init_octahedron_base(double l);
+ void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
+ void translate(double x,double y,double z);
+ double volume();
+ double max_radius_squared();
+ double total_edge_distance();
+ double surface_area();
+ void centroid(double &cx,double &cy,double &cz);
+ int number_of_faces();
+ int number_of_edges();
+ void vertex_orders(std::vector<int> &v);
+ void vertices(std::vector<double> &v);
+ void vertices(double x,double y,double z,std::vector<double> &v);
+ void face_areas(std::vector<double> &v);
+ void face_orders(std::vector<int> &v);
+ void face_freq_table(std::vector<int> &v);
+ void face_vertices(std::vector<int> &v);
+ void face_perimeters(std::vector<double> &v);
+ void normals(std::vector<double> &v);
+ template<class vc_class>
+ bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
+ bool plane_intersects(double x,double y,double z,double rsq);
+ bool plane_intersects_guess(double x,double y,double z,double rsq);
+ void construct_relations();
+ void check_relations();
+ void check_duplicates();
+ /** Returns a list of IDs of neighboring particles
+ * corresponding to each face.
+ * \param[out] v a reference to a vector in which to return the
+ * results. If no neighbor information is
+ * available, a blank vector is returned. */
+ virtual void neighbors(std::vector<int> &v) {v.clear();}
+ /** This a virtual function that is overridden by a routine to
+ * print the neighboring particle IDs for a given vertex. By
+ * default, when no neighbor information is available, the
+ * routine does nothing.
+ * \param[in] i the vertex to consider. */
+ /** This is a simple inline function for picking out the index
+ * of the next edge counterclockwise at the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return 0 if a=nu[p]-1, or a+1 otherwise. */
+ inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
+ /** This is a simple inline function for picking out the index
+ * of the next edge clockwise from the current vertex.
+ * \param[in] a the index of an edge of the current vertex.
+ * \param[in] p the number of the vertex.
+ * \return nu[p]-1 if a=0, or a-1 otherwise. */
+ inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
+ protected:
+ /** This a one dimensional array that holds the current sizes
+ * of the memory allocations for them mep array.*/
+ int *mem;
+ /** This is a one dimensional array that holds the current
+ * number of vertices of order p that are stored in the mep[p]
+ * array. */
+ int *mec;
+ /** This is a two dimensional array for holding the information
+ * about the edges of the Voronoi cell. mep[p] is a
+ * one-dimensional array for holding the edge information about
+ * all vertices of order p, with each vertex holding 2*p+1
+ * integers of information. The total number of vertices held
+ * on mep[p] is stored in mem[p]. If the space runs out, the
+ * code allocates more using the add_memory() routine. */
+ int **mep;
+ inline void reset_edges();
+ template<class vc_class>
+ void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
+ void copy(voronoicell_base* vb);
+ private:
+ /** This is the delete stack, used to store the vertices which
+ * are going to be deleted during the plane cutting procedure.
+ */
+ int *ds,*stacke;
+ /** This is the auxiliary delete stack, which has size set by
+ * current_delete2_size. */
+ int *ds2,*stacke2;
+ /** This stores the current memory allocation for the marginal
+ * cases. */
+ int current_marginal;
+ /** This stores the total number of marginal points which are
+ * currently in the buffer. */
+ int n_marg;
+ /** This array contains a list of the marginal points, and also
+ * the outcomes of the marginal tests. */
+ int *marg;
+ /** The x coordinate of the normal vector to the test plane. */
+ double px;
+ /** The y coordinate of the normal vector to the test plane. */
+ double py;
+ /** The z coordinate of the normal vector to the test plane. */
+ double pz;
+ /** The magnitude of the normal vector to the test plane. */
+ double prsq;
+ template<class vc_class>
+ void add_memory(vc_class &vc,int i,int *stackp2);
+ template<class vc_class>
+ void add_memory_vertices(vc_class &vc);
+ template<class vc_class>
+ void add_memory_vorder(vc_class &vc);
+ void add_memory_ds(int *&stackp);
+ void add_memory_ds2(int *&stackp2);
+ template<class vc_class>
+ inline bool collapse_order1(vc_class &vc);
+ template<class vc_class>
+ inline bool collapse_order2(vc_class &vc);
+ template<class vc_class>
+ inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
+ template<class vc_class>
+ inline bool search_for_outside_edge(vc_class &vc,int &up);
+ template<class vc_class>
+ inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
+ inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
+ inline void normals_search(std::vector<double> &v,int i,int j,int k);
+ inline bool search_edge(int l,int &m,int &k);
+ inline int m_test(int n,double &ans);
+ int check_marginal(int n,double &ans);
+ friend class voronoicell;
+ friend class voronoicell_neighbor;
+};
+
+/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
+ * with neighbor information.
+ *
+ * This class is an extension of the voronoicell_base class, in cases when the
+ * IDs of neighboring particles associated with each face of the Voronoi cell.
+ * It contains additional data structures mne and ne for storing this
+ * information. */
+class voronoicell_neighbor : public voronoicell_base {
+ public:
+ using voronoicell_base::nplane;
+ /** This two dimensional array holds the neighbor information
+ * associated with each vertex. mne[p] is a one dimensional
+ * array which holds all of the neighbor information for
+ * vertices of order p. */
+ int **mne;
+ /** This is a two dimensional array that holds the neighbor
+ * information associated with each vertex. ne[i] points to a
+ * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
+ * neighbor information associated with the jth edge of vertex
+ * i. It is set to the ID number of the plane that made the
+ * face that is clockwise from the jth edge. */
+ int **ne;
+ voronoicell_neighbor();
+ ~voronoicell_neighbor();
+ void operator=(voronoicell_neighbor &c);
+ /** Cuts the Voronoi cell by a particle whose center is at a
+ * separation of (x,y,z) from the cell center. The value of rsq
+ * should be initially set to \f$x^2+y^2+z^2\f$.
+ * \param[in] (x,y,z) the normal vector to the plane.
+ * \param[in] rsq the distance along this vector of the plane.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool nplane(double x,double y,double z,double rsq,int p_id) {
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This routine calculates the modulus squared of the vector
+ * before passing it to the main nplane() routine with full
+ * arguments.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] p_id the plane ID (for neighbor tracking only).
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool nplane(double x,double y,double z,int p_id) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,p_id);
+ }
+ /** This version of the plane routine just makes up the plane
+ * ID to be zero. It will only be referenced if neighbor
+ * tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \param[in] rsq the modulus squared of the vector.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z,double rsq) {
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ /** Cuts a Voronoi cell using the influence of a particle at
+ * (x,y,z), first calculating the modulus squared of this
+ * vector before passing it to the main nplane() routine. Zero
+ * is supplied as the plane ID, which will be ignored unless
+ * neighbor tracking is enabled.
+ * \param[in] (x,y,z) the vector to cut the cell by.
+ * \return False if the plane cut deleted the cell entirely,
+ * true otherwise. */
+ inline bool plane(double x,double y,double z) {
+ double rsq=x*x+y*y+z*z;
+ return nplane(*this,x,y,z,rsq,0);
+ }
+ void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
+ void check_facets();
+ virtual void neighbors(std::vector<int> &v);
+
+ private:
+ int *paux1;
+ int *paux2;
+ inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
+ inline void n_add_memory_vertices(int i) {
+ int **pp=new int*[i];
+ for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
+ delete [] ne;ne=pp;
+ }
+ inline void n_add_memory_vorder(int i) {
+ int **p2=new int*[i];
+ for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
+ delete [] mne;mne=p2;
+ }
+ inline void n_set_pointer(int p,int n) {
+ ne[p]=mne[n]+n*mec[n];
+ }
+ inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
+ inline void n_set(int a,int b,int c) {ne[a][b]=c;}
+ inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
+ inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
+ inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
+ inline void n_set_aux2_copy(int a,int b) {
+ paux2=mne[b]+b*mec[b];
+ for(int i=0;i<b;i++) ne[a][i]=paux2[i];
+ }
+ inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
+ inline void n_set_to_aux1(int j) {ne[j]=paux1;}
+ inline void n_set_to_aux2(int j) {ne[j]=paux2;}
+ inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
+ inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
+ inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
+ inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
+ friend class voronoicell_base;
+};
+
+}
+
+#endif
+
diff --git a/src/PTM/ptm_voronoi_config.h b/src/PTM/ptm_voronoi_config.h
new file mode 100644
index 0000000000..86257e60cc
--- /dev/null
+++ b/src/PTM/ptm_voronoi_config.h
@@ -0,0 +1,129 @@
+// Voro++, a 3D cell-based Voronoi library
+//
+// Author : Chris H. Rycroft (LBL / UC Berkeley)
+// Email : chr@alum.mit.edu
+// Date : August 30th 2011
+//
+// Modified by PM Larsen for use in Polyhedral Template Matching
+
+/** \file config.hh
+ * \brief Master configuration file for setting various compile-time options. */
+
+#ifndef PTM_VOROPP_CONFIG_HH
+#define PTM_VOROPP_CONFIG_HH
+
+namespace voro {
+
+// These constants set the initial memory allocation for the Voronoi cell
+/** The initial memory allocation for the number of vertices. */
+const int init_vertices=256;
+/** The initial memory allocation for the maximum vertex order. */
+const int init_vertex_order=64;
+/** The initial memory allocation for the number of regular vertices of order
+ * 3. */
+const int init_3_vertices=256;
+/** The initial memory allocation for the number of vertices of higher order.
+ */
+const int init_n_vertices=8;
+/** The initial buffer size for marginal cases used by the suretest class. */
+const int init_marginal=64;
+/** The initial size for the delete stack. */
+const int init_delete_size=256;
+/** The initial size for the auxiliary delete stack. */
+const int init_delete2_size=256;
+/** The initial size for the wall pointer array. */
+const int init_wall_size=32;
+/** The default initial size for the ordering class. */
+const int init_ordering_size=4096;
+/** The initial size of the pre_container chunk index. */
+const int init_chunk_size=256;
+
+// If the initial memory is too small, the program dynamically allocates more.
+// However, if the limits below are reached, then the program bails out.
+/** The maximum memory allocation for the number of vertices. */
+const int max_vertices=16777216;
+/** The maximum memory allocation for the maximum vertex order. */
+const int max_vertex_order=2048;
+/** The maximum memory allocation for the any particular order of vertex. */
+const int max_n_vertices=16777216;
+/** The maximum buffer size for marginal cases used by the suretest class. */
+const int max_marginal=16777216;
+/** The maximum size for the delete stack. */
+const int max_delete_size=16777216;
+/** The maximum size for the auxiliary delete stack. */
+const int max_delete2_size=16777216;
+/** The maximum amount of particle memory allocated for a single region. */
+const int max_particle_memory=16777216;
+/** The maximum size for the wall pointer array. */
+const int max_wall_size=2048;
+/** The maximum size for the ordering class. */
+const int max_ordering_size=67108864;
+/** The maximum size for the pre_container chunk index. */
+const int max_chunk_size=65536;
+
+/** The chunk size in the pre_container classes. */
+const int pre_container_chunk_size=1024;
+
+#ifndef VOROPP_VERBOSE
+/** Voro++ can print a number of different status and debugging messages to
+ * notify the user of special behavior, and this macro sets the amount which
+ * are displayed. At level 0, no messages are printed. At level 1, messages
+ * about unusual cases during cell construction are printed, such as when the
+ * plane routine bails out due to floating point problems. At level 2, general
+ * messages about memory expansion are printed. At level 3, technical details
+ * about memory management are printed. */
+#define VOROPP_VERBOSE 0
+#endif
+
+/** If a point is within this distance of a cutting plane, then the code
+ * assumes that point exactly lies on the plane. */
+const double tolerance=1e-11;
+
+/** If a point is within this distance of a cutting plane, then the code stores
+ * whether this point is inside, outside, or exactly on the cutting plane in
+ * the marginal cases buffer, to prevent the test giving a different result on
+ * a subsequent evaluation due to floating point rounding errors. */
+const double tolerance2=2e-11;
+
+/** The square of the tolerance, used when deciding whether some squared
+ * quantities are large enough to be used. */
+const double tolerance_sq=tolerance*tolerance;
+
+/** A large number that is used in the computation. */
+const double large_number=1e30;
+
+/** A radius to use as a placeholder when no other information is available. */
+const double default_radius=0.5;
+
+/** The maximum number of shells of periodic images to test over. */
+const int max_unit_voro_shells=10;
+
+/** A guess for the optimal number of particles per block, used to set up the
+ * container grid. */
+const double optimal_particles=5.6;
+
+/** If this is set to 1, then the code reports any instances of particles being
+ * put outside of the container geometry. */
+#define VOROPP_REPORT_OUT_OF_BOUNDS 0
+
+/** Voro++ returns this status code if there is a file-related error, such as
+ * not being able to open file. */
+#define VOROPP_FILE_ERROR 1
+
+/** Voro++ returns this status code if there is a memory allocation error, if
+ * one of the safe memory limits is exceeded. */
+#define VOROPP_MEMORY_ERROR 2
+
+/** Voro++ returns this status code if there is any type of internal error, if
+ * it detects that representation of the Voronoi cell is inconsistent. This
+ * status code will generally indicate a bug, and the developer should be
+ * contacted. */
+#define VOROPP_INTERNAL_ERROR 3
+
+/** Voro++ returns this status code if it could not interpret the command line
+ * arguments passed to the command line utility. */
+#define VOROPP_CMD_LINE_ERROR 4
+
+}
+
+#endif
--
GitLab
From 37201beda545bcd04419d07971e78548b6378ed1 Mon Sep 17 00:00:00 2001
From: pmla <pete.mahler.larsen@gmail.com>
Date: Thu, 20 Sep 2018 00:04:07 -0400
Subject: [PATCH 274/332] Fixed folder structure
---
src/PTM/compute_ptm_atom.cpp | 307 ---
src/PTM/compute_ptm_atom.h | 48 -
src/PTM/ptm_constants.h | 174 --
src/PTM/ptm_functions.h | 27 -
src/USER-PTM/alloy_types.cpp | 101 -
src/USER-PTM/alloy_types.h | 9 -
src/USER-PTM/canonical_coloured.cpp | 167 --
src/USER-PTM/canonical_coloured.h | 9 -
src/USER-PTM/cell.cpp | 1368 -----------
src/USER-PTM/cell.h | 324 ---
src/USER-PTM/config.h | 129 --
src/USER-PTM/convex_hull_incremental.cpp | 363 ---
src/USER-PTM/convex_hull_incremental.h | 27 -
src/USER-PTM/deformation_gradient.cpp | 37 -
src/USER-PTM/deformation_gradient.h | 142 --
src/USER-PTM/fundamental_mappings.h | 180 --
src/USER-PTM/graph_data.cpp | 2059 -----------------
src/USER-PTM/graph_data.h | 37 -
src/USER-PTM/graph_tools.cpp | 52 -
src/USER-PTM/graph_tools.h | 11 -
src/USER-PTM/index_ptm.cpp | 218 --
src/USER-PTM/initialize_data.cpp | 71 -
src/USER-PTM/initialize_data.h | 61 -
src/USER-PTM/neighbour_ordering.cpp | 203 --
src/USER-PTM/neighbour_ordering.h | 13 -
src/USER-PTM/normalize_vertices.cpp | 55 -
src/USER-PTM/normalize_vertices.h | 8 -
src/USER-PTM/polar.cpp | 337 ---
src/USER-PTM/polar.h | 12 -
src/{PTM => USER-PTM}/ptm_alloy_types.cpp | 0
src/{PTM => USER-PTM}/ptm_alloy_types.h | 0
.../ptm_canonical_coloured.cpp | 0
.../ptm_canonical_coloured.h | 0
.../ptm_convex_hull_incremental.cpp | 0
.../ptm_convex_hull_incremental.h | 0
.../ptm_deformation_gradient.cpp | 0
.../ptm_deformation_gradient.h | 0
src/USER-PTM/ptm_functions.h | 2 +-
.../ptm_fundamental_mappings.h | 0
src/{PTM => USER-PTM}/ptm_graph_data.cpp | 0
src/{PTM => USER-PTM}/ptm_graph_data.h | 0
src/{PTM => USER-PTM}/ptm_graph_tools.cpp | 0
src/{PTM => USER-PTM}/ptm_graph_tools.h | 0
src/{PTM => USER-PTM}/ptm_index.cpp | 0
src/{PTM => USER-PTM}/ptm_initialize_data.cpp | 0
src/{PTM => USER-PTM}/ptm_initialize_data.h | 0
.../ptm_neighbour_ordering.cpp | 0
.../ptm_neighbour_ordering.h | 0
.../ptm_normalize_vertices.cpp | 0
.../ptm_normalize_vertices.h | 0
src/{PTM => USER-PTM}/ptm_polar.cpp | 0
src/{PTM => USER-PTM}/ptm_polar.h | 0
src/{PTM => USER-PTM}/ptm_quat.cpp | 0
src/{PTM => USER-PTM}/ptm_quat.h | 0
.../ptm_structure_matcher.cpp | 0
src/{PTM => USER-PTM}/ptm_structure_matcher.h | 0
src/{PTM => USER-PTM}/ptm_voronoi_cell.cpp | 0
src/{PTM => USER-PTM}/ptm_voronoi_cell.h | 0
src/{PTM => USER-PTM}/ptm_voronoi_config.h | 0
src/USER-PTM/quat.cpp | 396 ----
src/USER-PTM/quat.h | 32 -
src/USER-PTM/structure_matcher.cpp | 294 ---
src/USER-PTM/structure_matcher.h | 21 -
63 files changed, 1 insertion(+), 7293 deletions(-)
delete mode 100644 src/PTM/compute_ptm_atom.cpp
delete mode 100644 src/PTM/compute_ptm_atom.h
delete mode 100644 src/PTM/ptm_constants.h
delete mode 100644 src/PTM/ptm_functions.h
delete mode 100644 src/USER-PTM/alloy_types.cpp
delete mode 100644 src/USER-PTM/alloy_types.h
delete mode 100644 src/USER-PTM/canonical_coloured.cpp
delete mode 100644 src/USER-PTM/canonical_coloured.h
delete mode 100644 src/USER-PTM/cell.cpp
delete mode 100644 src/USER-PTM/cell.h
delete mode 100644 src/USER-PTM/config.h
delete mode 100644 src/USER-PTM/convex_hull_incremental.cpp
delete mode 100644 src/USER-PTM/convex_hull_incremental.h
delete mode 100644 src/USER-PTM/deformation_gradient.cpp
delete mode 100644 src/USER-PTM/deformation_gradient.h
delete mode 100644 src/USER-PTM/fundamental_mappings.h
delete mode 100644 src/USER-PTM/graph_data.cpp
delete mode 100644 src/USER-PTM/graph_data.h
delete mode 100644 src/USER-PTM/graph_tools.cpp
delete mode 100644 src/USER-PTM/graph_tools.h
delete mode 100644 src/USER-PTM/index_ptm.cpp
delete mode 100644 src/USER-PTM/initialize_data.cpp
delete mode 100644 src/USER-PTM/initialize_data.h
delete mode 100644 src/USER-PTM/neighbour_ordering.cpp
delete mode 100644 src/USER-PTM/neighbour_ordering.h
delete mode 100644 src/USER-PTM/normalize_vertices.cpp
delete mode 100644 src/USER-PTM/normalize_vertices.h
delete mode 100644 src/USER-PTM/polar.cpp
delete mode 100644 src/USER-PTM/polar.h
rename src/{PTM => USER-PTM}/ptm_alloy_types.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_alloy_types.h (100%)
rename src/{PTM => USER-PTM}/ptm_canonical_coloured.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_canonical_coloured.h (100%)
rename src/{PTM => USER-PTM}/ptm_convex_hull_incremental.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_convex_hull_incremental.h (100%)
rename src/{PTM => USER-PTM}/ptm_deformation_gradient.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_deformation_gradient.h (100%)
rename src/{PTM => USER-PTM}/ptm_fundamental_mappings.h (100%)
rename src/{PTM => USER-PTM}/ptm_graph_data.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_graph_data.h (100%)
rename src/{PTM => USER-PTM}/ptm_graph_tools.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_graph_tools.h (100%)
rename src/{PTM => USER-PTM}/ptm_index.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_initialize_data.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_initialize_data.h (100%)
rename src/{PTM => USER-PTM}/ptm_neighbour_ordering.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_neighbour_ordering.h (100%)
rename src/{PTM => USER-PTM}/ptm_normalize_vertices.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_normalize_vertices.h (100%)
rename src/{PTM => USER-PTM}/ptm_polar.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_polar.h (100%)
rename src/{PTM => USER-PTM}/ptm_quat.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_quat.h (100%)
rename src/{PTM => USER-PTM}/ptm_structure_matcher.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_structure_matcher.h (100%)
rename src/{PTM => USER-PTM}/ptm_voronoi_cell.cpp (100%)
rename src/{PTM => USER-PTM}/ptm_voronoi_cell.h (100%)
rename src/{PTM => USER-PTM}/ptm_voronoi_config.h (100%)
delete mode 100644 src/USER-PTM/quat.cpp
delete mode 100644 src/USER-PTM/quat.h
delete mode 100644 src/USER-PTM/structure_matcher.cpp
delete mode 100644 src/USER-PTM/structure_matcher.h
diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp
deleted file mode 100644
index b6b4a9786c..0000000000
--- a/src/PTM/compute_ptm_atom.cpp
+++ /dev/null
@@ -1,307 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed
-under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: PM Larsen (MIT)
-------------------------------------------------------------------------- */
-
-#include <algorithm>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
-
-#include "atom.h"
-#include "comm.h"
-#include "compute_ptm_atom.h"
-#include "error.h"
-#include "force.h"
-#include "memory.h"
-#include "modify.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "neighbor.h"
-#include "pair.h"
-#include "update.h"
-
-#include "ptm_functions.h"
-
-#define MAX_NEIGHBORS 30
-#define NUM_COLUMNS 7
-#define UNKNOWN 0
-#define OTHER 8
-
-using namespace LAMMPS_NS;
-
-static const char cite_user_ptm_package[] =
- "USER-PTM package:\n\n"
- "@Article{larsen2016ptm,\n"
- " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, "
- "Jakob},\n"
- " title={Robust structural identification via polyhedral template "
- "matching},\n"
- " journal={Modelling~Simul.~Mater.~Sci.~Eng.},\n"
- " year={2016},\n"
- " number={5},\n"
- " volume={24},\n"
- " pages={055007},\n"
- " DOI = {10.1088/0965-0393/24/5/055007}"
- "}\n\n";
-
-/* ---------------------------------------------------------------------- */
-
-ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
- : Compute(lmp, narg, arg), list(NULL), output(NULL) {
- if (narg != 5)
- error->all(FLERR, "Illegal compute ptm/atom command");
-
- char *structures = arg[3];
- char *ptr = structures;
-
- const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc",
- "dcub", "dhex", "all", "default"};
- int32_t flags[] = {
- PTM_CHECK_FCC,
- PTM_CHECK_HCP,
- PTM_CHECK_BCC,
- PTM_CHECK_ICO,
- PTM_CHECK_SC,
- PTM_CHECK_DCUB,
- PTM_CHECK_DHEX,
- PTM_CHECK_ALL,
- PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO};
-
- input_flags = 0;
- while (*ptr != '\0') {
-
- bool found = false;
- for (int i = 0; i < 9; i++) {
- int len = strlen(strings[i]);
- if (strncmp(ptr, strings[i], len) == 0) {
- input_flags |= flags[i];
- ptr += len;
- found = true;
- break;
- }
- }
-
- if (!found)
- error->all(FLERR,
- "Illegal compute ptm/atom command (invalid structure type)");
-
- if (*ptr == '\0')
- break;
-
- if (*ptr != '-')
- error->all(FLERR,
- "Illegal compute ptm/atom command (invalid structure type)");
-
- ptr++;
- }
-
- double threshold = force->numeric(FLERR, arg[4]);
- if (threshold < 0.0)
- error->all(FLERR,
- "Illegal compute ptm/atom command (threshold is negative)");
- rmsd_threshold = threshold;
- if (rmsd_threshold == 0)
- rmsd_threshold = INFINITY;
-
- peratom_flag = 1;
- size_peratom_cols = NUM_COLUMNS;
- create_attribute = 1;
- nmax = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-ComputePTMAtom::~ComputePTMAtom() { memory->destroy(output); }
-
-/* ---------------------------------------------------------------------- */
-
-void ComputePTMAtom::init() {
- if (force->pair == NULL)
- error->all(FLERR, "Compute ptm/atom requires a pair style be defined");
-
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "ptm/atom") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute ptm/atom defined");
-
- // need an occasional full neighbor list
-
- int irequest = neighbor->request(this, instance_me);
- neighbor->requests[irequest]->pair = 0;
- neighbor->requests[irequest]->compute = 1;
- neighbor->requests[irequest]->half = 0;
- neighbor->requests[irequest]->full = 1;
- neighbor->requests[irequest]->occasional = 1;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; }
-
-/* ---------------------------------------------------------------------- */
-
-typedef struct {
- int index;
- double d;
-} ptmnbr_t;
-
-static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
- return a.d < b.d;
-}
-
-static int get_neighbors(double *pos, int jnum, int *jlist, double **x,
- double (*nbr)[3]) {
-
- ptmnbr_t *nbr_order = new ptmnbr_t[jnum];
-
- for (int jj = 0; jj < jnum; jj++) {
- int j = jlist[jj];
- j &= NEIGHMASK;
-
- double dx = pos[0] - x[j][0];
- double dy = pos[1] - x[j][1];
- double dz = pos[2] - x[j][2];
- double rsq = dx * dx + dy * dy + dz * dz;
-
- nbr_order[jj].index = j;
- nbr_order[jj].d = rsq;
- }
-
- std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare);
- int num_nbrs = std::min(MAX_NEIGHBORS, jnum);
-
- nbr[0][0] = nbr[0][1] = nbr[0][2] = 0;
- for (int jj = 0; jj < num_nbrs; jj++) {
-
- int j = nbr_order[jj].index;
- nbr[jj + 1][0] = x[j][0] - pos[0];
- nbr[jj + 1][1] = x[j][1] - pos[1];
- nbr[jj + 1][2] = x[j][2] - pos[2];
- }
-
- delete[] nbr_order;
- return num_nbrs;
-}
-
-void ComputePTMAtom::compute_peratom() {
- // PTM global initialization. If already initialized this function does
- // nothing.
- ptm_initialize_global();
-
- // initialize PTM local storage
- ptm_local_handle_t local_handle = ptm_initialize_local();
-
- invoked_peratom = update->ntimestep;
-
- // grow arrays if necessary
- if (atom->nmax > nmax) {
- memory->destroy(output);
- nmax = atom->nmax;
-
- memory->create(output, nmax, NUM_COLUMNS, "ptm:ptm_output");
- array_atom = output;
- }
-
- // invoke full neighbor list (will copy or build if necessary)
- neighbor->build_one(list);
-
- int inum = list->inum;
- int *ilist = list->ilist;
- int *numneigh = list->numneigh;
- int **firstneigh = list->firstneigh;
-
- double **x = atom->x;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int ii = 0; ii < inum; ii++) {
-
- int i = ilist[ii];
- output[i][0] = UNKNOWN;
- if (!(mask[i] & groupbit))
- continue;
-
- double *pos = x[i];
-
- int *jlist = firstneigh[i];
- int jnum = numneigh[i];
- if (jnum <= 0)
- continue;
-
- // get neighbours ordered by increasing distance
- double nbr[MAX_NEIGHBORS + 1][3];
- int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr);
-
- // check that we have enough neighbours for the desired structure types
- int32_t flags = 0;
- if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC))
- flags |= PTM_CHECK_SC;
- if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC))
- flags |= PTM_CHECK_FCC;
- if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP))
- flags |= PTM_CHECK_HCP;
- if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO))
- flags |= PTM_CHECK_ICO;
- if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC))
- flags |= PTM_CHECK_BCC;
- if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB))
- flags |= PTM_CHECK_DCUB;
- if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX))
- flags |= PTM_CHECK_DHEX;
-
- // now run PTM
- int8_t mapping[MAX_NEIGHBORS + 1];
- int32_t type, alloy_type;
- double scale, rmsd, interatomic_distance, lattice_constant;
- double q[4], F[9], F_res[3], U[9], P[9];
- ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type,
- &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping,
- &interatomic_distance, &lattice_constant);
-
- if (rmsd > rmsd_threshold) {
- type = PTM_MATCH_NONE;
- }
-
- // printf("%d type=%d rmsd=%f\n", i, type, rmsd);
-
- if (type == PTM_MATCH_NONE)
- type = OTHER;
-
- output[i][0] = type;
- output[i][1] = rmsd;
- output[i][2] = interatomic_distance;
- output[i][3] = q[0];
- output[i][4] = q[1];
- output[i][5] = q[2];
- output[i][6] = q[3];
- }
-
- // printf("finished ptm analysis\n");
- ptm_uninitialize_local(local_handle);
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based array
-------------------------------------------------------------------------- */
-
-double ComputePTMAtom::memory_usage() {
- double bytes = nmax * NUM_COLUMNS * sizeof(double);
- bytes += nmax * sizeof(double);
- return bytes;
-}
diff --git a/src/PTM/compute_ptm_atom.h b/src/PTM/compute_ptm_atom.h
deleted file mode 100644
index 5c10e0c443..0000000000
--- a/src/PTM/compute_ptm_atom.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef COMPUTE_CLASS
-
-ComputeStyle(ptm/atom,ComputePTMAtom)
-
-#else
-
-#ifndef LMP_COMPUTE_PTM_ATOM_H
-#define LMP_COMPUTE_PTM_ATOM_H
-
-#include "compute.h"
-
-namespace LAMMPS_NS {
-
-class ComputePTMAtom : public Compute {
- public:
- ComputePTMAtom(class LAMMPS *, int, char **);
- ~ComputePTMAtom();
- void init();
- void init_list(int, class NeighList *);
- void compute_peratom();
- double memory_usage();
-
- private:
- int nmax;
- int32_t input_flags;
- double rmsd_threshold;
- class NeighList *list;
- double **output;
-};
-
-}
-
-#endif
-#endif
-
diff --git a/src/PTM/ptm_constants.h b/src/PTM/ptm_constants.h
deleted file mode 100644
index f868f51e84..0000000000
--- a/src/PTM/ptm_constants.h
+++ /dev/null
@@ -1,174 +0,0 @@
-#ifndef PTM_CONSTANTS_H
-#define PTM_CONSTANTS_H
-
-//------------------------------------
-// definitions
-//------------------------------------
-#define PTM_NO_ERROR 0
-
-
-#define PTM_CHECK_FCC (1 << 0)
-#define PTM_CHECK_HCP (1 << 1)
-#define PTM_CHECK_BCC (1 << 2)
-#define PTM_CHECK_ICO (1 << 3)
-#define PTM_CHECK_SC (1 << 4)
-#define PTM_CHECK_DCUB (1 << 5)
-#define PTM_CHECK_DHEX (1 << 6)
-#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)
-#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX)
-
-#define PTM_MATCH_NONE 0
-#define PTM_MATCH_FCC 1
-#define PTM_MATCH_HCP 2
-#define PTM_MATCH_BCC 3
-#define PTM_MATCH_ICO 4
-#define PTM_MATCH_SC 5
-#define PTM_MATCH_DCUB 6
-#define PTM_MATCH_DHEX 7
-
-#define PTM_ALLOY_NONE 0
-#define PTM_ALLOY_PURE 1
-#define PTM_ALLOY_L10 2
-#define PTM_ALLOY_L12_CU 3
-#define PTM_ALLOY_L12_AU 4
-#define PTM_ALLOY_B2 5
-#define PTM_ALLOY_SIC 6
-
-
-#define PTM_MAX_INPUT_POINTS 35
-#define PTM_MAX_NBRS 16
-#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1)
-#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4
-#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6
-
-
-//------------------------------------
-// number of neighbours
-//------------------------------------
-#define PTM_NUM_NBRS_FCC 12
-#define PTM_NUM_NBRS_HCP 12
-#define PTM_NUM_NBRS_BCC 14
-#define PTM_NUM_NBRS_ICO 12
-#define PTM_NUM_NBRS_SC 6
-#define PTM_NUM_NBRS_DCUB 16
-#define PTM_NUM_NBRS_DHEX 16
-
-#define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1)
-#define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1)
-#define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1)
-#define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1)
-#define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1)
-#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1)
-#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1)
-
-const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX};
-
-//------------------------------------
-// template structures
-//------------------------------------
-
-//these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1
-
-const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. },
- { 0. , 0.707106781187, 0.707106781187 },
- { 0. , -0.707106781187, -0.707106781187 },
- { 0. , 0.707106781187, -0.707106781187 },
- { 0. , -0.707106781187, 0.707106781187 },
- { 0.707106781187, 0. , 0.707106781187 },
- { -0.707106781187, 0. , -0.707106781187 },
- { 0.707106781187, 0. , -0.707106781187 },
- { -0.707106781187, 0. , 0.707106781187 },
- { 0.707106781187, 0.707106781187, 0. },
- { -0.707106781187, -0.707106781187, 0. },
- { 0.707106781187, -0.707106781187, 0. },
- { -0.707106781187, 0.707106781187, 0. } };
-
-const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. },
- { 0.707106781186, 0. , 0.707106781186 },
- { -0.235702260395, -0.942809041583, -0.235702260395 },
- { 0.707106781186, 0.707106781186, 0. },
- { -0.235702260395, -0.235702260395, -0.942809041583 },
- { 0. , 0.707106781186, 0.707106781186 },
- { -0.942809041583, -0.235702260395, -0.235702260395 },
- { -0.707106781186, 0.707106781186, 0. },
- { 0. , 0.707106781186, -0.707106781186 },
- { 0.707106781186, 0. , -0.707106781186 },
- { 0.707106781186, -0.707106781186, 0. },
- { -0.707106781186, 0. , 0.707106781186 },
- { 0. , -0.707106781186, 0.707106781186 } };
-
-const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. },
- { -0.541451884327, -0.541451884327, -0.541451884327 },
- { 0.541451884327, 0.541451884327, 0.541451884327 },
- { 0.541451884327, -0.541451884327, -0.541451884327 },
- { -0.541451884327, 0.541451884327, 0.541451884327 },
- { -0.541451884327, 0.541451884327, -0.541451884327 },
- { 0.541451884327, -0.541451884327, 0.541451884327 },
- { -0.541451884327, -0.541451884327, 0.541451884327 },
- { 0.541451884327, 0.541451884327, -0.541451884327 },
- { 0. , 0. , -1.082903768655 },
- { 0. , 0. , 1.082903768655 },
- { 0. , -1.082903768655, 0. },
- { 0. , 1.082903768655, 0. },
- { -1.082903768655, 0. , 0. },
- { 1.082903768655, 0. , 0. } };
-
-const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. },
- { 0. , 0.525731112119, 0.850650808352 },
- { 0. , -0.525731112119, -0.850650808352 },
- { 0. , 0.525731112119, -0.850650808352 },
- { 0. , -0.525731112119, 0.850650808352 },
- { -0.525731112119, -0.850650808352, 0. },
- { 0.525731112119, 0.850650808352, 0. },
- { 0.525731112119, -0.850650808352, 0. },
- { -0.525731112119, 0.850650808352, 0. },
- { -0.850650808352, 0. , -0.525731112119 },
- { 0.850650808352, 0. , 0.525731112119 },
- { 0.850650808352, 0. , -0.525731112119 },
- { -0.850650808352, 0. , 0.525731112119 } };
-
-const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. },
- { 0. , 0. , -1. },
- { 0. , 0. , 1. },
- { 0. , -1. , 0. },
- { 0. , 1. , 0. },
- { -1. , 0. , 0. },
- { 1. , 0. , 0. } };
-
-const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. },
- { -0.391491627053, 0.391491627053, 0.391491627053 },
- { -0.391491627053, -0.391491627053, -0.391491627053 },
- { 0.391491627053, -0.391491627053, 0.391491627053 },
- { 0.391491627053, 0.391491627053, -0.391491627053 },
- { -0.782983254107, 0. , 0.782983254107 },
- { -0.782983254107, 0.782983254107, 0. },
- { 0. , 0.782983254107, 0.782983254107 },
- { -0.782983254107, -0.782983254107, 0. },
- { -0.782983254107, 0. , -0.782983254107 },
- { 0. , -0.782983254107, -0.782983254107 },
- { 0. , -0.782983254107, 0.782983254107 },
- { 0.782983254107, -0.782983254107, 0. },
- { 0.782983254107, 0. , 0.782983254107 },
- { 0. , 0.782983254107, -0.782983254107 },
- { 0.782983254107, 0. , -0.782983254107 },
- { 0.782983254107, 0.782983254107, 0. } };
-
-const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. },
- { -0.391491627053, -0.391491627053, -0.391491627053 },
- { 0.391491627053, -0.391491627053, 0.391491627053 },
- { -0.391491627053, 0.391491627053, 0.391491627053 },
- { 0.391491627053, 0.391491627053, -0.391491627053 },
- { -0.260994418036, -1.043977672142, -0.260994418036 },
- { -1.043977672142, -0.260994418036, -0.260994418036 },
- { -0.260994418036, -0.260994418036, -1.043977672142 },
- { 0.782983254107, 0. , 0.782983254107 },
- { 0.782983254107, -0.782983254107, 0. },
- { 0. , -0.782983254107, 0.782983254107 },
- { 0. , 0.782983254107, 0.782983254107 },
- { -0.782983254107, 0.782983254107, 0. },
- { -0.782983254107, 0. , 0.782983254107 },
- { 0.782983254107, 0.782983254107, 0. },
- { 0. , 0.782983254107, -0.782983254107 },
- { 0.782983254107, 0. , -0.782983254107 } };
-#endif
-
diff --git a/src/PTM/ptm_functions.h b/src/PTM/ptm_functions.h
deleted file mode 100644
index cd67d4940d..0000000000
--- a/src/PTM/ptm_functions.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef PTM_FUNCTIONS_H
-#define PTM_FUNCTIONS_H
-
-#include <stdint.h>
-#include <stdbool.h>
-#include "ptm_initialize_data.h"
-#include "ptm_constants.h"
-
-
-//------------------------------------
-// function declarations
-//------------------------------------
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-int ptm_index( ptm_local_handle_t local_handle, int32_t flags, int num_points, double (*atomic_positions)[3], int32_t* atomic_numbers, bool topological_ordering, //inputs
- int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant); //outputs
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
-
diff --git a/src/USER-PTM/alloy_types.cpp b/src/USER-PTM/alloy_types.cpp
deleted file mode 100644
index bde51c19b1..0000000000
--- a/src/USER-PTM/alloy_types.cpp
+++ /dev/null
@@ -1,101 +0,0 @@
-#include <algorithm>
-#include "ptm_constants.h"
-#include "initialize_data.h"
-
-
-#define NUM_ALLOY_TYPES 3
-static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
- {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe},
- {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e},
- {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe},
-};
-
-static bool test_pure(int num_nbrs, int32_t* numbers)
-{
- for (int i=1;i<num_nbrs + 1;i++)
- if (numbers[i] != numbers[0])
- return false;
- return true;
-}
-
-static bool test_binary(int num_nbrs, int32_t* numbers)
-{
- int a = numbers[0], b = -1;
- for (int i=1;i<num_nbrs + 1;i++)
- {
- if (numbers[i] != a)
- {
- if (b == -1)
- b = numbers[i];
- else if (numbers[i] != b)
- return false;
- }
- }
-
- return true;
-}
-
-static bool test_shell_structure(const refdata_t* ref, int8_t* mapping, int32_t* numbers, int num_inner)
-{
- int8_t binary[PTM_MAX_POINTS];
- for (int i=0;i<ref->num_nbrs+1;i++)
- binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
-
- for (int i=1;i<num_inner + 1;i++)
- if (binary[i] == binary[0])
- return false;
-
- for (int i=num_inner+1;i<ref->num_nbrs+1;i++)
- if (binary[i] != binary[0])
- return false;
-
- return true;
-}
-
-static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
-{
- int8_t binary[PTM_MAX_POINTS];
- for (int i=0;i<ref->num_nbrs+1;i++)
- binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1;
-
- int8_t temp[PTM_MAX_POINTS];
- uint32_t best = 0xFFFFFFFF;
- for (int j=0;j<ref->num_mappings;j++)
- {
- for (int i=0;i<ref->num_nbrs+1;i++)
- temp[ref->mapping[j][i]] = binary[i];
-
- uint32_t code = 0;
- for (int i=0;i<ref->num_nbrs+1;i++)
- code |= (temp[i] << i);
-
- best = std::min(best, code);
- }
-
- return best;
-}
-
-int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
-{
- if (test_pure(ref->num_nbrs, numbers))
- return PTM_ALLOY_PURE;
-
- if (!test_binary(ref->num_nbrs, numbers))
- return PTM_ALLOY_NONE;
-
- uint32_t code = canonical_alloy_representation(ref, mapping, numbers);
- for (int i=0;i<NUM_ALLOY_TYPES;i++)
- if ((uint32_t)ref->type == typedata[i][0] && code == typedata[i][2])
- return typedata[i][1];
-
- if (ref->type == PTM_MATCH_BCC)
- if (test_shell_structure(ref, mapping, numbers, 8))
- return PTM_ALLOY_B2;
-
- if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)
- if (test_shell_structure(ref, mapping, numbers, 4))
- return PTM_ALLOY_SIC;
-
- return PTM_ALLOY_NONE;
-}
-
diff --git a/src/USER-PTM/alloy_types.h b/src/USER-PTM/alloy_types.h
deleted file mode 100644
index 1f2980593a..0000000000
--- a/src/USER-PTM/alloy_types.h
+++ /dev/null
@@ -1,9 +0,0 @@
-#ifndef ALLOY_TYPES_H
-#define ALLOY_TYPES_H
-
-#include "initialize_data.h"
-
-int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
-
-#endif
-
diff --git a/src/USER-PTM/canonical_coloured.cpp b/src/USER-PTM/canonical_coloured.cpp
deleted file mode 100644
index af446e1a95..0000000000
--- a/src/USER-PTM/canonical_coloured.cpp
+++ /dev/null
@@ -1,167 +0,0 @@
-#include <string.h>
-#include <climits>
-#include <algorithm>
-#include "graph_tools.h"
-#include "ptm_constants.h"
-
-
-static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
-{
- bool m[PTM_MAX_NBRS][PTM_MAX_NBRS];
- memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS);
-
- int8_t index[PTM_MAX_NBRS];
- memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS);
-
-
- int n = 0;
- index[a] = colours[a] * num_nodes + n++;
- if (index[a] > best_code[0])
- return false;
-
- bool winning = false;
- if (index[a] < best_code[0])
- {
- best_code[0] = index[a];
- winning = true;
- }
-
- int c = -1;
- for (int it=1;it<2*num_edges;it++)
- {
- bool newvertex = index[b] == -1;
-
- if (newvertex)
- index[b] = colours[b] * num_nodes + n++;
-
- if (!winning && index[b] > best_code[it])
- return false;
-
- if (winning || index[b] < best_code[it])
- {
- winning = true;
- best_code[it] = index[b];
- }
-
- if (newvertex)
- {
- //When a new vertex is reached, take the right-most edge
- //relative to the edge on which the vertex is reached.
-
- c = common[a][b];
- }
- else if (m[b][a] == false)
- {
- //When an old vertex is reached on a new path, go back
- //in the opposite direction.
-
- c = a;
- }
- else
- {
- //When an old vertex is reached on an old path, leave the
- //vertex on the right-most edge that has not previously
- //been traversed in that direction.
-
- c = common[a][b];
- while (m[b][c] == true)
- c = common[c][b];
- }
-
- m[a][b] = true;
- a = b;
- b = c;
- }
-
- if (winning)
- {
- memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes);
- return true;
- }
-
- return false;
-}
-
-int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash)
-{
- int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}};
- int num_edges = 3 * num_facets / 2;
- if (!build_facet_map(num_facets, facets, common))
- return -1;
-
- memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES);
-
- bool equal = true;
- for (int i = 1;i<num_nodes;i++)
- if (degree[i] != degree[0] || colours[i] != colours[0])
- equal = false;
-
- if (equal)
- {
- weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, facets[0][0], facets[0][1]);
- }
- else
- {
- uint32_t best_degree = 0;
- for (int i = 0;i<num_facets;i++)
- {
- int a = facets[i][0];
- int b = facets[i][1];
- int c = facets[i][2];
-
- //int da = colours[a] * num_nodes + degree[a];
- //int db = colours[b] * num_nodes + degree[b];
- //int dc = colours[c] * num_nodes + degree[c];
-
- int da = degree[a];
- int db = degree[b];
- int dc = degree[c];
-
- best_degree = std::max(best_degree, ((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0));
- best_degree = std::max(best_degree, ((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8));
- best_degree = std::max(best_degree, ((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16));
- }
-
- for (int i = 0;i<num_facets;i++)
- {
- int a = facets[i][0];
- int b = facets[i][1];
- int c = facets[i][2];
-
- //int da = colours[a] * num_nodes + degree[a];
- //int db = colours[b] * num_nodes + degree[b];
- //int dc = colours[c] * num_nodes + degree[c];
-
- int da = degree[a];
- int db = degree[b];
- int dc = degree[c];
-
- if (best_degree == (((uint32_t)da << 16) | ((uint32_t)db << 8) | ((uint32_t)dc << 0)))
- weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, a, b);
-
- if (best_degree == (((uint32_t)da << 0) | ((uint32_t)db << 16) | ((uint32_t)dc << 8)))
- weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, b, c);
-
- if (best_degree == (((uint32_t)da << 8) | ((uint32_t)db << 0) | ((uint32_t)dc << 16)))
- weinberg_coloured(num_nodes, num_edges, common, colours, best_code, canonical_labelling, c, a);
- }
- }
-
- for (int i = num_nodes-1;i>=0;i--)
- canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1;
- canonical_labelling[0] = 0;
-
- uint64_t hash = 0;
- for (int i = 0;i<2 * num_edges;i++)
- {
- uint64_t e = best_code[i];
- e += i % 8;
- e &= 0xF;
- e <<= (4 * i) % 64;
- hash ^= e;
- }
-
- *p_hash = hash;
- return PTM_NO_ERROR;
-}
-
diff --git a/src/USER-PTM/canonical_coloured.h b/src/USER-PTM/canonical_coloured.h
deleted file mode 100644
index 4a7b5f5a4a..0000000000
--- a/src/USER-PTM/canonical_coloured.h
+++ /dev/null
@@ -1,9 +0,0 @@
-#ifndef CANONICAL_COLOURED_H
-#define CANONICAL_COLOURED_H
-
-#include <stdint.h>
-
-int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
-
-#endif
-
diff --git a/src/USER-PTM/cell.cpp b/src/USER-PTM/cell.cpp
deleted file mode 100644
index f88e310b74..0000000000
--- a/src/USER-PTM/cell.cpp
+++ /dev/null
@@ -1,1368 +0,0 @@
-// Voro++, a 3D cell-based Voronoi library
-//
-// Author : Chris H. Rycroft (LBL / UC Berkeley)
-// Email : chr@alum.mit.edu
-// Date : August 30th 2011
-//
-// Modified by PM Larsen for use in Polyhedral Template Matching
-
-/** \file cell.cc
- * \brief Function implementations for the voronoicell and related classes. */
-
-#include <cmath>
-#include <cstring>
-#include <cstdlib>
-#include "config.h"
-#include "cell.h"
-
-namespace voro {
-
-inline void voro_fatal_error(const char *p,int status) {
- fprintf(stderr,"voro++: %s\n",p);
- exit(status);
- //return -1;//status;
-}
-
-/** Constructs a Voronoi cell and sets up the initial memory. */
-voronoicell_base::voronoicell_base() :
- current_vertices(init_vertices), current_vertex_order(init_vertex_order),
- current_delete_size(init_delete_size), current_delete2_size(init_delete2_size),
- ed(new int*[current_vertices]), nu(new int[current_vertices]),
- pts(new double[3*current_vertices]), mem(new int[current_vertex_order]),
- mec(new int[current_vertex_order]), mep(new int*[current_vertex_order]),
- ds(new int[current_delete_size]), stacke(ds+current_delete_size),
- ds2(new int[current_delete2_size]), stacke2(ds2+current_delete_size),
- current_marginal(init_marginal), marg(new int[current_marginal]) {
- int i;
- for(i=0;i<3;i++) {
- mem[i]=init_n_vertices;mec[i]=0;
- mep[i]=new int[init_n_vertices*((i<<1)+1)];
- }
- mem[3]=init_3_vertices;mec[3]=0;
- mep[3]=new int[init_3_vertices*7];
- for(i=4;i<current_vertex_order;i++) {
- mem[i]=init_n_vertices;mec[i]=0;
- mep[i]=new int[init_n_vertices*((i<<1)+1)];
- }
-}
-
-/** The voronoicell destructor deallocates all the dynamic memory. */
-voronoicell_base::~voronoicell_base() {
- for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mep[i];
- delete [] marg;
- delete [] ds2;delete [] ds;
- delete [] mep;delete [] mec;
- delete [] mem;delete [] pts;
- delete [] nu;delete [] ed;
-}
-
-/** Ensures that enough memory is allocated prior to carrying out a copy.
- * \param[in] vc a reference to the specialized version of the calling class.
- * \param[in] vb a pointered to the class to be copied. */
-template<class vc_class>
-void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) {
- while(current_vertex_order<vb->current_vertex_order) add_memory_vorder(vc);
- for(int i=0;i<current_vertex_order;i++) while(mem[i]<vb->mec[i]) add_memory(vc,i,ds2);
- while(current_vertices<vb->p) add_memory_vertices(vc);
-}
-
-/** Increases the memory storage for a particular vertex order, by increasing
- * the size of the of the corresponding mep array. If the arrays already exist,
- * their size is doubled; if they don't exist, then new ones of size
- * init_n_vertices are allocated. The routine also ensures that the pointers in
- * the ed array are updated, by making use of the back pointers. For the cases
- * where the back pointer has been temporarily overwritten in the marginal
- * vertex code, the auxiliary delete stack is scanned to find out how to update
- * the ed value. If the template has been instantiated with the neighbor
- * tracking turned on, then the routine also reallocates the corresponding mne
- * array.
- * \param[in] i the order of the vertex memory to be increased. */
-template<class vc_class>
-void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) {
- int s=(i<<1)+1;
- if(mem[i]==0) {
- vc.n_allocate(i,init_n_vertices);
- mep[i]=new int[init_n_vertices*s];
- mem[i]=init_n_vertices;
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Order %d vertex memory created\n",i);
-#endif
- } else {
- int j=0,k,*l;
- mem[i]<<=1;
- if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]);
-#endif
- l=new int[s*mem[i]];
- int m=0;
- vc.n_allocate_aux1(i);
- while(j<s*mec[i]) {
- k=mep[i][j+(i<<1)];
- if(k>=0) {
- ed[k]=l+j;
- vc.n_set_to_aux1_offset(k,m);
- } else {
- int *dsp;
- for(dsp=ds2;dsp<stackp2;dsp++) {
- if(ed[*dsp]==mep[i]+j) {
- ed[*dsp]=l+j;
- vc.n_set_to_aux1_offset(*dsp,m);
- break;
- }
- }
- if(dsp==stackp2) voro_fatal_error("Couldn't relocate dangling pointer",VOROPP_INTERNAL_ERROR);
-#if VOROPP_VERBOSE >=3
- fputs("Relocated dangling pointer",stderr);
-#endif
- }
- for(k=0;k<s;k++,j++) l[j]=mep[i][j];
- for(k=0;k<i;k++,m++) vc.n_copy_to_aux1(i,m);
- }
- delete [] mep[i];
- mep[i]=l;
- vc.n_switch_to_aux1(i);
- }
-}
-
-/** Doubles the maximum number of vertices allowed, by reallocating the ed, nu,
- * and pts arrays. If the allocation exceeds the absolute maximum set in
- * max_vertices, then the routine exits with a fatal error. If the template has
- * been instantiated with the neighbor tracking turned on, then the routine
- * also reallocates the ne array. */
-template<class vc_class>
-void voronoicell_base::add_memory_vertices(vc_class &vc) {
-
-printf("nope: %d\n", current_vertices);
-exit(3);
-
- int i=(current_vertices<<1),j,**pp,*pnu;
- if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Vertex memory scaled up to %d\n",i);
-#endif
- double *ppts;
- pp=new int*[i];
- for(j=0;j<current_vertices;j++) pp[j]=ed[j];
- delete [] ed;ed=pp;
- vc.n_add_memory_vertices(i);
- pnu=new int[i];
- for(j=0;j<current_vertices;j++) pnu[j]=nu[j];
- delete [] nu;nu=pnu;
- ppts=new double[3*i];
- for(j=0;j<3*current_vertices;j++) ppts[j]=pts[j];
- delete [] pts;pts=ppts;
- current_vertices=i;
-}
-
-/** Doubles the maximum allowed vertex order, by reallocating mem, mep, and mec
- * arrays. If the allocation exceeds the absolute maximum set in
- * max_vertex_order, then the routine causes a fatal error. If the template has
- * been instantiated with the neighbor tracking turned on, then the routine
- * also reallocates the mne array. */
-template<class vc_class>
-void voronoicell_base::add_memory_vorder(vc_class &vc) {
- int i=(current_vertex_order<<1),j,*p1,**p2;
- if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Vertex order memory scaled up to %d\n",i);
-#endif
- p1=new int[i];
- for(j=0;j<current_vertex_order;j++) p1[j]=mem[j];while(j<i) p1[j++]=0;
- delete [] mem;mem=p1;
- p2=new int*[i];
- for(j=0;j<current_vertex_order;j++) p2[j]=mep[j];
- delete [] mep;mep=p2;
- p1=new int[i];
- for(j=0;j<current_vertex_order;j++) p1[j]=mec[j];while(j<i) p1[j++]=0;
- delete [] mec;mec=p1;
- vc.n_add_memory_vorder(i);
- current_vertex_order=i;
-}
-
-/** Doubles the size allocation of the main delete stack. If the allocation
- * exceeds the absolute maximum set in max_delete_size, then routine causes a
- * fatal error. */
-void voronoicell_base::add_memory_ds(int *&stackp) {
- current_delete_size<<=1;
- if(current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size);
-#endif
- int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds;
- while(dsp<stackp) *(dsnp++)=*(dsp++);
- delete [] ds;ds=dsn;stackp=dsnp;
- stacke=ds+current_delete_size;
-}
-
-/** Doubles the size allocation of the auxiliary delete stack. If the
- * allocation exceeds the absolute maximum set in max_delete2_size, then the
- * routine causes a fatal error. */
-void voronoicell_base::add_memory_ds2(int *&stackp2) {
- current_delete2_size<<=1;
- if(current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size);
-#endif
- int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2;
- while(dsp<stackp2) *(dsnp++)=*(dsp++);
- delete [] ds2;ds2=dsn;stackp2=dsnp;
- stacke2=ds2+current_delete2_size;
-}
-
-/** Initializes a Voronoi cell as a rectangular box with the given dimensions.
- * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
- * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
- * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
-void voronoicell_base::init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
- for(int i=0;i<current_vertex_order;i++) mec[i]=0;up=0;
- mec[3]=p=8;xmin*=2;xmax*=2;ymin*=2;ymax*=2;zmin*=2;zmax*=2;
- *pts=xmin;pts[1]=ymin;pts[2]=zmin;
- pts[3]=xmax;pts[4]=ymin;pts[5]=zmin;
- pts[6]=xmin;pts[7]=ymax;pts[8]=zmin;
- pts[9]=xmax;pts[10]=ymax;pts[11]=zmin;
- pts[12]=xmin;pts[13]=ymin;pts[14]=zmax;
- pts[15]=xmax;pts[16]=ymin;pts[17]=zmax;
- pts[18]=xmin;pts[19]=ymax;pts[20]=zmax;
- pts[21]=xmax;pts[22]=ymax;pts[23]=zmax;
- int *q=mep[3];
- *q=1;q[1]=4;q[2]=2;q[3]=2;q[4]=1;q[5]=0;q[6]=0;
- q[7]=3;q[8]=5;q[9]=0;q[10]=2;q[11]=1;q[12]=0;q[13]=1;
- q[14]=0;q[15]=6;q[16]=3;q[17]=2;q[18]=1;q[19]=0;q[20]=2;
- q[21]=2;q[22]=7;q[23]=1;q[24]=2;q[25]=1;q[26]=0;q[27]=3;
- q[28]=6;q[29]=0;q[30]=5;q[31]=2;q[32]=1;q[33]=0;q[34]=4;
- q[35]=4;q[36]=1;q[37]=7;q[38]=2;q[39]=1;q[40]=0;q[41]=5;
- q[42]=7;q[43]=2;q[44]=4;q[45]=2;q[46]=1;q[47]=0;q[48]=6;
- q[49]=5;q[50]=3;q[51]=6;q[52]=2;q[53]=1;q[54]=0;q[55]=7;
- *ed=q;ed[1]=q+7;ed[2]=q+14;ed[3]=q+21;
- ed[4]=q+28;ed[5]=q+35;ed[6]=q+42;ed[7]=q+49;
- *nu=nu[1]=nu[2]=nu[3]=nu[4]=nu[5]=nu[6]=nu[7]=3;
-}
-
-/** Starting from a point within the current cutting plane, this routine attempts
- * to find an edge to a point outside the cutting plane. This prevents the plane
- * routine from .
- * \param[in] vc a reference to the specialized version of the calling class.
- * \param[in,out] up */
-template<class vc_class>
-inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) {
- int i,lp,lw,*j(ds2),*stackp2(ds2);
- double l;
- *(stackp2++)=up;
- while(j<stackp2) {
- up=*(j++);
- for(i=0;i<nu[up];i++) {
- lp=ed[up][i];
- lw=m_test(lp,l);
- if(lw==-1) return true;
- else if(lw==0) add_to_stack(vc,lp,stackp2);
- }
- }
- return false;
-}
-
-/** Adds a point to the auxiliary delete stack if it is not already there.
- * \param[in] vc a reference to the specialized version of the calling class.
- * \param[in] lp the index of the point to add.
- * \param[in,out] stackp2 a pointer to the end of the stack entries. */
-template<class vc_class>
-inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) {
- for(int *k(ds2);k<stackp2;k++) if(*k==lp) return;
- if(stackp2==stacke2) add_memory_ds2(stackp2);
- *(stackp2++)=lp;
-}
-
-/** Cuts the Voronoi cell by a particle whose center is at a separation of
- * (x,y,z) from the cell center. The value of rsq should be initially set to
- * \f$x^2+y^2+z^2\f$.
- * \param[in] vc a reference to the specialized version of the calling class.
- * \param[in] (x,y,z) the normal vector to the plane.
- * \param[in] rsq the distance along this vector of the plane.
- * \param[in] p_id the plane ID (for neighbor tracking only).
- * \return False if the plane cut deleted the cell entirely, true otherwise. */
-template<class vc_class>
-bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) {
- int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp;
- int us=0,ls=0,qs,iqs,cs,uw,qw,lw;
- int *edp,*edd;
- double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false;
-
- // Initialize the safe testing routine
- n_marg=0;px=x;py=y;pz=z;prsq=rsq;
-
- // Test approximately sqrt(n)/4 points for their proximity to the plane
- // and keep the one which is closest
- uw=m_test(up,u);
-
- // Starting from an initial guess, we now move from vertex to vertex,
- // to try and find an edge which intersects the cutting plane,
- // or a vertex which is on the plane
- try {
- if(uw==1) {
-
- // The test point is inside the cutting plane.
- us=0;
- do {
- lp=ed[up][us];
- lw=m_test(lp,l);
- if(l<u) break;
- us++;
- } while (us<nu[up]);
-
- if(us==nu[up]) {
- return false;
- }
-
- ls=ed[up][nu[up]+us];
- while(lw==1) {
- if(++count>=p) throw true;
- u=l;up=lp;
- for(us=0;us<ls;us++) {
- lp=ed[up][us];
- lw=m_test(lp,l);
- if(l<u) break;
- }
- if(us==ls) {
- us++;
- while(us<nu[up]) {
- lp=ed[up][us];
- lw=m_test(lp,l);
- if(l<u) break;
- us++;
- }
- if(us==nu[up]) {
- return false;
- }
- }
- ls=ed[up][nu[up]+us];
- }
-
- // If the last point in the iteration is within the
- // plane, we need to do the complicated setup
- // routine. Otherwise, we use the regular iteration.
- if(lw==0) {
- up=lp;
- complicated_setup=true;
- } else complicated_setup=false;
- } else if(uw==-1) {
- us=0;
- do {
- qp=ed[up][us];
- qw=m_test(qp,q);
- if(u<q) break;
- us++;
- } while (us<nu[up]);
- if(us==nu[up]) return true;
-
- while(qw==-1) {
- qs=ed[up][nu[up]+us];
- if(++count>=p) throw true;
- u=q;up=qp;
- for(us=0;us<qs;us++) {
- qp=ed[up][us];
- qw=m_test(qp,q);
- if(u<q) break;
- }
- if(us==qs) {
- us++;
- while(us<nu[up]) {
- qp=ed[up][us];
- qw=m_test(qp,q);
- if(u<q) break;
- us++;
- }
- if(us==nu[up]) return true;
- }
- }
- if(qw==1) {
- lp=up;ls=us;l=u;
- up=qp;us=ed[lp][nu[lp]+ls];u=q;
- complicated_setup=false;
- } else {
- up=qp;
- complicated_setup=true;
- }
- } else {
-
- // Our original test point was on the plane, so we
- // automatically head for the complicated setup
- // routine
- complicated_setup=true;
- }
- }
- catch(bool except) {
- // This routine is a fall-back, in case floating point errors
- // cause the usual search routine to fail. In the fall-back
- // routine, we just test every edge to find one straddling
- // the plane.
-#if VOROPP_VERBOSE >=1
- fputs("Bailed out of convex calculation\n",stderr);
-#endif
- qw=1;lw=0;
- for(qp=0;qp<p;qp++) {
- qw=m_test(qp,q);
- if(qw==1) {
-
- // The point is inside the cutting space. Now
- // see if we can find a neighbor which isn't.
- for(us=0;us<nu[qp];us++) {
- lp=ed[qp][us];
- if(lp<qp) {
- lw=m_test(lp,l);
- if(lw!=1) break;
- }
- }
- if(us<nu[qp]) {
- up=qp;
- if(lw==0) {
- complicated_setup=true;
- } else {
- complicated_setup=false;
- u=q;
- ls=ed[up][nu[up]+us];
- }
- break;
- }
- } else if(qw==-1) {
-
- // The point is outside the cutting space. See
- // if we can find a neighbor which isn't.
- for(ls=0;ls<nu[qp];ls++) {
- up=ed[qp][ls];
- if(up<qp) {
- uw=m_test(up,u);
- if(uw!=-1) break;
- }
- }
- if(ls<nu[qp]) {
- if(uw==0) {
- up=qp;
- complicated_setup=true;
- } else {
- complicated_setup=false;
- lp=qp;l=q;
- us=ed[lp][nu[lp]+ls];
- }
- break;
- }
- } else {
-
- // The point is in the plane, so we just
- // proceed with the complicated setup routine
- up=qp;
- complicated_setup=true;
- break;
- }
- }
- if(qp==p) return qw==-1?true:false;
- }
-
- // We're about to add the first point of the new facet. In either
- // routine, we have to add a point, so first check there's space for
- // it.
- if(p==current_vertices) add_memory_vertices(vc);
-
- if(complicated_setup) {
-
- // We want to be strict about reaching the conclusion that the
- // cell is entirely within the cutting plane. It's not enough
- // to find a vertex that has edges which are all inside or on
- // the plane. If the vertex has neighbors that are also on the
- // plane, we should check those too.
- if(!search_for_outside_edge(vc,up)) return false;
-
- // The search algorithm found a point which is on the cutting
- // plane. We leave that point in place, and create a new one at
- // the same location.
- pts[3*p]=pts[3*up];
- pts[3*p+1]=pts[3*up+1];
- pts[3*p+2]=pts[3*up+2];
-
- // Search for a collection of edges of the test vertex which
- // are outside of the cutting space. Begin by testing the
- // zeroth edge.
- i=0;
- lp=*ed[up];
- lw=m_test(lp,l);
- if(lw!=-1) {
-
- // The first edge is either inside the cutting space,
- // or lies within the cutting plane. Test the edges
- // sequentially until we find one that is outside.
- rp=lw;
- do {
- i++;
-
- // If we reached the last edge with no luck
- // then all of the vertices are inside
- // or on the plane, so the cell is completely
- // deleted
- if(i==nu[up]) return false;
- lp=ed[up][i];
- lw=m_test(lp,l);
- } while (lw!=-1);
- j=i+1;
-
- // We found an edge outside the cutting space. Keep
- // moving through these edges until we find one that's
- // inside or on the plane.
- while(j<nu[up]) {
- lp=ed[up][j];
- lw=m_test(lp,l);
- if(lw!=-1) break;
- j++;
- }
-
- // Compute the number of edges for the new vertex. In
- // general it will be the number of outside edges
- // found, plus two. But we need to recognize the
- // special case when all but one edge is outside, and
- // the remaining one is on the plane. For that case we
- // have to reduce the edge count by one to prevent
- // doubling up.
- if(j==nu[up]&&i==1&&rp==0) {
- nu[p]=nu[up];
- double_edge=true;
- } else nu[p]=j-i+2;
- k=1;
-
- // Add memory for the new vertex if needed, and
- // initialize
- while (nu[p]>=current_vertex_order) add_memory_vorder(vc);
- if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
- vc.n_set_pointer(p,nu[p]);
- ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
- ed[p][nu[p]<<1]=p;
-
- // Copy the edges of the original vertex into the new
- // one. Delete the edges of the original vertex, and
- // update the relational table.
- us=cycle_down(i,up);
- while(i<j) {
- qp=ed[up][i];
- qs=ed[up][nu[up]+i];
- vc.n_copy(p,k,up,i);
- ed[p][k]=qp;
- ed[p][nu[p]+k]=qs;
- ed[qp][qs]=p;
- ed[qp][nu[qp]+qs]=k;
- ed[up][i]=-1;
- i++;k++;
- }
- qs=i==nu[up]?0:i;
- } else {
-
- // In this case, the zeroth edge is outside the cutting
- // plane. Begin by searching backwards from the last
- // edge until we find an edge which isn't outside.
- i=nu[up]-1;
- lp=ed[up][i];
- lw=m_test(lp,l);
- while(lw==-1) {
- i--;
-
- // If i reaches zero, then we have a point in
- // the plane all of whose edges are outside
- // the cutting space, so we just exit
- if(i==0) return true;
- lp=ed[up][i];
- lw=m_test(lp,l);
- }
-
- // Now search forwards from zero
- j=1;
- qp=ed[up][j];
- qw=m_test(qp,q);
- while(qw==-1) {
- j++;
- qp=ed[up][j];
- qw=m_test(qp,l);
- }
-
- // Compute the number of edges for the new vertex. In
- // general it will be the number of outside edges
- // found, plus two. But we need to recognize the
- // special case when all but one edge is outside, and
- // the remaining one is on the plane. For that case we
- // have to reduce the edge count by one to prevent
- // doubling up.
- if(i==j&&qw==0) {
- double_edge=true;
- nu[p]=nu[up];
- } else {
- nu[p]=nu[up]-i+j+1;
- }
-
- // Add memory to store the vertex if it doesn't exist
- // already
- k=1;
- while(nu[p]>=current_vertex_order) add_memory_vorder(vc);
- if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2);
-
- // Copy the edges of the original vertex into the new
- // one. Delete the edges of the original vertex, and
- // update the relational table.
- vc.n_set_pointer(p,nu[p]);
- ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++;
- ed[p][nu[p]<<1]=p;
- us=i++;
- while(i<nu[up]) {
- qp=ed[up][i];
- qs=ed[up][nu[up]+i];
- vc.n_copy(p,k,up,i);
- ed[p][k]=qp;
- ed[p][nu[p]+k]=qs;
- ed[qp][qs]=p;
- ed[qp][nu[qp]+qs]=k;
- ed[up][i]=-1;
- i++;k++;
- }
- i=0;
- while(i<j) {
- qp=ed[up][i];
- qs=ed[up][nu[up]+i];
- vc.n_copy(p,k,up,i);
- ed[p][k]=qp;
- ed[p][nu[p]+k]=qs;
- ed[qp][qs]=p;
- ed[qp][nu[qp]+qs]=k;
- ed[up][i]=-1;
- i++;k++;
- }
- qs=j;
- }
- if(!double_edge) {
- vc.n_copy(p,k,up,qs);
- vc.n_set(p,0,p_id);
- } else vc.n_copy(p,0,up,qs);
-
- // Add this point to the auxiliary delete stack
- if(stackp2==stacke2) add_memory_ds2(stackp2);
- *(stackp2++)=up;
-
- // Look at the edges on either side of the group that was
- // detected. We're going to commence facet computation by
- // moving along one of them. We are going to end up coming back
- // along the other one.
- cs=k;
- qp=up;q=u;
- i=ed[up][us];
- us=ed[up][nu[up]+us];
- up=i;
- ed[qp][nu[qp]<<1]=-p;
-
- } else {
-
- // The search algorithm found an intersected edge between the
- // points lp and up. Create a new vertex between them which
- // lies on the cutting plane. Since u and l differ by at least
- // the tolerance, this division should never screw up.
- if(stackp==stacke) add_memory_ds(stackp);
- *(stackp++)=up;
- r=u/(u-l);l=1-r;
- pts[3*p]=pts[3*lp]*r+pts[3*up]*l;
- pts[3*p+1]=pts[3*lp+1]*r+pts[3*up+1]*l;
- pts[3*p+2]=pts[3*lp+2]*r+pts[3*up+2]*l;
-
- // This point will always have three edges. Connect one of them
- // to lp.
- nu[p]=3;
- if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
- vc.n_set_pointer(p,3);
- vc.n_set(p,0,p_id);
- vc.n_copy(p,1,up,us);
- vc.n_copy(p,2,lp,ls);
- ed[p]=mep[3]+7*mec[3]++;
- ed[p][6]=p;
- ed[up][us]=-1;
- ed[lp][ls]=p;
- ed[lp][nu[lp]+ls]=1;
- ed[p][1]=lp;
- ed[p][nu[p]+1]=ls;
- cs=2;
-
- // Set the direction to move in
- qs=cycle_up(us,up);
- qp=up;q=u;
- }
-
- // When the code reaches here, we have initialized the first point, and
- // we have a direction for moving it to construct the rest of the facet
- cp=p;rp=p;p++;
- while(qp!=up||qs!=us) {
-
- // We're currently tracing round an intersected facet. Keep
- // moving around it until we find a point or edge which
- // intersects the plane.
- lp=ed[qp][qs];
- lw=m_test(lp,l);
-
- if(lw==1) {
-
- // The point is still in the cutting space. Just add it
- // to the delete stack and keep moving.
- qs=cycle_up(ed[qp][nu[qp]+qs],lp);
- qp=lp;
- q=l;
- if(stackp==stacke) add_memory_ds(stackp);
- *(stackp++)=qp;
-
- } else if(lw==-1) {
-
- // The point is outside of the cutting space, so we've
- // found an intersected edge. Introduce a regular point
- // at the point of intersection. Connect it to the
- // point we just tested. Also connect it to the previous
- // new point in the facet we're constructing.
- if(p==current_vertices) add_memory_vertices(vc);
- r=q/(q-l);l=1-r;
- pts[3*p]=pts[3*lp]*r+pts[3*qp]*l;
- pts[3*p+1]=pts[3*lp+1]*r+pts[3*qp+1]*l;
- pts[3*p+2]=pts[3*lp+2]*r+pts[3*qp+2]*l;
- nu[p]=3;
- if(mec[3]==mem[3]) add_memory(vc,3,stackp2);
- ls=ed[qp][qs+nu[qp]];
- vc.n_set_pointer(p,3);
- vc.n_set(p,0,p_id);
- vc.n_copy(p,1,qp,qs);
- vc.n_copy(p,2,lp,ls);
- ed[p]=mep[3]+7*mec[3]++;
- *ed[p]=cp;
- ed[p][1]=lp;
- ed[p][3]=cs;
- ed[p][4]=ls;
- ed[p][6]=p;
- ed[lp][ls]=p;
- ed[lp][nu[lp]+ls]=1;
- ed[cp][cs]=p;
- ed[cp][nu[cp]+cs]=0;
- ed[qp][qs]=-1;
- qs=cycle_up(qs,qp);
- cp=p++;
- cs=2;
- } else {
-
- // We've found a point which is on the cutting plane.
- // We're going to introduce a new point right here, but
- // first we need to figure out the number of edges it
- // has.
- if(p==current_vertices) add_memory_vertices(vc);
-
- // If the previous vertex detected a double edge, our
- // new vertex will have one less edge.
- k=double_edge?0:1;
- qs=ed[qp][nu[qp]+qs];
- qp=lp;
- iqs=qs;
-
- // Start testing the edges of the current point until
- // we find one which isn't outside the cutting space
- do {
- k++;
- qs=cycle_up(qs,qp);
- lp=ed[qp][qs];
- lw=m_test(lp,l);
- } while (lw==-1);
-
- // Now we need to find out whether this marginal vertex
- // we are on has been visited before, because if that's
- // the case, we need to add vertices to the existing
- // new vertex, rather than creating a fresh one. We also
- // need to figure out whether we're in a case where we
- // might be creating a duplicate edge.
- j=-ed[qp][nu[qp]<<1];
- if(qp==up&&qs==us) {
-
- // If we're heading into the final part of the
- // new facet, then we never worry about the
- // duplicate edge calculation.
- new_double_edge=false;
- if(j>0) k+=nu[j];
- } else {
- if(j>0) {
-
- // This vertex was visited before, so
- // count those vertices to the ones we
- // already have.
- k+=nu[j];
-
- // The only time when we might make a
- // duplicate edge is if the point we're
- // going to move to next is also a
- // marginal point, so test for that
- // first.
- if(lw==0) {
-
- // Now see whether this marginal point
- // has been visited before.
- i=-ed[lp][nu[lp]<<1];
- if(i>0) {
-
- // Now see if the last edge of that other
- // marginal point actually ends up here.
- if(ed[i][nu[i]-1]==j) {
- new_double_edge=true;
- k-=1;
- } else new_double_edge=false;
- } else {
-
- // That marginal point hasn't been visited
- // before, so we probably don't have to worry
- // about duplicate edges, except in the
- // case when that's the way into the end
- // of the facet, because that way always creates
- // an edge.
- if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) {
- new_double_edge=true;
- k-=1;
- } else new_double_edge=false;
- }
- } else new_double_edge=false;
- } else {
-
- // The vertex hasn't been visited
- // before, but let's see if it's
- // marginal
- if(lw==0) {
-
- // If it is, we need to check
- // for the case that it's a
- // small branch, and that we're
- // heading right back to where
- // we came from
- i=-ed[lp][nu[lp]<<1];
- if(i==cp) {
- new_double_edge=true;
- k-=1;
- } else new_double_edge=false;
- } else new_double_edge=false;
- }
- }
-
- // k now holds the number of edges of the new vertex
- // we are forming. Add memory for it if it doesn't exist
- // already.
- while(k>=current_vertex_order) add_memory_vorder(vc);
- if(mec[k]==mem[k]) add_memory(vc,k,stackp2);
-
- // Now create a new vertex with order k, or augment
- // the existing one
- if(j>0) {
-
- // If we're augmenting a vertex but we don't
- // actually need any more edges, just skip this
- // routine to avoid memory confusion
- if(nu[j]!=k) {
- // Allocate memory and copy the edges
- // of the previous instance into it
- vc.n_set_aux1(k);
- edp=mep[k]+((k<<1)+1)*mec[k]++;
- i=0;
- while(i<nu[j]) {
- vc.n_copy_aux1(j,i);
- edp[i]=ed[j][i];
- edp[k+i]=ed[j][nu[j]+i];
- i++;
- }
- edp[k<<1]=j;
-
- // Remove the previous instance with
- // fewer vertices from the memory
- // structure
- edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
- if(edd!=ed[j]) {
- for(lw=0;lw<=(nu[j]<<1);lw++) ed[j][lw]=edd[lw];
- vc.n_set_aux2_copy(j,nu[j]);
- vc.n_copy_pointer(edd[nu[j]<<1],j);
- ed[edd[nu[j]<<1]]=ed[j];
- }
- vc.n_set_to_aux1(j);
- ed[j]=edp;
- } else i=nu[j];
- } else {
-
- // Allocate a new vertex of order k
- vc.n_set_pointer(p,k);
- ed[p]=mep[k]+((k<<1)+1)*mec[k]++;
- ed[p][k<<1]=p;
- if(stackp2==stacke2) add_memory_ds2(stackp2);
- *(stackp2++)=qp;
- pts[3*p]=pts[3*qp];
- pts[3*p+1]=pts[3*qp+1];
- pts[3*p+2]=pts[3*qp+2];
- ed[qp][nu[qp]<<1]=-p;
- j=p++;
- i=0;
- }
- nu[j]=k;
-
- // Unless the previous case was a double edge, connect
- // the first available edge of the new vertex to the
- // last one in the facet
- if(!double_edge) {
- ed[j][i]=cp;
- ed[j][nu[j]+i]=cs;
- vc.n_set(j,i,p_id);
- ed[cp][cs]=j;
- ed[cp][nu[cp]+cs]=i;
- i++;
- }
-
- // Copy in the edges of the underlying vertex,
- // and do one less if this was a double edge
- qs=iqs;
- while(i<(new_double_edge?k:k-1)) {
- qs=cycle_up(qs,qp);
- lp=ed[qp][qs];ls=ed[qp][nu[qp]+qs];
- vc.n_copy(j,i,qp,qs);
- ed[j][i]=lp;
- ed[j][nu[j]+i]=ls;
- ed[lp][ls]=j;
- ed[lp][nu[lp]+ls]=i;
- ed[qp][qs]=-1;
- i++;
- }
- qs=cycle_up(qs,qp);
- cs=i;
- cp=j;
- vc.n_copy(j,new_double_edge?0:cs,qp,qs);
-
- // Update the double_edge flag, to pass it
- // to the next instance of this routine
- double_edge=new_double_edge;
- }
- }
-
- // Connect the final created vertex to the initial one
- ed[cp][cs]=rp;
- *ed[rp]=cp;
- ed[cp][nu[cp]+cs]=0;
- ed[rp][nu[rp]]=cs;
-
- // Delete points: first, remove any duplicates
- dsp=ds;
- while(dsp<stackp) {
- j=*dsp;
- if(ed[j][nu[j]]!=-1) {
- ed[j][nu[j]]=-1;
- dsp++;
- } else *dsp=*(--stackp);
- }
-
- // Add the points in the auxiliary delete stack,
- // and reset their back pointers
- for(dsp=ds2;dsp<stackp2;dsp++) {
- j=*dsp;
- ed[j][nu[j]<<1]=j;
- if(ed[j][nu[j]]!=-1) {
- ed[j][nu[j]]=-1;
- if(stackp==stacke) add_memory_ds(stackp);
- *(stackp++)=j;
- }
- }
-
- // Scan connections and add in extras
- for(dsp=ds;dsp<stackp;dsp++) {
- cp=*dsp;
- for(edp=ed[cp];edp<ed[cp]+nu[cp];edp++) {
- qp=*edp;
- if(qp!=-1&&ed[qp][nu[qp]]!=-1) {
- if(stackp==stacke) {
- int dis=stackp-dsp;
- add_memory_ds(stackp);
- dsp=ds+dis;
- }
- *(stackp++)=qp;
- ed[qp][nu[qp]]=-1;
- }
- }
- }
- up=0;
-
- // Delete them from the array structure
- while(stackp>ds) {
- --p;
- while(ed[p][nu[p]]==-1) {
- j=nu[p];
- edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]);
- while(edp<ed[p]+(j<<1)+1) *(edp++)=*(edd++);
- vc.n_set_aux2_copy(p,j);
- vc.n_copy_pointer(ed[p][(j<<1)],p);
- ed[ed[p][(j<<1)]]=ed[p];
- --p;
- }
- up=*(--stackp);
- if(up<p) {
-
- // Vertex management
- pts[3*up]=pts[3*p];
- pts[3*up+1]=pts[3*p+1];
- pts[3*up+2]=pts[3*p+2];
-
- // Memory management
- j=nu[up];
- edp=ed[up];edd=(mep[j]+((j<<1)+1)*--mec[j]);
- while(edp<ed[up]+(j<<1)+1) *(edp++)=*(edd++);
- vc.n_set_aux2_copy(up,j);
- vc.n_copy_pointer(ed[up][j<<1],up);
- vc.n_copy_pointer(up,p);
- ed[ed[up][j<<1]]=ed[up];
-
- // Edge management
- ed[up]=ed[p];
- nu[up]=nu[p];
- for(i=0;i<nu[up];i++) ed[ed[up][i]][ed[up][nu[up]+i]]=up;
- ed[up][nu[up]<<1]=up;
- } else up=p++;
- }
-
- // Check for any vertices of zero order
- if(*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR);
-
- // Collapse any order 2 vertices and exit
- return collapse_order2(vc);
-}
-
-/** During the creation of a new facet in the plane routine, it is possible
- * that some order two vertices may arise. This routine removes them.
- * Suppose an order two vertex joins c and d. If there's a edge between
- * c and d already, then the order two vertex is just removed; otherwise,
- * the order two vertex is removed and c and d are joined together directly.
- * It is possible this process will create order two or order one vertices,
- * and the routine is continually run until all of them are removed.
- * \return False if the vertex removal was unsuccessful, indicative of the cell
- * reducing to zero volume and disappearing; true if the vertex removal
- * was successful. */
-template<class vc_class>
-inline bool voronoicell_base::collapse_order2(vc_class &vc) {
- if(!collapse_order1(vc)) return false;
- int a,b,i,j,k,l;
- while(mec[2]>0) {
-
- // Pick a order 2 vertex and read in its edges
- i=--mec[2];
- j=mep[2][5*i];k=mep[2][5*i+1];
- if(j==k) {
-#if VOROPP_VERBOSE >=1
- fputs("Order two vertex joins itself",stderr);
-#endif
- return false;
- }
-
- // Scan the edges of j to see if joins k
- for(l=0;l<nu[j];l++) {
- if(ed[j][l]==k) break;
- }
-
- // If j doesn't already join k, join them together.
- // Otherwise delete the connection to the current
- // vertex from j and k.
- a=mep[2][5*i+2];b=mep[2][5*i+3];i=mep[2][5*i+4];
- if(l==nu[j]) {
- ed[j][a]=k;
- ed[k][b]=j;
- ed[j][nu[j]+a]=b;
- ed[k][nu[k]+b]=a;
- } else {
- if(!delete_connection(vc,j,a,false)) return false;
- if(!delete_connection(vc,k,b,true)) return false;
- }
-
- // Compact the memory
- --p;
- if(up==i) up=0;
- if(p!=i) {
- if(up==p) up=i;
- pts[3*i]=pts[3*p];
- pts[3*i+1]=pts[3*p+1];
- pts[3*i+2]=pts[3*p+2];
- for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
- vc.n_copy_pointer(i,p);
- ed[i]=ed[p];
- nu[i]=nu[p];
- ed[i][nu[i]<<1]=i;
- }
-
- // Collapse any order 1 vertices if they were created
- if(!collapse_order1(vc)) return false;
- }
- return true;
-}
-
-/** Order one vertices can potentially be created during the order two collapse
- * routine. This routine keeps removing them until there are none left.
- * \return False if the vertex removal was unsuccessful, indicative of the cell
- * having zero volume and disappearing; true if the vertex removal was
- * successful. */
-template<class vc_class>
-inline bool voronoicell_base::collapse_order1(vc_class &vc) {
- int i,j,k;
- while(mec[1]>0) {
- up=0;
-#if VOROPP_VERBOSE >=1
- fputs("Order one collapse\n",stderr);
-#endif
- i=--mec[1];
- j=mep[1][3*i];k=mep[1][3*i+1];
- i=mep[1][3*i+2];
- if(!delete_connection(vc,j,k,false)) return false;
- --p;
- if(up==i) up=0;
- if(p!=i) {
- if(up==p) up=i;
- pts[3*i]=pts[3*p];
- pts[3*i+1]=pts[3*p+1];
- pts[3*i+2]=pts[3*p+2];
- for(k=0;k<nu[p];k++) ed[ed[p][k]][ed[p][nu[p]+k]]=i;
- vc.n_copy_pointer(i,p);
- ed[i]=ed[p];
- nu[i]=nu[p];
- ed[i][nu[i]<<1]=i;
- }
- }
- return true;
-}
-
-/** This routine deletes the kth edge of vertex j and reorganizes the memory.
- * If the neighbor computation is enabled, we also have to supply an handedness
- * flag to decide whether to preserve the plane on the left or right of the
- * connection.
- * \return False if a zero order vertex was formed, indicative of the cell
- * disappearing; true if the vertex removal was successful. */
-template<class vc_class>
-inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) {
- int q=hand?k:cycle_up(k,j);
- int i=nu[j]-1,l,*edp,*edd,m;
-#if VOROPP_VERBOSE >=1
- if(i<1) {
- fputs("Zero order vertex formed\n",stderr);
- return false;
- }
-#endif
- if(mec[i]==mem[i]) add_memory(vc,i,ds2);
- vc.n_set_aux1(i);
- for(l=0;l<q;l++) vc.n_copy_aux1(j,l);
- while(l<i) {
- vc.n_copy_aux1_shift(j,l);
- l++;
- }
- edp=mep[i]+((i<<1)+1)*mec[i]++;
- edp[i<<1]=j;
- for(l=0;l<k;l++) {
- edp[l]=ed[j][l];
- edp[l+i]=ed[j][l+nu[j]];
- }
- while(l<i) {
- m=ed[j][l+1];
- edp[l]=m;
- k=ed[j][l+nu[j]+1];
- edp[l+i]=k;
- ed[m][nu[m]+k]--;
- l++;
- }
-
- edd=mep[nu[j]]+((nu[j]<<1)+1)*--mec[nu[j]];
- for(l=0;l<=(nu[j]<<1);l++) ed[j][l]=edd[l];
- vc.n_set_aux2_copy(j,nu[j]);
- vc.n_set_to_aux2(edd[nu[j]<<1]);
- vc.n_set_to_aux1(j);
- ed[edd[nu[j]<<1]]=edd;
- ed[j]=edp;
- nu[j]=i;
- return true;
-}
-
-/** Calculates the areas of each face of the Voronoi cell and prints the
- * results to an output stream.
- * \param[out] v the vector to store the results in. */
-void voronoicell_base::face_areas(std::vector<double> &v) {
- double area;
- v.clear();
- int i,j,k,l,m,n;
- double ux,uy,uz,vx,vy,vz,wx,wy,wz;
- for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
- k=ed[i][j];
- if(k>=0) {
- area=0;
- ed[i][j]=-1-k;
- l=cycle_up(ed[i][nu[i]+j],k);
- m=ed[k][l];ed[k][l]=-1-m;
- while(m!=i) {
- n=cycle_up(ed[k][nu[k]+l],m);
- ux=pts[3*k]-pts[3*i];
- uy=pts[3*k+1]-pts[3*i+1];
- uz=pts[3*k+2]-pts[3*i+2];
- vx=pts[3*m]-pts[3*i];
- vy=pts[3*m+1]-pts[3*i+1];
- vz=pts[3*m+2]-pts[3*i+2];
- wx=uy*vz-uz*vy;
- wy=uz*vx-ux*vz;
- wz=ux*vy-uy*vx;
- area+=sqrt(wx*wx+wy*wy+wz*wz);
- k=m;l=n;
- m=ed[k][l];ed[k][l]=-1-m;
- }
- v.push_back(0.125*area);
- }
- }
- reset_edges();
-}
-
-/** Several routines in the class that gather cell-based statistics internally
- * track their progress by flipping edges to negative so that they know what
- * parts of the cell have already been tested. This function resets them back
- * to positive. When it is called, it assumes that every edge in the routine
- * should have already been flipped to negative, and it bails out with an
- * internal error if it encounters a positive edge. */
-inline void voronoicell_base::reset_edges() {
- int i,j;
- for(i=0;i<p;i++) for(j=0;j<nu[i];j++) {
- if(ed[i][j]>=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR);
- ed[i][j]=-1-ed[i][j];
- }
-}
-
-/** Checks to see if a given vertex is inside, outside or within the test
- * plane. If the point is far away from the test plane, the routine immediately
- * returns whether it is inside or outside. If the routine is close the the
- * plane and within the specified tolerance, then the special check_marginal()
- * routine is called.
- * \param[in] n the vertex to test.
- * \param[out] ans the result of the scalar product used in evaluating the
- * location of the point.
- * \return -1 if the point is inside the plane, 1 if the point is outside the
- * plane, or 0 if the point is within the plane. */
-inline int voronoicell_base::m_test(int n,double &ans) {
- double *pp=pts+n+(n<<1);
- ans=*(pp++)*px;
- ans+=*(pp++)*py;
- ans+=*pp*pz-prsq;
- if(ans<-tolerance2) {
- return -1;
- } else if(ans>tolerance2) {
- return 1;
- }
- return check_marginal(n,ans);
-}
-
-/** Checks to see if a given vertex is inside, outside or within the test
- * plane, for the case when the point has been detected to be very close to the
- * plane. The routine ensures that the returned results are always consistent
- * with previous tests, by keeping a table of any marginal results. The routine
- * first sees if the vertex is in the table, and if it finds a previously
- * computed result it uses that. Otherwise, it computes a result for this
- * vertex and adds it the table.
- * \param[in] n the vertex to test.
- * \param[in] ans the result of the scalar product used in evaluating
- * the location of the point.
- * \return -1 if the point is inside the plane, 1 if the point is outside the
- * plane, or 0 if the point is within the plane. */
-int voronoicell_base::check_marginal(int n,double &ans) {
- int i;
- for(i=0;i<n_marg;i+=2) if(marg[i]==n) return marg[i+1];
- if(n_marg==current_marginal) {
- current_marginal<<=1;
- if(current_marginal>max_marginal)
- voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR);
-#if VOROPP_VERBOSE >=2
- fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i);
-#endif
- int *pmarg=new int[current_marginal];
- for(int j=0;j<n_marg;j++) pmarg[j]=marg[j];
- delete [] marg;
- marg=pmarg;
- }
- marg[n_marg++]=n;
- marg[n_marg++]=ans>tolerance?1:(ans<-tolerance?-1:0);
- return marg[n_marg-1];
-}
-
-/** This initializes the class to be a rectangular box. It calls the base class
- * initialization routine to set up the edge and vertex information, and then
- * sets up the neighbor information, with initial faces being assigned ID
- * numbers from -1 to -6.
- * \param[in] (xmin,xmax) the minimum and maximum x coordinates.
- * \param[in] (ymin,ymax) the minimum and maximum y coordinates.
- * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */
-void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) {
- init_base(xmin,xmax,ymin,ymax,zmin,zmax);
- int *q=mne[3];
- *q=-5;q[1]=-3;q[2]=-1;
- q[3]=-5;q[4]=-2;q[5]=-3;
- q[6]=-5;q[7]=-1;q[8]=-4;
- q[9]=-5;q[10]=-4;q[11]=-2;
- q[12]=-6;q[13]=-1;q[14]=-3;
- q[15]=-6;q[16]=-3;q[17]=-2;
- q[18]=-6;q[19]=-4;q[20]=-1;
- q[21]=-6;q[22]=-2;q[23]=-4;
- *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9;
- ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21;
-}
-
-/** This routine checks to make sure the neighbor information of each face is
- * consistent. */
-void voronoicell_neighbor::check_facets() {
- int i,j,k,l,m,q;
- for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
- k=ed[i][j];
- if(k>=0) {
- ed[i][j]=-1-k;
- q=ne[i][j];
- l=cycle_up(ed[i][nu[i]+j],k);
- do {
- m=ed[k][l];
- ed[k][l]=-1-m;
- if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q);
- l=cycle_up(ed[k][nu[k]+l],m);
- k=m;
- } while (k!=i);
- }
- }
- reset_edges();
-}
-
-/** The class constructor allocates memory for storing neighbor information. */
-voronoicell_neighbor::voronoicell_neighbor() {
- int i;
- mne=new int*[current_vertex_order];
- ne=new int*[current_vertices];
- for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i];
- mne[3]=new int[init_3_vertices*3];
- for(i=4;i<current_vertex_order;i++) mne[i]=new int[init_n_vertices*i];
-}
-
-/** The class destructor frees the dynamically allocated memory for storing
- * neighbor information. */
-voronoicell_neighbor::~voronoicell_neighbor() {
- for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mne[i];
- delete [] mne;
- delete [] ne;
-}
-
-/** Computes a vector list of neighbors. */
-void voronoicell_neighbor::neighbors(std::vector<int> &v) {
- v.clear();
- int i,j,k,l,m;
- for(i=1;i<p;i++) for(j=0;j<nu[i];j++) {
- k=ed[i][j];
- if(k>=0) {
- v.push_back(ne[i][j]);
- ed[i][j]=-1-k;
- l=cycle_up(ed[i][nu[i]+j],k);
- do {
- m=ed[k][l];
- ed[k][l]=-1-m;
- l=cycle_up(ed[k][nu[k]+l],m);
- k=m;
- } while (k!=i);
- }
- }
- reset_edges();
-}
-
-// Explicit instantiation
-template bool voronoicell_base::nplane(voronoicell_neighbor&,double,double,double,double,int);
-template void voronoicell_base::check_memory_for_copy(voronoicell_neighbor&,voronoicell_base*);
-
-}
-
diff --git a/src/USER-PTM/cell.h b/src/USER-PTM/cell.h
deleted file mode 100644
index 51a0cbb9ef..0000000000
--- a/src/USER-PTM/cell.h
+++ /dev/null
@@ -1,324 +0,0 @@
-// Voro++, a 3D cell-based Voronoi library
-//
-// Author : Chris H. Rycroft (LBL / UC Berkeley)
-// Email : chr@alum.mit.edu
-// Date : August 30th 2011
-//
-// Modified by PM Larsen for use in Polyhedral Template Matching
-
-/** \file cell.hh
- * \brief Header file for the voronoicell and related classes. */
-
-#ifndef VOROPP_CELL_HH
-#define VOROPP_CELL_HH
-
-#include <vector>
-#include <cstdio>
-
-#include "config.h"
-
-namespace voro {
-
-/** \brief A class representing a single Voronoi cell.
- *
- * This class represents a single Voronoi cell, as a collection of vertices
- * that are connected by edges. The class contains routines for initializing
- * the Voronoi cell to be simple shapes such as a box, tetrahedron, or octahedron.
- * It the contains routines for recomputing the cell based on cutting it
- * by a plane, which forms the key routine for the Voronoi cell computation.
- * It contains numerous routine for computing statistics about the Voronoi cell,
- * and it can output the cell in several formats.
- *
- * This class is not intended for direct use, but forms the base of the
- * voronoicell and voronoicell_neighbor classes, which extend it based on
- * whether neighboring particle ID information needs to be tracked. */
-class voronoicell_base {
- public:
- /** This holds the current size of the arrays ed and nu, which
- * hold the vertex information. If more vertices are created
- * than can fit in this array, then it is dynamically extended
- * using the add_memory_vertices routine. */
- int current_vertices;
- /** This holds the current maximum allowed order of a vertex,
- * which sets the size of the mem, mep, and mec arrays. If a
- * vertex is created with more vertices than this, the arrays
- * are dynamically extended using the add_memory_vorder routine.
- */
- int current_vertex_order;
- /** This sets the size of the main delete stack. */
- int current_delete_size;
- /** This sets the size of the auxiliary delete stack. */
- int current_delete2_size;
- /** This sets the total number of vertices in the current cell.
- */
- int p;
- /** This is the index of particular point in the cell, which is
- * used to start the tracing routines for plane intersection
- * and cutting. These routines will work starting from any
- * point, but it's often most efficient to start from the last
- * point considered, since in many cases, the cell construction
- * algorithm may consider many planes with similar vectors
- * concurrently. */
- int up;
- /** This is a two dimensional array that holds information
- * about the edge connections of the vertices that make up the
- * cell. The two dimensional array is not allocated in the
- * usual method. To account for the fact the different vertices
- * have different orders, and thus require different amounts of
- * storage, the elements of ed[i] point to one-dimensional
- * arrays in the mep[] array of different sizes.
- *
- * More specifically, if vertex i has order m, then ed[i]
- * points to a one-dimensional array in mep[m] that has 2*m+1
- * entries. The first m elements hold the neighboring edges, so
- * that the jth edge of vertex i is held in ed[i][j]. The next
- * m elements hold a table of relations which is redundant but
- * helps speed up the computation. It satisfies the relation
- * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back
- * pointer, so that ed[i+2*m]=i. The back pointers are used
- * when rearranging the memory. */
- int **ed;
- /** This array holds the order of the vertices in the Voronoi
- * cell. This array is dynamically allocated, with its current
- * size held by current_vertices. */
- int *nu;
- /** This in an array with size 3*current_vertices for holding
- * the positions of the vertices. */
- double *pts;
- voronoicell_base();
- virtual ~voronoicell_base();
- void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
- void init_octahedron_base(double l);
- void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3);
- void translate(double x,double y,double z);
- double volume();
- double max_radius_squared();
- double total_edge_distance();
- double surface_area();
- void centroid(double &cx,double &cy,double &cz);
- int number_of_faces();
- int number_of_edges();
- void vertex_orders(std::vector<int> &v);
- void vertices(std::vector<double> &v);
- void vertices(double x,double y,double z,std::vector<double> &v);
- void face_areas(std::vector<double> &v);
- void face_orders(std::vector<int> &v);
- void face_freq_table(std::vector<int> &v);
- void face_vertices(std::vector<int> &v);
- void face_perimeters(std::vector<double> &v);
- void normals(std::vector<double> &v);
- template<class vc_class>
- bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id);
- bool plane_intersects(double x,double y,double z,double rsq);
- bool plane_intersects_guess(double x,double y,double z,double rsq);
- void construct_relations();
- void check_relations();
- void check_duplicates();
- /** Returns a list of IDs of neighboring particles
- * corresponding to each face.
- * \param[out] v a reference to a vector in which to return the
- * results. If no neighbor information is
- * available, a blank vector is returned. */
- virtual void neighbors(std::vector<int> &v) {v.clear();}
- /** This a virtual function that is overridden by a routine to
- * print the neighboring particle IDs for a given vertex. By
- * default, when no neighbor information is available, the
- * routine does nothing.
- * \param[in] i the vertex to consider. */
- /** This is a simple inline function for picking out the index
- * of the next edge counterclockwise at the current vertex.
- * \param[in] a the index of an edge of the current vertex.
- * \param[in] p the number of the vertex.
- * \return 0 if a=nu[p]-1, or a+1 otherwise. */
- inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;}
- /** This is a simple inline function for picking out the index
- * of the next edge clockwise from the current vertex.
- * \param[in] a the index of an edge of the current vertex.
- * \param[in] p the number of the vertex.
- * \return nu[p]-1 if a=0, or a-1 otherwise. */
- inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;}
- protected:
- /** This a one dimensional array that holds the current sizes
- * of the memory allocations for them mep array.*/
- int *mem;
- /** This is a one dimensional array that holds the current
- * number of vertices of order p that are stored in the mep[p]
- * array. */
- int *mec;
- /** This is a two dimensional array for holding the information
- * about the edges of the Voronoi cell. mep[p] is a
- * one-dimensional array for holding the edge information about
- * all vertices of order p, with each vertex holding 2*p+1
- * integers of information. The total number of vertices held
- * on mep[p] is stored in mem[p]. If the space runs out, the
- * code allocates more using the add_memory() routine. */
- int **mep;
- inline void reset_edges();
- template<class vc_class>
- void check_memory_for_copy(vc_class &vc,voronoicell_base* vb);
- void copy(voronoicell_base* vb);
- private:
- /** This is the delete stack, used to store the vertices which
- * are going to be deleted during the plane cutting procedure.
- */
- int *ds,*stacke;
- /** This is the auxiliary delete stack, which has size set by
- * current_delete2_size. */
- int *ds2,*stacke2;
- /** This stores the current memory allocation for the marginal
- * cases. */
- int current_marginal;
- /** This stores the total number of marginal points which are
- * currently in the buffer. */
- int n_marg;
- /** This array contains a list of the marginal points, and also
- * the outcomes of the marginal tests. */
- int *marg;
- /** The x coordinate of the normal vector to the test plane. */
- double px;
- /** The y coordinate of the normal vector to the test plane. */
- double py;
- /** The z coordinate of the normal vector to the test plane. */
- double pz;
- /** The magnitude of the normal vector to the test plane. */
- double prsq;
- template<class vc_class>
- void add_memory(vc_class &vc,int i,int *stackp2);
- template<class vc_class>
- void add_memory_vertices(vc_class &vc);
- template<class vc_class>
- void add_memory_vorder(vc_class &vc);
- void add_memory_ds(int *&stackp);
- void add_memory_ds2(int *&stackp2);
- template<class vc_class>
- inline bool collapse_order1(vc_class &vc);
- template<class vc_class>
- inline bool collapse_order2(vc_class &vc);
- template<class vc_class>
- inline bool delete_connection(vc_class &vc,int j,int k,bool hand);
- template<class vc_class>
- inline bool search_for_outside_edge(vc_class &vc,int &up);
- template<class vc_class>
- inline void add_to_stack(vc_class &vc,int lp,int *&stackp2);
- inline bool plane_intersects_track(double x,double y,double z,double rs,double g);
- inline void normals_search(std::vector<double> &v,int i,int j,int k);
- inline bool search_edge(int l,int &m,int &k);
- inline int m_test(int n,double &ans);
- int check_marginal(int n,double &ans);
- friend class voronoicell;
- friend class voronoicell_neighbor;
-};
-
-/** \brief Extension of the voronoicell_base class to represent a Voronoi cell
- * with neighbor information.
- *
- * This class is an extension of the voronoicell_base class, in cases when the
- * IDs of neighboring particles associated with each face of the Voronoi cell.
- * It contains additional data structures mne and ne for storing this
- * information. */
-class voronoicell_neighbor : public voronoicell_base {
- public:
- using voronoicell_base::nplane;
- /** This two dimensional array holds the neighbor information
- * associated with each vertex. mne[p] is a one dimensional
- * array which holds all of the neighbor information for
- * vertices of order p. */
- int **mne;
- /** This is a two dimensional array that holds the neighbor
- * information associated with each vertex. ne[i] points to a
- * one-dimensional array in mne[nu[i]]. ne[i][j] holds the
- * neighbor information associated with the jth edge of vertex
- * i. It is set to the ID number of the plane that made the
- * face that is clockwise from the jth edge. */
- int **ne;
- voronoicell_neighbor();
- ~voronoicell_neighbor();
- void operator=(voronoicell_neighbor &c);
- /** Cuts the Voronoi cell by a particle whose center is at a
- * separation of (x,y,z) from the cell center. The value of rsq
- * should be initially set to \f$x^2+y^2+z^2\f$.
- * \param[in] (x,y,z) the normal vector to the plane.
- * \param[in] rsq the distance along this vector of the plane.
- * \param[in] p_id the plane ID (for neighbor tracking only).
- * \return False if the plane cut deleted the cell entirely,
- * true otherwise. */
- inline bool nplane(double x,double y,double z,double rsq,int p_id) {
- return nplane(*this,x,y,z,rsq,p_id);
- }
- /** This routine calculates the modulus squared of the vector
- * before passing it to the main nplane() routine with full
- * arguments.
- * \param[in] (x,y,z) the vector to cut the cell by.
- * \param[in] p_id the plane ID (for neighbor tracking only).
- * \return False if the plane cut deleted the cell entirely,
- * true otherwise. */
- inline bool nplane(double x,double y,double z,int p_id) {
- double rsq=x*x+y*y+z*z;
- return nplane(*this,x,y,z,rsq,p_id);
- }
- /** This version of the plane routine just makes up the plane
- * ID to be zero. It will only be referenced if neighbor
- * tracking is enabled.
- * \param[in] (x,y,z) the vector to cut the cell by.
- * \param[in] rsq the modulus squared of the vector.
- * \return False if the plane cut deleted the cell entirely,
- * true otherwise. */
- inline bool plane(double x,double y,double z,double rsq) {
- return nplane(*this,x,y,z,rsq,0);
- }
- /** Cuts a Voronoi cell using the influence of a particle at
- * (x,y,z), first calculating the modulus squared of this
- * vector before passing it to the main nplane() routine. Zero
- * is supplied as the plane ID, which will be ignored unless
- * neighbor tracking is enabled.
- * \param[in] (x,y,z) the vector to cut the cell by.
- * \return False if the plane cut deleted the cell entirely,
- * true otherwise. */
- inline bool plane(double x,double y,double z) {
- double rsq=x*x+y*y+z*z;
- return nplane(*this,x,y,z,rsq,0);
- }
- void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax);
- void check_facets();
- virtual void neighbors(std::vector<int> &v);
-
- private:
- int *paux1;
- int *paux2;
- inline void n_allocate(int i,int m) {mne[i]=new int[m*i];}
- inline void n_add_memory_vertices(int i) {
- int **pp=new int*[i];
- for(int j=0;j<current_vertices;j++) pp[j]=ne[j];
- delete [] ne;ne=pp;
- }
- inline void n_add_memory_vorder(int i) {
- int **p2=new int*[i];
- for(int j=0;j<current_vertex_order;j++) p2[j]=mne[j];
- delete [] mne;mne=p2;
- }
- inline void n_set_pointer(int p,int n) {
- ne[p]=mne[n]+n*mec[n];
- }
- inline void n_copy(int a,int b,int c,int d) {ne[a][b]=ne[c][d];}
- inline void n_set(int a,int b,int c) {ne[a][b]=c;}
- inline void n_set_aux1(int k) {paux1=mne[k]+k*mec[k];}
- inline void n_copy_aux1(int a,int b) {paux1[b]=ne[a][b];}
- inline void n_copy_aux1_shift(int a,int b) {paux1[b]=ne[a][b+1];}
- inline void n_set_aux2_copy(int a,int b) {
- paux2=mne[b]+b*mec[b];
- for(int i=0;i<b;i++) ne[a][i]=paux2[i];
- }
- inline void n_copy_pointer(int a,int b) {ne[a]=ne[b];}
- inline void n_set_to_aux1(int j) {ne[j]=paux1;}
- inline void n_set_to_aux2(int j) {ne[j]=paux2;}
- inline void n_allocate_aux1(int i) {paux1=new int[i*mem[i]];}
- inline void n_switch_to_aux1(int i) {delete [] mne[i];mne[i]=paux1;}
- inline void n_copy_to_aux1(int i,int m) {paux1[m]=mne[i][m];}
- inline void n_set_to_aux1_offset(int k,int m) {ne[k]=paux1+m;}
- friend class voronoicell_base;
-};
-
-}
-
-#endif
-
diff --git a/src/USER-PTM/config.h b/src/USER-PTM/config.h
deleted file mode 100644
index eba69b3373..0000000000
--- a/src/USER-PTM/config.h
+++ /dev/null
@@ -1,129 +0,0 @@
-// Voro++, a 3D cell-based Voronoi library
-//
-// Author : Chris H. Rycroft (LBL / UC Berkeley)
-// Email : chr@alum.mit.edu
-// Date : August 30th 2011
-//
-// Modified by PM Larsen for use in Polyhedral Template Matching
-
-/** \file config.hh
- * \brief Master configuration file for setting various compile-time options. */
-
-#ifndef VOROPP_CONFIG_HH
-#define VOROPP_CONFIG_HH
-
-namespace voro {
-
-// These constants set the initial memory allocation for the Voronoi cell
-/** The initial memory allocation for the number of vertices. */
-const int init_vertices=256;
-/** The initial memory allocation for the maximum vertex order. */
-const int init_vertex_order=64;
-/** The initial memory allocation for the number of regular vertices of order
- * 3. */
-const int init_3_vertices=256;
-/** The initial memory allocation for the number of vertices of higher order.
- */
-const int init_n_vertices=8;
-/** The initial buffer size for marginal cases used by the suretest class. */
-const int init_marginal=64;
-/** The initial size for the delete stack. */
-const int init_delete_size=256;
-/** The initial size for the auxiliary delete stack. */
-const int init_delete2_size=256;
-/** The initial size for the wall pointer array. */
-const int init_wall_size=32;
-/** The default initial size for the ordering class. */
-const int init_ordering_size=4096;
-/** The initial size of the pre_container chunk index. */
-const int init_chunk_size=256;
-
-// If the initial memory is too small, the program dynamically allocates more.
-// However, if the limits below are reached, then the program bails out.
-/** The maximum memory allocation for the number of vertices. */
-const int max_vertices=16777216;
-/** The maximum memory allocation for the maximum vertex order. */
-const int max_vertex_order=2048;
-/** The maximum memory allocation for the any particular order of vertex. */
-const int max_n_vertices=16777216;
-/** The maximum buffer size for marginal cases used by the suretest class. */
-const int max_marginal=16777216;
-/** The maximum size for the delete stack. */
-const int max_delete_size=16777216;
-/** The maximum size for the auxiliary delete stack. */
-const int max_delete2_size=16777216;
-/** The maximum amount of particle memory allocated for a single region. */
-const int max_particle_memory=16777216;
-/** The maximum size for the wall pointer array. */
-const int max_wall_size=2048;
-/** The maximum size for the ordering class. */
-const int max_ordering_size=67108864;
-/** The maximum size for the pre_container chunk index. */
-const int max_chunk_size=65536;
-
-/** The chunk size in the pre_container classes. */
-const int pre_container_chunk_size=1024;
-
-#ifndef VOROPP_VERBOSE
-/** Voro++ can print a number of different status and debugging messages to
- * notify the user of special behavior, and this macro sets the amount which
- * are displayed. At level 0, no messages are printed. At level 1, messages
- * about unusual cases during cell construction are printed, such as when the
- * plane routine bails out due to floating point problems. At level 2, general
- * messages about memory expansion are printed. At level 3, technical details
- * about memory management are printed. */
-#define VOROPP_VERBOSE 0
-#endif
-
-/** If a point is within this distance of a cutting plane, then the code
- * assumes that point exactly lies on the plane. */
-const double tolerance=1e-11;
-
-/** If a point is within this distance of a cutting plane, then the code stores
- * whether this point is inside, outside, or exactly on the cutting plane in
- * the marginal cases buffer, to prevent the test giving a different result on
- * a subsequent evaluation due to floating point rounding errors. */
-const double tolerance2=2e-11;
-
-/** The square of the tolerance, used when deciding whether some squared
- * quantities are large enough to be used. */
-const double tolerance_sq=tolerance*tolerance;
-
-/** A large number that is used in the computation. */
-const double large_number=1e30;
-
-/** A radius to use as a placeholder when no other information is available. */
-const double default_radius=0.5;
-
-/** The maximum number of shells of periodic images to test over. */
-const int max_unit_voro_shells=10;
-
-/** A guess for the optimal number of particles per block, used to set up the
- * container grid. */
-const double optimal_particles=5.6;
-
-/** If this is set to 1, then the code reports any instances of particles being
- * put outside of the container geometry. */
-#define VOROPP_REPORT_OUT_OF_BOUNDS 0
-
-/** Voro++ returns this status code if there is a file-related error, such as
- * not being able to open file. */
-#define VOROPP_FILE_ERROR 1
-
-/** Voro++ returns this status code if there is a memory allocation error, if
- * one of the safe memory limits is exceeded. */
-#define VOROPP_MEMORY_ERROR 2
-
-/** Voro++ returns this status code if there is any type of internal error, if
- * it detects that representation of the Voronoi cell is inconsistent. This
- * status code will generally indicate a bug, and the developer should be
- * contacted. */
-#define VOROPP_INTERNAL_ERROR 3
-
-/** Voro++ returns this status code if it could not interpret the command line
- * arguments passed to the command line utility. */
-#define VOROPP_CMD_LINE_ERROR 4
-
-}
-
-#endif
diff --git a/src/USER-PTM/convex_hull_incremental.cpp b/src/USER-PTM/convex_hull_incremental.cpp
deleted file mode 100644
index bfe173cc02..0000000000
--- a/src/USER-PTM/convex_hull_incremental.cpp
+++ /dev/null
@@ -1,363 +0,0 @@
-#include <cmath>
-#include <cfloat>
-#include <string.h>
-#include <cassert>
-#include <algorithm>
-#include "convex_hull_incremental.h"
-#include "ptm_constants.h"
-
-
-#define VISIBLE 1
-#define INVISIBLE 2
-#define BOTH 3
-#define TOLERANCE 1E-8
-
-static double norm_squared(double* p)
-{
- double x = p[0];
- double y = p[1];
- double z = p[2];
-
- return x*x + y*y + z*z;
-}
-
-static double dot_product(const double* a, const double* b)
-{
- return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
-}
-
-static void cross_product(double* a, double* b, double* c)
-{
- c[0] = a[1] * b[2] - a[2] * b[1];
- c[1] = a[2] * b[0] - a[0] * b[2];
- c[2] = a[0] * b[1] - a[1] * b[0];
-}
-
-static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal)
-{
- double u[3] = { points[b][0] - points[a][0],
- points[b][1] - points[a][1],
- points[b][2] - points[a][2] };
-
- double v[3] = { points[c][0] - points[a][0],
- points[c][1] - points[a][1],
- points[c][2] - points[a][2] };
-
- cross_product(u, v, plane_normal);
- double norm = sqrt(norm_squared(plane_normal));
- plane_normal[0] /= norm;
- plane_normal[1] /= norm;
- plane_normal[2] /= norm;
-}
-
-static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross)
-{
- return plane_cross[0] * (plane_point[0] - w[0])
- + plane_cross[1] * (plane_point[1] - w[1])
- + plane_cross[2] * (plane_point[2] - w[2]);
-}
-
-static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index)
-{
- for (int j=0;j<3;j++)
- {
- double dmin = DBL_MAX, dmax = -DBL_MAX;
- int imin = 0, imax = 0;
-
- for (int i = 0;i<num_points;i++)
- {
- double d = points[i][j];
- if (d < dmin)
- {
- dmin = d;
- imin = i;
- }
- if (d > dmax)
- {
- dmax = d;
- imax = i;
- }
- }
-
- if (imin == imax)
- return false; //degenerate point set
-
- min_index[j] = imin;
- max_index[j] = imax;
- }
-
- return true;
-}
-
-static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c)
-{
- const double* x1 = points[a];
- const double* x2 = points[b];
-
- double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]};
- double ns_x2x1 = norm_squared(x2x1);
-
- int bi = -1;
- double max_dist = 0.0;
- for (int i = 0;i<num_points;i++)
- {
- if (i == a || i == b)
- continue;
-
- const double* x0 = points[i];
-
- double x1x0[3] = {x1[0] - x0[0], x1[1] - x0[1], x1[2] - x0[2]};
- double dot = dot_product(x1x0, x2x1);
- double dist = (norm_squared(x1x0) * ns_x2x1 - dot*dot) / ns_x2x1;
-
- if (dist > max_dist)
- {
- max_dist = dist;
- bi = i;
- }
- }
-
- *p_c = bi;
- return max_dist > TOLERANCE;
-}
-
-static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d)
-{
- double plane_normal[3];
- calculate_plane_normal(points, a, b, c, plane_normal);
-
-
- int bi = -1;
- double max_dist = 0.0;
- for (int i = 0;i<num_points;i++)
- {
- if (i == a || i == b || i == c)
- continue;
-
- const double* x0 = points[i];
- double dist = fabs(point_plane_distance(x0, points[a], plane_normal));
- if (dist > max_dist)
- {
- max_dist = dist;
- bi = i;
- }
- }
-
- *p_d = bi;
- return max_dist > TOLERANCE;
-}
-
-static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices)
-{
- int min_index[3] = {0};
- int max_index[3] = {0};
- if (!calc_max_extent(num_points, points, min_index, max_index))
- return -1;
-
- int bi = -1;
- double max_dist = 0.0;
- for (int i = 0;i<3;i++)
- {
- int a = min_index[i], b = max_index[i];
- double delta[3] = { points[a][0] - points[b][0],
- points[a][1] - points[b][1],
- points[a][2] - points[b][2] };
- double dist = norm_squared(delta);
- if (dist > max_dist)
- {
- bi = i;
- max_dist = dist;
- }
- }
-
- //first two points are (a, b)
- int a = min_index[bi], b = max_index[bi], c = -1, d = -1;
-
- if (!find_third_point(num_points, points, a, b, &c))
- return -2;
-
- if (!find_fourth_point(num_points, points, a, b, c, &d))
- return -3;
-
- initial_vertices[0] = a;
- initial_vertices[1] = b;
- initial_vertices[2] = c;
- initial_vertices[3] = d;
- return 0;
-}
-
-static bool visible(const double* w, const double* plane_point, const double* plane_normal)
-{
- return point_plane_distance(w, plane_point, plane_normal) > 0;
-}
-
-void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre)
-{
- calculate_plane_normal(points, a, b, c, plane_normal);
- if (visible(barycentre, points[a], plane_normal))
- {
- plane_normal[0] = -plane_normal[0];
- plane_normal[1] = -plane_normal[1];
- plane_normal[2] = -plane_normal[2];
-
- facet[0] = b;
- facet[1] = a;
- facet[2] = c;
- }
- else
- {
- facet[0] = a;
- facet[1] = b;
- facet[2] = c;
- }
-}
-
-static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre)
-{
- memset(processed, 0, PTM_MAX_POINTS * sizeof(bool));
- memset(barycentre, 0, 3 * sizeof(double));
- int ret = initial_simplex(num_points, points, initial_vertices);
- if (ret != 0)
- return ret;
-
- for (int i = 0;i<4;i++)
- {
- int a = initial_vertices[i];
- processed[a] = true;
-
- barycentre[0] += points[a][0];
- barycentre[1] += points[a][1];
- barycentre[2] += points[a][2];
- }
- barycentre[0] /= 4;
- barycentre[1] /= 4;
- barycentre[2] /= 4;
-
- add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre);
- add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre);
- add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre);
- add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre);
- return 0;
-}
-
-int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3])
-{
- assert( num_points == PTM_NUM_POINTS_FCC
- || num_points == PTM_NUM_POINTS_HCP
- || num_points == PTM_NUM_POINTS_BCC
- || num_points == PTM_NUM_POINTS_ICO
- || num_points == PTM_NUM_POINTS_SC
- || num_points == PTM_NUM_POINTS_DCUB
- || num_points == PTM_NUM_POINTS_DHEX);
-
- int ret = 0;
- int num_prev = ch->num_prev;
- ch->num_prev = num_points;
- if (!ch->ok || 0)
- {
- ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre);
- if (ret != 0)
- return ret;
-
- ch->num_facets = 4;
- num_prev = 0;
- }
-
- for (int i = num_prev;i<num_points;i++)
- {
- if (ch->processed[i])
- continue;
- ch->processed[i] = true;
-
- int num_to_add = 0;
- int8_t to_add[PTM_MAX_FACETS][3];
- int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS];
- memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS);
- for (int j = 0;j<ch->num_facets;j++)
- {
- int a = ch->facets[j][0];
- int b = ch->facets[j][1];
- int c = ch->facets[j][2];
-
- int u = 0, v = 0, w = 0;
-
- double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]);
- bool vis = distance > TOLERANCE;
- if (vis)
- {
- u = edge_visible[a][b] |= VISIBLE;
- edge_visible[b][a] |= VISIBLE;
-
- v = edge_visible[b][c] |= VISIBLE;
- edge_visible[c][b] |= VISIBLE;
-
- w = edge_visible[c][a] |= VISIBLE;
- edge_visible[a][c] |= VISIBLE;
-
- memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t));
- memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double));
- ch->num_facets--;
- j--;
- }
- else
- {
- u = edge_visible[a][b] |= INVISIBLE;
- edge_visible[b][a] |= INVISIBLE;
-
- v = edge_visible[b][c] |= INVISIBLE;
- edge_visible[c][b] |= INVISIBLE;
-
- w = edge_visible[c][a] |= INVISIBLE;
- edge_visible[a][c] |= INVISIBLE;
- }
-
- if (u == BOTH)
- {
- to_add[num_to_add][0] = i;
- to_add[num_to_add][1] = a;
- to_add[num_to_add][2] = b;
- num_to_add++;
- }
-
- if (v == BOTH)
- {
- to_add[num_to_add][0] = i;
- to_add[num_to_add][1] = b;
- to_add[num_to_add][2] = c;
- num_to_add++;
- }
-
- if (w == BOTH)
- {
- to_add[num_to_add][0] = i;
- to_add[num_to_add][1] = c;
- to_add[num_to_add][2] = a;
- num_to_add++;
- }
- }
-
- for (int j = 0;j<num_to_add;j++)
- {
- if (ch->num_facets >= PTM_MAX_FACETS)
- return -4;
-
- add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++;
- }
- }
-
- for (int i=0;i<ch->num_facets;i++)
- {
- int a = ch->facets[i][0];
- int b = ch->facets[i][1];
- int c = ch->facets[i][2];
- if (a == 0 || b == 0 || c == 0)
- return 1; //central atom contained in convex hull
-
- simplex[i][0] = a - 1;
- simplex[i][1] = b - 1;
- simplex[i][2] = c - 1;
- }
-
- return ret;
-}
-
diff --git a/src/USER-PTM/convex_hull_incremental.h b/src/USER-PTM/convex_hull_incremental.h
deleted file mode 100644
index d384a0457e..0000000000
--- a/src/USER-PTM/convex_hull_incremental.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef CONVEX_HULL_INCREMENTAL_H
-#define CONVEX_HULL_INCREMENTAL_H
-
-
-#include <stdint.h>
-#include <stdbool.h>
-#include "ptm_constants.h"
-
-
-typedef struct
-{
- int8_t facets[PTM_MAX_FACETS][3];
- double plane_normal[PTM_MAX_FACETS][3];
- bool processed[PTM_MAX_POINTS];
- int initial_vertices[4];
- double barycentre[3];
- int num_facets;
- int num_prev;
- bool ok;
-
-} convexhull_t;
-
-void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
-int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
-
-#endif
-
diff --git a/src/USER-PTM/deformation_gradient.cpp b/src/USER-PTM/deformation_gradient.cpp
deleted file mode 100644
index 9a86dff6a3..0000000000
--- a/src/USER-PTM/deformation_gradient.cpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#include "deformation_gradient.h"
-
-
-void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
-{
- for (int i = 0;i<3;i++)
- {
- for (int j = 0;j<3;j++)
- {
- double acc = 0.0;
- for (int k = 0;k<num_points;k++)
- acc += penrose[k][j] * normalized[mapping[k]][i];
-
- F[i*3 + j] = acc;
- }
- }
-
- res[0] = 0;
- res[1] = 0;
- res[2] = 0;
-
- for (int k = 0;k<num_points;k++)
- {
- for (int i = 0;i<3;i++)
- {
- double acc = 0.0;
- for (int j = 0;j<3;j++)
- {
- acc += F[i*3 + j] * ideal_points[k][j];
- }
-
- double delta = acc - normalized[mapping[k]][i];
- res[i] += delta * delta;
- }
- }
-}
-
diff --git a/src/USER-PTM/deformation_gradient.h b/src/USER-PTM/deformation_gradient.h
deleted file mode 100644
index 059a06fdec..0000000000
--- a/src/USER-PTM/deformation_gradient.h
+++ /dev/null
@@ -1,142 +0,0 @@
-#ifndef DEFORMATION_GRADIENT_H
-#define DEFORMATION_GRADIENT_H
-
-#include <stdint.h>
-#include "ptm_constants.h"
-
-void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
-
-//sc
-#define k_sc 0.5
-const double penrose_sc[PTM_NUM_POINTS_SC][3] = {
- {0, 0, 0},
- {0, 0, -k_sc},
- {0, 0, k_sc},
- {0, -k_sc, 0},
- {0, k_sc, 0},
- {-k_sc, 0, 0},
- {k_sc, 0, 0},
- };
-
-//fcc
-#define k_fcc 0.17677669529663678216
-const double penrose_fcc[PTM_NUM_POINTS_FCC][3] = {
- {0, 0, 0},
- {0, k_fcc, k_fcc},
- {0, -k_fcc, -k_fcc},
- {0, k_fcc, -k_fcc},
- {0, -k_fcc, k_fcc},
- {k_fcc, 0, k_fcc},
- {-k_fcc, 0, -k_fcc},
- {k_fcc, 0, -k_fcc},
- {-k_fcc, 0, k_fcc},
- {k_fcc, k_fcc, -0},
- {-k_fcc, -k_fcc, 0},
- {k_fcc, -k_fcc, 0},
- {-k_fcc, k_fcc, -0},
- };
-
-//hcp
-#define k_hcp 0.17677669529663678216
-const double penrose_hcp[PTM_NUM_POINTS_HCP][3] = {
- {0, 0, 0},
- {k_hcp, 0, k_hcp},
- {-k_hcp/3, -4*k_hcp/3, -k_hcp/3},
- {k_hcp, k_hcp, 0},
- {-k_hcp/3, -k_hcp/3, -4*k_hcp/3},
- {0, k_hcp, k_hcp},
- {-4*k_hcp/3, -k_hcp/3, -k_hcp/3},
- {-k_hcp, k_hcp, -0},
- {0, k_hcp, -k_hcp},
- {k_hcp, 0, -k_hcp},
- {k_hcp, -k_hcp, 0},
- {-k_hcp, 0, k_hcp},
- {0, -k_hcp, k_hcp},
- };
-
-//ico
-#define k_ico 0.13143277802974323576
-#define phi 1.61803398874989490253
-//((1.0 + sqrt(5)) / 2)
-const double penrose_ico[PTM_NUM_POINTS_ICO][3] = {
- {0, 0, 0},
- {0, k_ico, phi*k_ico},
- {0, -k_ico, -phi*k_ico},
- {0, k_ico, -phi*k_ico},
- {0, -k_ico, phi*k_ico},
- {-k_ico, -phi*k_ico, -0},
- {k_ico, phi*k_ico, 0},
- {k_ico, -phi*k_ico, 0},
- {-k_ico, phi*k_ico, -0},
- {-phi*k_ico, 0, -k_ico},
- {phi*k_ico, 0, k_ico},
- {phi*k_ico, 0, -k_ico},
- {-phi*k_ico, 0, k_ico},
- };
-
-//bcc
-#define k_bcc 0.11543038598460284017
-const double penrose_bcc[PTM_NUM_POINTS_BCC][3] = {
- {0, 0, 0},
- {-k_bcc, -k_bcc, -k_bcc},
- {k_bcc, k_bcc, k_bcc},
- {k_bcc, -k_bcc, -k_bcc},
- {-k_bcc, k_bcc, k_bcc},
- {-k_bcc, k_bcc, -k_bcc},
- {k_bcc, -k_bcc, k_bcc},
- {-k_bcc, -k_bcc, k_bcc},
- {k_bcc, k_bcc, -k_bcc},
- {0, 0, -2*k_bcc},
- {0, 0, 2*k_bcc},
- {0, -2*k_bcc, 0},
- {0, 2*k_bcc, 0},
- {-2*k_bcc, 0, 0},
- {2*k_bcc, 0, -0},
- };
-
-//dcub
-#define kdcub 0.07095369570691034689
-const double penrose_dcub[PTM_NUM_POINTS_DCUB][3] = {
- { 0, 0, 0 },
- { -kdcub, kdcub, kdcub },
- { -kdcub, -kdcub, -kdcub },
- { kdcub, -kdcub, kdcub },
- { kdcub, kdcub, -kdcub },
- { -2 * kdcub, 0, 2 * kdcub },
- { -2 * kdcub, 2 * kdcub, 0 },
- { 0, 2 * kdcub, 2 * kdcub },
- { -2 * kdcub, -2 * kdcub, 0 },
- { -2 * kdcub, 0, -2 * kdcub },
- { 0, -2 * kdcub, -2 * kdcub },
- { 0, -2 * kdcub, 2 * kdcub },
- { 2 * kdcub, -2 * kdcub, 0 },
- { 2 * kdcub, 0, 2 * kdcub },
- { 0, 2 * kdcub, -2 * kdcub },
- { 2 * kdcub, 0, -2 * kdcub },
- { 2 * kdcub, 2 * kdcub, 0 },
- };
-
-
-#define kdhex 0.04730246380471011397
-const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
- { 0, 0, 0 },
- { -kdcub, -kdcub, -kdcub },
- { kdcub, -kdcub, kdcub },
- { -kdcub, kdcub, kdcub },
- { kdcub, kdcub, -kdcub },
- { -kdhex, -4 * kdhex, -kdhex },
- { -4 * kdhex, -kdhex, -kdhex },
- { -kdhex, -kdhex, -4 * kdhex },
- { 2 * kdcub, 0, 2 * kdcub },
- { 2 * kdcub, -2 * kdcub, 0 },
- { 0, -2 * kdcub, 2 * kdcub },
- { 0, 2 * kdcub, 2 * kdcub },
- { -2 * kdcub, 2 * kdcub, 0 },
- { -2 * kdcub, 0, 2 * kdcub },
- { 2 * kdcub, 2 * kdcub, 0 },
- { 0, 2 * kdcub, -2 * kdcub },
- { 2 * kdcub, 0, -2 * kdcub },
- };
-#endif
-
-
diff --git a/src/USER-PTM/fundamental_mappings.h b/src/USER-PTM/fundamental_mappings.h
deleted file mode 100644
index 9030d3a2b2..0000000000
--- a/src/USER-PTM/fundamental_mappings.h
+++ /dev/null
@@ -1,180 +0,0 @@
-#ifndef FUNDAMENTAL_MAPPINGS_H
-#define FUNDAMENTAL_MAPPINGS_H
-
-#include <stdint.h>
-
-#define NUM_CUBIC_MAPPINGS 24
-#define NUM_ICO_MAPPINGS 60
-#define NUM_HEX_MAPPINGS 6
-#define NUM_DCUB_MAPPINGS 12
-#define NUM_DHEX_MAPPINGS 3
-
-const int8_t mapping_sc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6},
- {0, 2, 1, 4, 3, 5, 6},
- {0, 2, 1, 3, 4, 6, 5},
- {0, 1, 2, 4, 3, 6, 5},
- {0, 3, 4, 5, 6, 1, 2},
- {0, 5, 6, 2, 1, 4, 3},
- {0, 6, 5, 1, 2, 4, 3},
- {0, 4, 3, 5, 6, 2, 1},
- {0, 5, 6, 1, 2, 3, 4},
- {0, 4, 3, 6, 5, 1, 2},
- {0, 3, 4, 6, 5, 2, 1},
- {0, 6, 5, 2, 1, 3, 4},
- {0, 3, 4, 2, 1, 5, 6},
- {0, 6, 5, 3, 4, 1, 2},
- {0, 1, 2, 5, 6, 4, 3},
- {0, 4, 3, 1, 2, 5, 6},
- {0, 5, 6, 3, 4, 2, 1},
- {0, 1, 2, 6, 5, 3, 4},
- {0, 2, 1, 5, 6, 3, 4},
- {0, 5, 6, 4, 3, 1, 2},
- {0, 3, 4, 1, 2, 6, 5},
- {0, 2, 1, 6, 5, 4, 3},
- {0, 6, 5, 4, 3, 2, 1},
- {0, 4, 3, 2, 1, 6, 5} };
-
-const int8_t mapping_fcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
- {0, 2, 1, 4, 3, 7, 8, 5, 6, 11, 12, 9, 10},
- {0, 3, 4, 1, 2, 6, 5, 8, 7, 12, 11, 10, 9},
- {0, 4, 3, 2, 1, 8, 7, 6, 5, 10, 9, 12, 11},
- {0, 9, 10, 11, 12, 1, 2, 4, 3, 5, 6, 8, 7},
- {0, 7, 8, 6, 5, 11, 12, 10, 9, 2, 1, 4, 3},
- {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
- {0, 11, 12, 9, 10, 2, 1, 3, 4, 7, 8, 6, 5},
- {0, 5, 6, 8, 7, 9, 10, 12, 11, 1, 2, 3, 4},
- {0, 10, 9, 12, 11, 4, 3, 1, 2, 8, 7, 5, 6},
- {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
- {0, 6, 5, 7, 8, 12, 11, 9, 10, 3, 4, 1, 2},
- {0, 3, 4, 2, 1, 9, 10, 11, 12, 7, 8, 5, 6},
- {0, 12, 11, 9, 10, 8, 7, 5, 6, 1, 2, 4, 3},
- {0, 5, 6, 7, 8, 4, 3, 2, 1, 11, 12, 10, 9},
- {0, 4, 3, 1, 2, 11, 12, 9, 10, 5, 6, 7, 8},
- {0, 9, 10, 12, 11, 7, 8, 6, 5, 3, 4, 2, 1},
- {0, 8, 7, 6, 5, 1, 2, 3, 4, 12, 11, 9, 10},
- {0, 7, 8, 5, 6, 3, 4, 1, 2, 9, 10, 12, 11},
- {0, 11, 12, 10, 9, 5, 6, 8, 7, 4, 3, 1, 2},
- {0, 1, 2, 4, 3, 12, 11, 10, 9, 8, 7, 6, 5},
- {0, 6, 5, 8, 7, 2, 1, 4, 3, 10, 9, 11, 12},
- {0, 10, 9, 11, 12, 6, 5, 7, 8, 2, 1, 3, 4},
- {0, 2, 1, 3, 4, 10, 9, 12, 11, 6, 5, 8, 7} };
-
-const int8_t mapping_bcc[NUM_CUBIC_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14},
- {0, 4, 3, 2, 1, 7, 8, 5, 6, 10, 9, 12, 11, 13, 14},
- {0, 6, 5, 7, 8, 2, 1, 3, 4, 10, 9, 11, 12, 14, 13},
- {0, 8, 7, 5, 6, 3, 4, 2, 1, 9, 10, 12, 11, 14, 13},
- {0, 1, 2, 7, 8, 3, 4, 5, 6, 11, 12, 13, 14, 9, 10},
- {0, 4, 3, 7, 8, 5, 6, 2, 1, 13, 14, 10, 9, 12, 11},
- {0, 8, 7, 3, 4, 2, 1, 5, 6, 14, 13, 9, 10, 12, 11},
- {0, 4, 3, 5, 6, 2, 1, 7, 8, 12, 11, 13, 14, 10, 9},
- {0, 1, 2, 5, 6, 7, 8, 3, 4, 13, 14, 9, 10, 11, 12},
- {0, 8, 7, 2, 1, 5, 6, 3, 4, 12, 11, 14, 13, 9, 10},
- {0, 6, 5, 3, 4, 7, 8, 2, 1, 11, 12, 14, 13, 10, 9},
- {0, 6, 5, 2, 1, 3, 4, 7, 8, 14, 13, 10, 9, 11, 12},
- {0, 7, 8, 6, 5, 1, 2, 4, 3, 11, 12, 10, 9, 13, 14},
- {0, 3, 4, 6, 5, 8, 7, 1, 2, 14, 13, 11, 12, 9, 10},
- {0, 5, 6, 1, 2, 8, 7, 4, 3, 9, 10, 13, 14, 12, 11},
- {0, 5, 6, 8, 7, 4, 3, 1, 2, 12, 11, 9, 10, 13, 14},
- {0, 7, 8, 1, 2, 4, 3, 6, 5, 13, 14, 11, 12, 10, 9},
- {0, 3, 4, 8, 7, 1, 2, 6, 5, 9, 10, 14, 13, 11, 12},
- {0, 7, 8, 4, 3, 6, 5, 1, 2, 10, 9, 13, 14, 11, 12},
- {0, 5, 6, 4, 3, 1, 2, 8, 7, 13, 14, 12, 11, 9, 10},
- {0, 3, 4, 1, 2, 6, 5, 8, 7, 11, 12, 9, 10, 14, 13},
- {0, 2, 1, 6, 5, 4, 3, 8, 7, 10, 9, 14, 13, 12, 11},
- {0, 2, 1, 8, 7, 6, 5, 4, 3, 14, 13, 12, 11, 10, 9},
- {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9, 14, 13} };
-
-const int8_t mapping_ico[NUM_ICO_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
- {0, 10, 9, 8, 7, 5, 6, 2, 1, 12, 11, 3, 4},
- {0, 1, 2, 9, 10, 7, 8, 11, 12, 5, 6, 3, 4},
- {0, 4, 3, 8, 7, 2, 1, 11, 12, 9, 10, 6, 5},
- {0, 6, 5, 9, 10, 4, 3, 7, 8, 12, 11, 2, 1},
- {0, 12, 11, 3, 4, 7, 8, 10, 9, 2, 1, 6, 5},
- {0, 4, 3, 6, 5, 9, 10, 2, 1, 8, 7, 11, 12},
- {0, 8, 7, 2, 1, 4, 3, 10, 9, 5, 6, 11, 12},
- {0, 10, 9, 3, 4, 12, 11, 5, 6, 8, 7, 2, 1},
- {0, 12, 11, 6, 5, 2, 1, 7, 8, 3, 4, 10, 9},
- {0, 1, 2, 11, 12, 9, 10, 5, 6, 3, 4, 7, 8},
- {0, 8, 7, 11, 12, 5, 6, 4, 3, 2, 1, 10, 9},
- {0, 6, 5, 2, 1, 12, 11, 4, 3, 9, 10, 7, 8},
- {0, 3, 4, 5, 6, 1, 2, 10, 9, 12, 11, 7, 8},
- {0, 3, 4, 7, 8, 12, 11, 1, 2, 5, 6, 10, 9},
- {0, 6, 5, 7, 8, 9, 10, 12, 11, 2, 1, 4, 3},
- {0, 9, 10, 11, 12, 4, 3, 1, 2, 7, 8, 6, 5},
- {0, 11, 12, 9, 10, 1, 2, 4, 3, 8, 7, 5, 6},
- {0, 8, 7, 5, 6, 10, 9, 11, 12, 4, 3, 2, 1},
- {0, 10, 9, 2, 1, 8, 7, 12, 11, 3, 4, 5, 6},
- {0, 12, 11, 2, 1, 10, 9, 6, 5, 7, 8, 3, 4},
- {0, 9, 10, 6, 5, 7, 8, 4, 3, 11, 12, 1, 2},
- {0, 8, 7, 10, 9, 2, 1, 5, 6, 11, 12, 4, 3},
- {0, 6, 5, 12, 11, 7, 8, 2, 1, 4, 3, 9, 10},
- {0, 11, 12, 8, 7, 4, 3, 5, 6, 1, 2, 9, 10},
- {0, 4, 3, 11, 12, 8, 7, 9, 10, 6, 5, 2, 1},
- {0, 4, 3, 9, 10, 11, 12, 6, 5, 2, 1, 8, 7},
- {0, 12, 11, 10, 9, 3, 4, 2, 1, 6, 5, 7, 8},
- {0, 5, 6, 8, 7, 11, 12, 10, 9, 3, 4, 1, 2},
- {0, 7, 8, 6, 5, 12, 11, 9, 10, 1, 2, 3, 4},
- {0, 10, 9, 12, 11, 2, 1, 3, 4, 5, 6, 8, 7},
- {0, 7, 8, 1, 2, 9, 10, 3, 4, 12, 11, 6, 5},
- {0, 5, 6, 1, 2, 3, 4, 11, 12, 8, 7, 10, 9},
- {0, 7, 8, 12, 11, 3, 4, 6, 5, 9, 10, 1, 2},
- {0, 1, 2, 5, 6, 11, 12, 3, 4, 7, 8, 9, 10},
- {0, 11, 12, 1, 2, 5, 6, 9, 10, 4, 3, 8, 7},
- {0, 5, 6, 3, 4, 10, 9, 1, 2, 11, 12, 8, 7},
- {0, 5, 6, 10, 9, 8, 7, 3, 4, 1, 2, 11, 12},
- {0, 3, 4, 12, 11, 10, 9, 7, 8, 1, 2, 5, 6},
- {0, 9, 10, 7, 8, 1, 2, 6, 5, 4, 3, 11, 12},
- {0, 9, 10, 1, 2, 11, 12, 7, 8, 6, 5, 4, 3},
- {0, 7, 8, 3, 4, 1, 2, 12, 11, 6, 5, 9, 10},
- {0, 11, 12, 5, 6, 8, 7, 1, 2, 9, 10, 4, 3},
- {0, 1, 2, 7, 8, 3, 4, 9, 10, 11, 12, 5, 6},
- {0, 3, 4, 10, 9, 5, 6, 12, 11, 7, 8, 1, 2},
- {0, 2, 1, 4, 3, 8, 7, 6, 5, 12, 11, 10, 9},
- {0, 2, 1, 12, 11, 6, 5, 10, 9, 8, 7, 4, 3},
- {0, 9, 10, 4, 3, 6, 5, 11, 12, 1, 2, 7, 8},
- {0, 11, 12, 4, 3, 9, 10, 8, 7, 5, 6, 1, 2},
- {0, 2, 1, 10, 9, 12, 11, 8, 7, 4, 3, 6, 5},
- {0, 5, 6, 11, 12, 1, 2, 8, 7, 10, 9, 3, 4},
- {0, 10, 9, 5, 6, 3, 4, 8, 7, 2, 1, 12, 11},
- {0, 12, 11, 7, 8, 6, 5, 3, 4, 10, 9, 2, 1},
- {0, 7, 8, 9, 10, 6, 5, 1, 2, 3, 4, 12, 11},
- {0, 2, 1, 8, 7, 10, 9, 4, 3, 6, 5, 12, 11},
- {0, 8, 7, 4, 3, 11, 12, 2, 1, 10, 9, 5, 6},
- {0, 6, 5, 4, 3, 2, 1, 9, 10, 7, 8, 12, 11},
- {0, 2, 1, 6, 5, 4, 3, 12, 11, 10, 9, 8, 7},
- {0, 3, 4, 1, 2, 7, 8, 5, 6, 10, 9, 12, 11},
- {0, 4, 3, 2, 1, 6, 5, 8, 7, 11, 12, 9, 10} };
-
-const int8_t mapping_hcp[NUM_HEX_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
- {0, 5, 6, 1, 2, 3, 4, 9, 10, 12, 11, 8, 7},
- {0, 3, 4, 5, 6, 1, 2, 12, 11, 7, 8, 10, 9},
- {0, 4, 3, 2, 1, 6, 5, 11, 12, 10, 9, 7, 8},
- {0, 2, 1, 6, 5, 4, 3, 8, 7, 11, 12, 9, 10},
- {0, 6, 5, 4, 3, 2, 1, 10, 9, 8, 7, 12, 11} };
-
-const int8_t mapping_dcub[NUM_DCUB_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- {0, 2, 1, 4, 3, 9, 8, 10, 6, 5, 7, 14, 16, 15, 11, 13, 12},
- {0, 4, 3, 2, 1, 15, 16, 14, 12, 13, 11, 10, 8, 9, 7, 5, 6},
- {0, 3, 4, 1, 2, 13, 12, 11, 16, 15, 14, 7, 6, 5, 10, 9, 8},
- {0, 4, 2, 1, 3, 14, 15, 16, 9, 10, 8, 6, 5, 7, 12, 11, 13},
- {0, 4, 1, 3, 2, 16, 14, 15, 7, 6, 5, 13, 11, 12, 9, 8, 10},
- {0, 1, 4, 2, 3, 6, 7, 5, 14, 16, 15, 9, 10, 8, 13, 12, 11},
- {0, 3, 1, 2, 4, 11, 13, 12, 5, 7, 6, 8, 9, 10, 16, 14, 15},
- {0, 3, 2, 4, 1, 12, 11, 13, 10, 8, 9, 15, 14, 16, 5, 6, 7},
- {0, 2, 4, 3, 1, 10, 9, 8, 15, 14, 16, 12, 13, 11, 6, 7, 5},
- {0, 1, 3, 4, 2, 7, 5, 6, 13, 11, 12, 16, 15, 14, 8, 10, 9},
- {0, 2, 3, 1, 4, 8, 10, 9, 11, 12, 13, 5, 7, 6, 15, 16, 14} };
-
-const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
- {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- {0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
- {0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
-
-#endif
-
diff --git a/src/USER-PTM/graph_data.cpp b/src/USER-PTM/graph_data.cpp
deleted file mode 100644
index aea2e59eac..0000000000
--- a/src/USER-PTM/graph_data.cpp
+++ /dev/null
@@ -1,2059 +0,0 @@
-#include "graph_data.h"
-
-
-int8_t automorphisms[65][17] = {
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 4, 3, 10, 9, 5, 6, 12, 11, 8, 7, 1, 2, -1, -1, -1, -1},
- { 0, 5, 6, 11, 12, 8, 7, 2, 1, 4, 3, 10, 9, -1, -1, -1, -1},
- { 0, 8, 7, 1, 2, 4, 3, 9, 10, 5, 6, 11, 12, -1, -1, -1, -1},
- { 0, 8, 7, 10, 9, 1, 2, 6, 5, 12, 11, 3, 4, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 12, 3, 2, 7, 10, 8, 4, 6, 11, 5, 9, 1, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 4, 11, 8, 1, 9, 12, 10, 3, 5, 7, 2, 6, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 2, 1, 6, 5, 4, 3, 9, 8, 7, 11, 10, 12, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 1, 7, 10, 11, 9, 6, 4, 2, 12, 5, 8, 3, -1, -1, -1, -1},
- { 0, 1, 11, 9, 2, 3, 6, 8, 4, 10, 12, 7, 5, -1, -1, -1, -1},
- { 0, 3, 6, 1, 11, 9, 2, 10, 12, 5, 7, 4, 8, -1, -1, -1, -1},
- { 0, 3, 11, 9, 12, 8, 2, 4, 10, 1, 5, 6, 7, -1, -1, -1, -1},
- { 0, 8, 2, 3, 11, 9, 12, 1, 5, 7, 6, 10, 4, -1, -1, -1, -1},
- { 0, 9, 2, 3, 6, 1, 11, 5, 7, 8, 4, 12, 10, -1, -1, -1, -1},
- { 0, 9, 6, 1, 7, 10, 11, 12, 5, 3, 8, 2, 4, -1, -1, -1, -1},
- { 0, 9, 12, 8, 2, 3, 11, 7, 6, 4, 10, 5, 1, -1, -1, -1, -1},
- { 0, 10, 11, 9, 6, 1, 7, 3, 8, 4, 2, 5, 12, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
- { 0, 3, 2, 8, 6, 5, 12, 11, 7, 4, 9, 1, 10, -1, -1, -1, -1},
- { 0, 3, 11, 10, 6, 9, 7, 4, 2, 12, 1, 8, 5, -1, -1, -1, -1},
- { 0, 3, 12, 9, 6, 8, 11, 7, 4, 2, 10, 5, 1, -1, -1, -1, -1},
- { 0, 5, 12, 3, 2, 8, 6, 4, 9, 10, 1, 7, 11, -1, -1, -1, -1},
- { 0, 8, 6, 5, 12, 3, 2, 10, 1, 11, 7, 9, 4, -1, -1, -1, -1},
- { 0, 8, 11, 3, 12, 9, 6, 2, 10, 1, 5, 4, 7, -1, -1, -1, -1},
- { 0, 9, 6, 8, 11, 3, 12, 1, 5, 7, 4, 10, 2, -1, -1, -1, -1},
- { 0, 9, 7, 3, 11, 10, 6, 12, 1, 5, 8, 2, 4, -1, -1, -1, -1},
- { 0, 10, 6, 9, 7, 3, 11, 5, 8, 4, 2, 1, 12, -1, -1, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 3, 4, 6, 5, 2, 1, 9, 10, 14, 13, 11, 12, 8, 7, -1, -1},
- { 0, 4, 3, 1, 2, 5, 6, 10, 9, 13, 14, 7, 8, 12, 11, -1, -1},
- { 0, 6, 5, 1, 2, 4, 3, 14, 13, 7, 8, 11, 12, 10, 9, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 6, 5, 4, 3, 2, 1, 11, 12, 10, 9, 7, 8, 14, 13, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 12, 11, 10, 9, 13, 14, 8, 7, 4, 3, 2, 1, 5, 6, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 9, 10, 13, 14, 11, 12, 8, 7, 1, 2, 5, 6, 3, 4, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 3, 10, 14, 5, 9, 7, 13, 2, 8, 4, 11, 12, 1, 6, -1, -1},
- { 0, 13, 8, 1, 10, 4, 14, 6, 9, 5, 2, 11, 12, 7, 3, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 11, 12, 14, 13, 9, 10, 7, 8, 3, 4, 6, 5, 1, 2, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, -1, -1},
- { 0, 13, 14, 11, 12, 5, 6, 10, 9, 1, 2, 7, 8, 4, 3, -1, -1},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- { 0, 4, 1, 3, 2, 15, 14, 16, 5, 7, 6, 13, 11, 12, 10, 8, 9},
- { 0, 4, 2, 1, 3, 16, 15, 14, 10, 8, 9, 5, 6, 7, 13, 12, 11},
- { 0, 4, 3, 2, 1, 14, 16, 15, 13, 12, 11, 10, 9, 8, 5, 7, 6},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- { 0, 3, 4, 1, 2, 12, 13, 11, 16, 14, 15, 7, 5, 6, 9, 10, 8},
- { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
- { 0, 4, 1, 3, 2, 16, 15, 14, 6, 5, 7, 13, 11, 12, 10, 8, 9},
- { 0, 4, 2, 1, 3, 14, 16, 15, 10, 8, 9, 6, 7, 5, 13, 12, 11},
- { 0, 4, 3, 2, 1, 15, 14, 16, 13, 12, 11, 10, 9, 8, 6, 5, 7},
-};
-
-graph_t graphs_sc[NUM_SC_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,4},{1,3,5},{0,3,4},{0,3,5},{1,2,5},{1,2,4},{0,2,4},{0,2,5}}},
-
-};
-
-graph_t graphs_ico[NUM_ICO_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,5,9},{1,2,8},{0,5,7},{2,7,8},{2,5,7},{1,4,8},{1,2,10},{5,9,10},{2,5,10},{4,8,11},{7,8,11},{0,7,11},{0,3,9},{0,3,11},{3,4,11},{3,6,9},{3,4,6},{6,9,10},{1,4,6},{1,6,10}}},
-
-};
-
-graph_t graphs_fcc[NUM_FCC_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
-
-{1,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
-
-{2,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{6,8,10},{4,8,10}}},
-
-{3,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{4,6,10},{4,6,8}}},
-
-{4,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
-
-{5,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{5,7,11},{5,7,9},{2,5,6},{1,5,6},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
-
-{6,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{1,2,6},{1,2,5},{3,9,10},{1,9,10},{4,6,10},{4,6,8}}},
-
-{7,
-0,
-1,
-5,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{0,4,8},{3,7,9},{2,5,11},{0,7,11},{1,5,9},{2,6,8},{3,4,10},{1,6,10},{3,4,7},{0,4,7},{0,2,11},{0,2,8},{7,9,11},{5,9,11},{2,5,6},{1,5,6},{1,3,10},{1,3,9},{6,8,10},{4,8,10}}},
-
-};
-
-graph_t graphs_hcp[NUM_HCP_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
-
-{1,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-{2,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
-
-{3,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
-
-{4,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
-
-{5,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-{6,
-0,
-6,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
-
-{7,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
-
-{8,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{2,6,7},{2,4,6}}},
-
-{9,
-0,
-8,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-{10,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{4,10,11},{0,4,11},{4,6,7},{2,4,7}}},
-
-{11,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-{12,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
-
-{13,
-0,
-10,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-{14,
-0,
-12,
-10,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{1,10,11},{1,5,10},{5,6,7},{3,5,7},{3,8,9},{1,3,9},{0,8,9},{0,2,8},{4,10,11},{0,4,11},{2,6,7},{2,4,6}}},
-
-{15,
-0,
-22,
-10,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,5},{5,6,10},{0,9,11},{1,9,11},{3,7,8},{2,7,8},{4,6,10},{0,2,4},{5,10,11},{1,5,11},{3,6,7},{3,5,6},{1,8,9},{1,3,8},{2,8,9},{0,2,9},{0,10,11},{0,4,10},{4,6,7},{2,4,7}}},
-
-};
-
-graph_t graphs_bcc[NUM_BCC_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}},
-
-{1,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}},
-
-{2,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{3,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{4,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
-
-{5,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{6,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{2,8,10},{0,8,10}}},
-
-{7,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{5,10,13},{2,10,13},{0,2,10},{0,2,8}}},
-
-{8,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
-
-{9,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{10,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
-
-{11,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{12,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{4,11,12},{3,11,12},{7,11,13},{1,11,13},{7,8,11},{4,8,11},{5,9,13},{1,9,13},{6,9,12},{3,9,12},{6,9,10},{5,9,10},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
-
-{13,
-0,
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-{209,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
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-{210,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{7,8,11},{4,8,11},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{211,
-0,
-49,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
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-{212,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{4,8,12},{0,8,12},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
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-{213,
-0,
-51,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{7,8,13},{2,8,13},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
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-{214,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{6,10,12},{0,10,12},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{215,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{2,8,10},{0,8,10}}},
-
-{216,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{3,9,11},{1,9,11},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-{217,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{1,3,11},{1,3,9},{3,4,12},{3,4,11},{1,7,13},{1,7,11},{4,7,11},{4,7,8},{1,5,13},{1,5,9},{3,6,12},{3,6,9},{5,6,10},{5,6,9},{0,4,12},{0,4,8},{0,6,12},{0,6,10},{2,7,13},{2,7,8},{2,5,13},{2,5,10},{0,2,10},{0,2,8}}},
-
-};
-
-graph_t graphs_dcub[NUM_DCUB_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}},
-
-{1,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}},
-
-{2,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
-
-{3,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}},
-
-{4,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}},
-
-{5,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
-
-{6,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}},
-
-{7,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{5,13,15},{5,6,15},{8,13,14},{8,9,14},{12,14,15},{11,12,14}}},
-
-{8,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{9,13,14},{8,9,13},{11,14,15},{11,12,15}}},
-
-{9,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{6,10,12},{4,6,10},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
-
-{10,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{5,7,8},{4,5,7},{4,10,12},{4,6,12},{9,10,11},{7,9,10},{6,13,15},{5,6,13},{8,13,14},{8,9,14},{11,14,15},{11,12,15}}},
-
-{11,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{4,7,10},{0,5,6},{0,4,5},{0,4,6},{2,11,12},{2,10,12},{2,10,11},{1,7,8},{1,8,9},{1,7,9},{6,12,15},{5,8,13},{3,13,15},{3,13,14},{9,11,14},{3,14,15},{4,7,8},{4,5,8},{6,10,12},{4,6,10},{7,10,11},{7,9,11},{5,13,15},{5,6,15},{9,13,14},{8,9,13},{12,14,15},{11,12,14}}},
-
-};
-
-graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
-
-{0,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{7,13,15},{7,8,15}}},
-
-{1,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{2,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
-
-{3,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{4,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{5,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
-
-{6,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{7,
-0,
-53,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{8,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
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-{9,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
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-{10,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
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-{11,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
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-{12,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
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-{13,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
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-{14,
-0,
-55,
-4,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{7,13,15},{7,8,15}}},
-
-{15,
-0,
-59,
-2,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{11,13,14},{10,11,13},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{16,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{17,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{18,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{19,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{9,10,12},{7,9,10},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{20,
-0,
-61,
-4,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{4,8,15},{4,6,15},{8,13,15},{7,8,13}}},
-
-{21,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{6,11,14},{5,6,11},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{22,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{5,9,12},{4,5,9},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-{23,
-0,
-0,
-1,
-{0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-{{7,10,13},{5,11,12},{6,14,15},{0,4,5},{0,5,6},{0,4,6},{4,8,9},{2,10,12},{2,10,11},{2,11,12},{3,13,14},{3,13,15},{3,14,15},{1,7,9},{1,7,8},{1,8,9},{7,10,12},{7,9,12},{4,9,12},{4,5,12},{10,13,14},{10,11,14},{5,11,14},{5,6,14},{6,8,15},{4,6,8},{8,13,15},{7,8,13}}},
-
-};
-
diff --git a/src/USER-PTM/graph_data.h b/src/USER-PTM/graph_data.h
deleted file mode 100644
index 3a8a5c7ae7..0000000000
--- a/src/USER-PTM/graph_data.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef GRAPH_DATA_H
-#define GRAPH_DATA_H
-
-#include <stdint.h>
-#include "ptm_constants.h"
-
-
-typedef struct
-{
- int id;
- uint64_t hash;
- int automorphism_index;
- int num_automorphisms;
- int8_t canonical_labelling[PTM_MAX_POINTS];
- int8_t facets[PTM_MAX_FACETS][3];
-} graph_t;
-
-#define NUM_SC_GRAPHS 1
-#define NUM_ICO_GRAPHS 1
-#define NUM_FCC_GRAPHS 8
-#define NUM_HCP_GRAPHS 16
-#define NUM_BCC_GRAPHS 218
-#define NUM_DCUB_GRAPHS 12
-#define NUM_DHEX_GRAPHS 24
-
-extern int8_t automorphisms[][PTM_MAX_POINTS];
-
-extern graph_t graphs_sc[NUM_SC_GRAPHS];
-extern graph_t graphs_fcc[NUM_FCC_GRAPHS];
-extern graph_t graphs_hcp[NUM_HCP_GRAPHS];
-extern graph_t graphs_ico[NUM_ICO_GRAPHS];
-extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
-extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
-extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
-
-#endif
-
diff --git a/src/USER-PTM/graph_tools.cpp b/src/USER-PTM/graph_tools.cpp
deleted file mode 100644
index 864e921b51..0000000000
--- a/src/USER-PTM/graph_tools.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include <string.h>
-#include <algorithm>
-#include "graph_tools.h"
-#include "ptm_constants.h"
-
-
-bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
-{
- memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
-
- for (int i = 0;i<num_facets;i++)
- {
- int a = facets[i][0];
- int b = facets[i][1];
- int c = facets[i][2];
-
- //assert(common[a][b] == -1);
- //assert(common[b][c] == -1);
- //assert(common[c][a] == -1);
- if (common[a][b] != -1 || common[b][c] != -1 || common[c][a] != -1)
- return false;
-
- common[a][b] = c;
- common[b][c] = a;
- common[c][a] = b;
- }
-
- return true;
-}
-
-int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree)
-{
- memset(degree, 0, sizeof(int8_t) * num_nodes);
-
- for (int i = 0;i<num_facets;i++)
- {
- int a = facets[i][0];
- int b = facets[i][1];
- int c = facets[i][2];
-
- degree[a]++;
- degree[b]++;
- degree[c]++;
- }
-
- int8_t max_degree = 0;
- for (int i = 0;i<num_nodes;i++)
- max_degree = std::max(max_degree, degree[i]);
-
- return max_degree;
-}
-
diff --git a/src/USER-PTM/graph_tools.h b/src/USER-PTM/graph_tools.h
deleted file mode 100644
index 791a44f9a6..0000000000
--- a/src/USER-PTM/graph_tools.h
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef GRAPH_TOOLS_H
-#define GRAPH_TOOLS_H
-
-#include <stdint.h>
-#include "ptm_constants.h"
-
-bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
-int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
-
-#endif
-
diff --git a/src/USER-PTM/index_ptm.cpp b/src/USER-PTM/index_ptm.cpp
deleted file mode 100644
index 2683323ac5..0000000000
--- a/src/USER-PTM/index_ptm.cpp
+++ /dev/null
@@ -1,218 +0,0 @@
-#include <cstdio>
-#include <cstdlib>
-#include <string.h>
-#include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
-#include "convex_hull_incremental.h"
-#include "graph_data.h"
-#include "deformation_gradient.h"
-#include "alloy_types.h"
-#include "neighbour_ordering.h"
-#include "normalize_vertices.h"
-#include "quat.h"
-#include "polar.h"
-#include "initialize_data.h"
-#include "structure_matcher.h"
-#include "ptm_functions.h"
-#include "ptm_constants.h"
-
-
-//todo: verify that c == norm(template[1])
-static double calculate_interatomic_distance(int type, double scale)
-{
- assert(type >= 1 && type <= 7);
- double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))};
- return c[type] / scale;
-}
-
-static double calculate_lattice_constant(int type, double interatomic_distance)
-{
- assert(type >= 1 && type <= 7);
- double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)};
- return c[type] * interatomic_distance;
-}
-
-static int rotate_into_fundamental_zone(int type, double* q)
-{
- if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
- if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
- if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
- return -1;
-}
-
-static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
- int8_t* ordering, double (*points)[3], int32_t* numbers)
-{
- if (topological_ordering)
- {
- double normalized_points[PTM_MAX_INPUT_POINTS][3];
- normalize_vertices(num_points, unpermuted_points, normalized_points);
- int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
- if (ret != 0)
- topological_ordering = false;
- }
-
- if (!topological_ordering)
- for (int i=0;i<num_points;i++)
- ordering[i] = i;
-
- for (int i=0;i<num_points;i++)
- {
- memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
-
- if (unpermuted_numbers != NULL)
- numbers[i] = unpermuted_numbers[ordering[i]];
- }
-}
-
-static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
- int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
- double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
-{
- *p_type = PTM_MATCH_NONE;
- if (p_alloy_type != NULL)
- *p_alloy_type = PTM_ALLOY_NONE;
-
- if (mapping != NULL)
- memset(mapping, -1, num_points * sizeof(int8_t));
-
- const refdata_t* ref = res->ref_struct;
- if (ref == NULL)
- return;
-
- *p_type = ref->type;
- if (p_alloy_type != NULL && unpermuted_numbers != NULL)
- *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
-
- int bi = rotate_into_fundamental_zone(ref->type, res->q);
- int8_t temp[PTM_MAX_POINTS];
- for (int i=0;i<ref->num_nbrs+1;i++)
- temp[ref->mapping[bi][i]] = res->mapping[i];
-
- memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t));
-
- if (F != NULL && F_res != NULL)
- {
- double scaled_points[PTM_MAX_INPUT_POINTS][3];
-
- subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
- for (int i = 0;i<ref->num_nbrs + 1;i++)
- {
- scaled_points[i][0] *= res->scale;
- scaled_points[i][1] *= res->scale;
- scaled_points[i][2] *= res->scale;
- }
- calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
-
- if (P != NULL && U != NULL)
- polar_decomposition_3x3(F, false, U, P);
- }
-
- if (mapping != NULL)
- for (int i=0;i<ref->num_nbrs + 1;i++)
- mapping[i] = ordering[res->mapping[i]];
-
- double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale);
- double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance);
-
- if (p_interatomic_distance != NULL)
- *p_interatomic_distance = interatomic_distance;
-
- if (p_lattice_constant != NULL)
- *p_lattice_constant = lattice_constant;
-
- *p_rmsd = res->rmsd;
- *p_scale = res->scale;
- memcpy(q, res->q, 4 * sizeof(double));
-}
-
-
-extern bool ptm_initialized;
-
-int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
- int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering,
- int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
- double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
-{
- assert(ptm_initialized);
- assert(num_points <= PTM_MAX_INPUT_POINTS);
-
- if (flags & PTM_CHECK_SC)
- assert(num_points >= PTM_NUM_POINTS_SC);
-
- if (flags & PTM_CHECK_BCC)
- assert(num_points >= PTM_NUM_POINTS_BCC);
-
- if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
- assert(num_points >= PTM_NUM_POINTS_FCC);
-
- if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
- assert(num_points >= PTM_NUM_POINTS_DCUB);
-
- int ret = 0;
- result_t res;
- res.ref_struct = NULL;
- res.rmsd = INFINITY;
-
- int8_t ordering[PTM_MAX_INPUT_POINTS];
- double points[PTM_MAX_POINTS][3];
- int32_t numbers[PTM_MAX_POINTS];
-
- int8_t dordering[PTM_MAX_INPUT_POINTS];
- double dpoints[PTM_MAX_POINTS][3];
- int32_t dnumbers[PTM_MAX_POINTS];
-
- convexhull_t ch;
- double ch_points[PTM_MAX_INPUT_POINTS][3];
-
- if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
- {
- int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
- order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
- normalize_vertices(num_lpoints, points, ch_points);
- ch.ok = false;
-
- if (flags & PTM_CHECK_SC)
- ret = match_general(&structure_sc, ch_points, points, &ch, &res);
-
- if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
- ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
-
- if (flags & PTM_CHECK_BCC)
- ret = match_general(&structure_bcc, ch_points, points, &ch, &res);
- }
-
- if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
- {
- ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
- if (ret == 0)
- {
- normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
- ch.ok = false;
-
- ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
- }
- }
-
- if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX))
- {
- output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering,
- p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
- U, P, mapping, p_interatomic_distance, p_lattice_constant);
- }
- else
- {
- output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering,
- p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res,
- U, P, mapping, p_interatomic_distance, p_lattice_constant);
- }
-
- return PTM_NO_ERROR;
-}
-
diff --git a/src/USER-PTM/initialize_data.cpp b/src/USER-PTM/initialize_data.cpp
deleted file mode 100644
index 6c177bfb70..0000000000
--- a/src/USER-PTM/initialize_data.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#include <cstdio>
-#include <cstdlib>
-#include <string.h>
-#include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
-#include "initialize_data.h"
-
-
-static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3])
-{
- double plane_normal[3];
- double origin[3] = {0, 0, 0};
-
- for (int i = 0;i<num_facets;i++)
- add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
-}
-
-static int initialize_graphs(const refdata_t* s, int8_t* colours)
-{
- for (int i = 0;i<s->num_graphs;i++)
- {
- int8_t code[2 * PTM_MAX_EDGES];
- int8_t degree[PTM_MAX_NBRS];
- int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
- assert(_max_degree <= s->max_degree);
-
- make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
- int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
- if (ret != 0)
- return ret;
- }
-
- return PTM_NO_ERROR;
-}
-
-bool ptm_initialized = false;
-int ptm_initialize_global()
-{
- if (ptm_initialized)
- return PTM_NO_ERROR;
-
- int8_t colours[PTM_MAX_POINTS] = {0};
- int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
-
- int ret = initialize_graphs(&structure_sc, colours);
- ret |= initialize_graphs(&structure_fcc, colours);
- ret |= initialize_graphs(&structure_hcp, colours);
- ret |= initialize_graphs(&structure_ico, colours);
- ret |= initialize_graphs(&structure_bcc, colours);
- ret |= initialize_graphs(&structure_dcub, dcolours);
- ret |= initialize_graphs(&structure_dhex, dcolours);
-
- if (ret == PTM_NO_ERROR)
- ptm_initialized = true;
-
- return ret;
-}
-
-ptm_local_handle_t ptm_initialize_local()
-{
- assert(ptm_initialized);
- return (ptm_local_handle_t)voronoi_initialize_local();
-}
-
-void ptm_uninitialize_local(ptm_local_handle_t ptr)
-{
- voronoi_uninitialize_local(ptr);
-}
-
diff --git a/src/USER-PTM/initialize_data.h b/src/USER-PTM/initialize_data.h
deleted file mode 100644
index 644dfea8c4..0000000000
--- a/src/USER-PTM/initialize_data.h
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef INITIALIZE_DATA_H
-#define INITIALIZE_DATA_H
-
-
-#include "graph_data.h"
-#include "graph_tools.h"
-#include "deformation_gradient.h"
-#include "fundamental_mappings.h"
-#include "neighbour_ordering.h"
-#include "canonical_coloured.h"
-#include "convex_hull_incremental.h"
-
-
-typedef struct
-{
- int type;
- int num_nbrs;
- int num_facets;
- int max_degree;
- int num_graphs;
- int num_mappings;
- graph_t* graphs;
- const double (*points)[3];
- const double (*penrose)[3];
- const int8_t (*mapping)[PTM_MAX_POINTS];
-} refdata_t;
-
-
-//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc };
-const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc };
-const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc };
-const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp };
-const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico };
-const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc };
-const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
-const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-typedef struct ptm_local_handle* ptm_local_handle_t;
-ptm_local_handle_t ptm_initialize_local();
-void ptm_uninitialize_local(ptm_local_handle_t ptr);
-
-int ptm_initialize_global();
-
-//------------------------------------
-// global initialization switch
-//------------------------------------
-extern bool ptm_initialized;
-
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#endif
-
diff --git a/src/USER-PTM/neighbour_ordering.cpp b/src/USER-PTM/neighbour_ordering.cpp
deleted file mode 100644
index 8e8b016cfc..0000000000
--- a/src/USER-PTM/neighbour_ordering.cpp
+++ /dev/null
@@ -1,203 +0,0 @@
-#include <cstdlib>
-#include <cmath>
-#include <cstring>
-#include <cassert>
-#include <algorithm>
-#include "ptm_constants.h"
-#include "cell.h"
-using namespace voro;
-
-
-
-typedef struct
-{
- double area;
- double dist;
- int index;
-} sorthelper_t;
-
-static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
-{
- if (a.area > b.area)
- return true;
-
- if (a.area < b.area)
- return false;
-
- if (a.dist < b.dist)
- return true;
-
- return false;
-}
-
-//todo: change voronoi code to return errors rather than exiting
-static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
-{
- const double k = 1000 * max_norm; //todo: reduce this constant
- v->init(-k,k,-k,k,-k,k);
-
- for (int i=1;i<num_points;i++)
- {
- double x = _points[i][0] - _points[0][0];
- double y = _points[i][1] - _points[0][1];
- double z = _points[i][2] - _points[0][2];
- v->nplane(x,y,z,normsq[i],i);
- }
-
- v->neighbors(nbr_indices);
- v->face_areas(face_areas);
- return 0;
-}
-
-int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering)
-{
- assert(num_points <= PTM_MAX_INPUT_POINTS);
-
- voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
-
- double max_norm = 0;
- double points[PTM_MAX_INPUT_POINTS][3];
- double normsq[PTM_MAX_INPUT_POINTS];
- for (int i = 0;i<num_points;i++)
- {
- double x = _points[i][0] - _points[0][0];
- double y = _points[i][1] - _points[0][1];
- double z = _points[i][2] - _points[0][2];
- points[i][0] = x;
- points[i][1] = y;
- points[i][2] = z;
-
- normsq[i] = x*x + y*y + z*z;
- max_norm = std::max(max_norm, normsq[i]);
-#ifdef DEBUG
- printf("point %d: %f\t%f\t%f\t%f\n", i, x, y, z, x*x + y*y + z*z);
-#endif
- }
-
- max_norm = sqrt(max_norm);
-
- std::vector<int> nbr_indices(num_points + 6);
- std::vector<double> face_areas(num_points + 6);
- int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas);
- if (ret != 0)
- return ret;
-
- double areas[PTM_MAX_INPUT_POINTS];
- memset(areas, 0, num_points * sizeof(double));
- areas[0] = INFINITY;
- for (size_t i=0;i<nbr_indices.size();i++)
- {
- int index = nbr_indices[i];
- if (index > 0)
- areas[index] = face_areas[i];
- }
-
- sorthelper_t data[PTM_MAX_INPUT_POINTS];
- for (int i=0;i<num_points;i++)
- {
- assert(areas[i] == areas[i]);
- data[i].area = areas[i];
- data[i].dist = normsq[i];
- data[i].index = i;
- }
-
- std::sort(data, data + num_points, &sorthelper_compare);
-
-#ifdef DEBUG
- for (int i=0;i<num_points;i++)
- printf("%d %f\n", data[i].index, data[i].area);
-#endif
-
- for (int i=0;i<num_points;i++)
- ordering[i] = data[i].index;
-
- return ret;
-}
-
-void* voronoi_initialize_local()
-{
- voronoicell_neighbor* ptr = new voronoicell_neighbor;
- return (void*)ptr;
-}
-
-void voronoi_uninitialize_local(void* _ptr)
-{
- voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
- delete ptr;
-}
-
-
-typedef struct
-{
- double dist;
- int p;
- int index;
-} diamond_t;
-
-static bool diamond_compare(diamond_t const& a, diamond_t const& b)
-{
- return a.dist < b.dist;
-}
-
-int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
- int8_t* ordering, double (*points)[3], int32_t* numbers)
-{
- assert(num_points <= PTM_MAX_INPUT_POINTS);
-
- diamond_t data[4 * (PTM_MAX_INPUT_POINTS - 5)];
- int index = 0;
- for (int i=5;i<num_points;i++)
- {
- for (int j=1;j<5;j++)
- {
- double dx = unpermuted_points[i][0] - unpermuted_points[j][0];
- double dy = unpermuted_points[i][1] - unpermuted_points[j][1];
- double dz = unpermuted_points[i][2] - unpermuted_points[j][2];
-
- double d = dx*dx + dy*dy + dz*dz;
-
- data[index].p = j - 1;
- data[index].index = i;
- data[index].dist = d;
- index++;
- }
- }
- int n = index;
-
- std::sort(data, data + n, &diamond_compare);
-
- for (index=0;index<5;index++)
- ordering[index] = index;
-
- int num_found = 0;
- bool hit[PTM_MAX_INPUT_POINTS] = {0};
- int counts[4] = {0};
- for (int i=0;i<n;i++)
- {
- int p = data[i].p;
- int q = data[i].index;
- if (hit[q] || counts[p] >= 3)
- continue;
-
- ordering[1 + 4 + 3 * p + counts[p]] = q;
- counts[p]++;
- index++;
- num_found++;
- if (num_found >= 12)
- break;
- }
-
- if (num_found != 12)
- return -1;
-
- for (int i=0;i<PTM_NUM_NBRS_DCUB+1;i++)
- {
- memcpy(points[i], &unpermuted_points[ordering[i]], 3 * sizeof(double));
-
- if (unpermuted_numbers != NULL)
- numbers[i] = unpermuted_numbers[ordering[i]];
- }
-
- return 0;
-}
-
diff --git a/src/USER-PTM/neighbour_ordering.h b/src/USER-PTM/neighbour_ordering.h
deleted file mode 100644
index 33160caa4f..0000000000
--- a/src/USER-PTM/neighbour_ordering.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef NEIGHBOUR_ORDERING_H
-#define NEIGHBOUR_ORDERING_H
-
-int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
-
-int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
- int8_t* ordering, double (*points)[3], int32_t* numbers);
-
-void* voronoi_initialize_local();
-void voronoi_uninitialize_local(void* ptr);
-
-#endif
-
diff --git a/src/USER-PTM/normalize_vertices.cpp b/src/USER-PTM/normalize_vertices.cpp
deleted file mode 100644
index 61dca5006f..0000000000
--- a/src/USER-PTM/normalize_vertices.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-#include <cmath>
-
-
-void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
-{
- //calculate barycentre
- double sum[3] = {0, 0, 0};
- for (int i=0;i<num;i++)
- {
- sum[0] += points[i][0];
- sum[1] += points[i][1];
- sum[2] += points[i][2];
- }
-
- sum[0] /= num;
- sum[1] /= num;
- sum[2] /= num;
-
- //subtract barycentre
- for (int i=0;i<num;i++)
- {
- normalized[i][0] = points[i][0] - sum[0];
- normalized[i][1] = points[i][1] - sum[1];
- normalized[i][2] = points[i][2] - sum[2];
- }
-}
-
-double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
-{
- subtract_barycentre(num, points, normalized);
-
- //calculate mean length
- double scale = 0.0;
- for (int i=1;i<num;i++)
- {
- double x = normalized[i][0];
- double y = normalized[i][1];
- double z = normalized[i][2];
-
- double norm = sqrt(x*x + y*y + z*z);
- scale += norm;
- }
- scale /= num;
-
- //scale vertices such that mean length is 1
- for (int i=0;i<num;i++)
- {
- normalized[i][0] /= scale;
- normalized[i][1] /= scale;
- normalized[i][2] /= scale;
- }
-
- return scale;
-}
-
diff --git a/src/USER-PTM/normalize_vertices.h b/src/USER-PTM/normalize_vertices.h
deleted file mode 100644
index e18990cd9b..0000000000
--- a/src/USER-PTM/normalize_vertices.h
+++ /dev/null
@@ -1,8 +0,0 @@
-#ifndef NORMALIZE_VERTICES_H
-#define NORMALIZE_VERTICES_H
-
-void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
-double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
-
-#endif
-
diff --git a/src/USER-PTM/polar.cpp b/src/USER-PTM/polar.cpp
deleted file mode 100644
index fdb759a1f3..0000000000
--- a/src/USER-PTM/polar.cpp
+++ /dev/null
@@ -1,337 +0,0 @@
-/*******************************************************************************
- * -/_|:|_|_\-
- *
- * This code is a modification of D.L. Theobald's QCP rotation code.
- * It has been adapted to calculate the polar decomposition of a 3x3 matrix
- * Adaption by P.M. Larsen
- *
- * Original Author(s): Douglas L. Theobald
- * Department of Biochemistry
- * MS 009
- * Brandeis University
- * 415 South St
- * Waltham, MA 02453
- * USA
- *
- * dtheobald@brandeis.edu
- *
- * Pu Liu
- * Johnson & Johnson Pharmaceutical Research and Development, L.L.C.
- * 665 Stockton Drive
- * Exton, PA 19341
- * USA
- *
- * pliu24@its.jnj.com
- *
- *
- * If you use this QCP rotation calculation method in a publication, please
- * reference:
- *
- * Douglas L. Theobald (2005)
- * "Rapid calculation of RMSD using a quaternion-based characteristic
- * polynomial."
- * Acta Crystallographica A 61(4):478-480.
- *
- * Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009)
- * "Fast determination of the optimal rotational matrix for macromolecular
- * superpositions."
- * Journal of Computational Chemistry 31(7):1561-1563.
- *
- *
- * Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification, are permitted
- * provided that the following conditions are met:
- *
- * * Redistributions of source code must retain the above copyright notice, this list of
- * conditions and the following disclaimer.
- * * Redistributions in binary form must reproduce the above copyright notice, this list
- * of conditions and the following disclaimer in the documentation and/or other materials
- * provided with the distribution.
- * * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to
- * endorse or promote products derived from this software without specific prior written
- * permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
- * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
- * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
- * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * Source: started anew.
- *
- * Change History:
- * 2009/04/13 Started source
- * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr
- * If trying all rows of the adjoint still gives too small
- * qsqr, then just return identity matrix. (DLT)
- * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct()
- * invalid mem access
- * 2011/02/21 Made CenterCoords use weights
- * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h
- * Also changed some functions to static
- * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error
- * 2012/07/26 minor changes to comments and main.c, more info (v.1.4)
- *
- * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix,
- * for use in Polyhedral Template Matching.
- *
- ******************************************************************************/
-
-#include <cmath>
-#include <algorithm>
-#include <string.h>
-#include "quat.h"
-
-
-static void matmul_3x3(double* A, double* x, double* b)
-{
- b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
- b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6];
- b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6];
-
- b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7];
- b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7];
- b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7];
-
- b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8];
- b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8];
- b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8];
-}
-
-static double matrix_determinant_3x3(double* A)
-{
- return A[0] * (A[4]*A[8] - A[5]*A[7])
- - A[1] * (A[3]*A[8] - A[5]*A[6])
- + A[2] * (A[3]*A[7] - A[4]*A[6]);
-}
-
-static void flip_matrix(double* A)
-{
- for (int i=0;i<9;i++)
- A[i] = -A[i];
-}
-
-static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt)
-{
- const double evecprec = 1e-6;
- const double evalprec = 1e-11;
-
- double Sxx = A[0], Sxy = A[1], Sxz = A[2],
- Syx = A[3], Syy = A[4], Syz = A[5],
- Szx = A[6], Szy = A[7], Szz = A[8];
-
- double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz,
- Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz,
- Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx;
-
- double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2;
-
- double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
- double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
- double SxzpSzx = Sxz + Szx;
- double SyzpSzy = Syz + Szy;
- double SxypSyx = Sxy + Syx;
- double SyzmSzy = Syz - Szy;
- double SxzmSzx = Sxz - Szx;
- double SxymSyx = Sxy - Syx;
- double SxxpSyy = Sxx + Syy;
- double SxxmSyy = Sxx - Syy;
- double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
-
- double C[3];
- C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
- + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
- + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz))
- + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz))
- + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz))
- + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz));
-
- C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz);
- C[2] = -2.0 * fnorm_squared;
-
- //Newton-Raphson
- double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0;
- if (mxEigenV > evalprec)
- {
- for (int i=0;i<50;i++)
- {
- double oldg = mxEigenV;
- double x2 = mxEigenV*mxEigenV;
- double b = (x2 + C[2])*mxEigenV;
- double a = b + C[1];
- double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a));
- mxEigenV -= delta;
- if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
- break;
- }
- }
- else
- {
- mxEigenV = 0.0;
- }
-
- (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV));
-
- double a11 = SxxpSyy + Szz - mxEigenV;
- double a12 = SyzmSzy;
- double a13 = -SxzmSzx;
- double a14 = SxymSyx;
-
- double a21 = SyzmSzy;
- double a22 = SxxmSyy - Szz -mxEigenV;
- double a23 = SxypSyx;
- double a24 = SxzpSzx;
-
- double a31 = a13;
- double a32 = a23;
- double a33 = Syy - Sxx - Szz - mxEigenV;
- double a34 = SyzpSzy;
-
- double a41 = a14;
- double a42 = a24;
- double a43 = a34;
- double a44 = Szz - SxxpSyy - mxEigenV;
-
- double a3344_4334 = a33 * a44 - a43 * a34;
- double a3244_4234 = a32 * a44 - a42 * a34;
- double a3243_4233 = a32 * a43 - a42 * a33;
- double a3143_4133 = a31 * a43 - a41 * a33;
- double a3144_4134 = a31 * a44 - a41 * a34;
- double a3142_4132 = a31 * a42 - a41 * a32;
- double a1324_1423 = a13 * a24 - a14 * a23;
- double a1224_1422 = a12 * a24 - a14 * a22;
- double a1223_1322 = a12 * a23 - a13 * a22;
- double a1124_1421 = a11 * a24 - a14 * a21;
- double a1123_1321 = a11 * a23 - a13 * a21;
- double a1122_1221 = a11 * a22 - a12 * a21;
-
- double q[4][4];
- q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233;
- q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
- q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132;
- q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132;
-
- q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
- q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133;
- q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
- q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132;
-
- q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
- q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321;
- q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
- q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221;
-
- q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
- q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321;
- q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
- q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
-
- double qsqr[4];
- for (int i=0;i<4;i++)
- qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3];
-
- int bi = 0;
- double max = 0;
- for (int i=0;i<4;i++)
- {
- if (qsqr[i] > max)
- {
- bi = i;
- max = qsqr[i];
- }
- }
-
- bool too_small = false;
- if (qsqr[bi] < evecprec)
- {
- //if qsqr is still too small, return the identity rotation.
- q[bi][0] = 1;
- q[bi][1] = 0;
- q[bi][2] = 0;
- q[bi][3] = 0;
- too_small = true;
- }
- else
- {
- double normq = sqrt(qsqr[bi]);
- q[bi][0] /= normq;
- q[bi][1] /= normq;
- q[bi][2] /= normq;
- q[bi][3] /= normq;
- }
-
- memcpy(qopt, q[bi], 4 * sizeof(double));
- return !too_small;
-}
-
-int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P)
-{
- double A[9];
- memcpy(A, _A, 9 * sizeof(double));
-
- double det = matrix_determinant_3x3(A);
- if (det < 0)
- flip_matrix(A);
-
- double q[4];
- double nrmsdsq = 0;
- optimal_quaternion(A, true, -1, &nrmsdsq, q);
- q[0] = -q[0];
- quaternion_to_rotation_matrix(q, U);
-
- if (det < 0)
- flip_matrix(U);
-
- double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]};
-
- if (right_sided)
- matmul_3x3(UT, _A, P);
- else
- matmul_3x3(_A, UT, P);
-
- return 0;
-}
-
-void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation)
-{
- A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0;
-
- for (int i = 0; i < num; ++i)
- {
- double x1 = coords1[i][0];
- double y1 = coords1[i][1];
- double z1 = coords1[i][2];
-
- double x2 = coords2[permutation[i]][0];
- double y2 = coords2[permutation[i]][1];
- double z2 = coords2[permutation[i]][2];
-
- A[0] += x1 * x2;
- A[1] += x1 * y2;
- A[2] += x1 * z2;
-
- A[3] += y1 * x2;
- A[4] += y1 * y2;
- A[5] += y1 * z2;
-
- A[6] += z1 * x2;
- A[7] += z1 * y2;
- A[8] += z1 * z2;
- }
-}
-
-int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U)
-{
- optimal_quaternion(A, false, E0, p_nrmsdsq, q);
- quaternion_to_rotation_matrix(q, U);
- return 0;
-}
-
diff --git a/src/USER-PTM/polar.h b/src/USER-PTM/polar.h
deleted file mode 100644
index 3ec025b806..0000000000
--- a/src/USER-PTM/polar.h
+++ /dev/null
@@ -1,12 +0,0 @@
-#ifndef POLAR_H
-#define POLAR_H
-
-#include <stdint.h>
-#include <stdbool.h>
-
-int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
-void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
-int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
-
-#endif
-
diff --git a/src/PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp
similarity index 100%
rename from src/PTM/ptm_alloy_types.cpp
rename to src/USER-PTM/ptm_alloy_types.cpp
diff --git a/src/PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h
similarity index 100%
rename from src/PTM/ptm_alloy_types.h
rename to src/USER-PTM/ptm_alloy_types.h
diff --git a/src/PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp
similarity index 100%
rename from src/PTM/ptm_canonical_coloured.cpp
rename to src/USER-PTM/ptm_canonical_coloured.cpp
diff --git a/src/PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h
similarity index 100%
rename from src/PTM/ptm_canonical_coloured.h
rename to src/USER-PTM/ptm_canonical_coloured.h
diff --git a/src/PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp
similarity index 100%
rename from src/PTM/ptm_convex_hull_incremental.cpp
rename to src/USER-PTM/ptm_convex_hull_incremental.cpp
diff --git a/src/PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h
similarity index 100%
rename from src/PTM/ptm_convex_hull_incremental.h
rename to src/USER-PTM/ptm_convex_hull_incremental.h
diff --git a/src/PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp
similarity index 100%
rename from src/PTM/ptm_deformation_gradient.cpp
rename to src/USER-PTM/ptm_deformation_gradient.cpp
diff --git a/src/PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h
similarity index 100%
rename from src/PTM/ptm_deformation_gradient.h
rename to src/USER-PTM/ptm_deformation_gradient.h
diff --git a/src/USER-PTM/ptm_functions.h b/src/USER-PTM/ptm_functions.h
index 69141a37c4..cd67d4940d 100644
--- a/src/USER-PTM/ptm_functions.h
+++ b/src/USER-PTM/ptm_functions.h
@@ -3,7 +3,7 @@
#include <stdint.h>
#include <stdbool.h>
-#include "initialize_data.h"
+#include "ptm_initialize_data.h"
#include "ptm_constants.h"
diff --git a/src/PTM/ptm_fundamental_mappings.h b/src/USER-PTM/ptm_fundamental_mappings.h
similarity index 100%
rename from src/PTM/ptm_fundamental_mappings.h
rename to src/USER-PTM/ptm_fundamental_mappings.h
diff --git a/src/PTM/ptm_graph_data.cpp b/src/USER-PTM/ptm_graph_data.cpp
similarity index 100%
rename from src/PTM/ptm_graph_data.cpp
rename to src/USER-PTM/ptm_graph_data.cpp
diff --git a/src/PTM/ptm_graph_data.h b/src/USER-PTM/ptm_graph_data.h
similarity index 100%
rename from src/PTM/ptm_graph_data.h
rename to src/USER-PTM/ptm_graph_data.h
diff --git a/src/PTM/ptm_graph_tools.cpp b/src/USER-PTM/ptm_graph_tools.cpp
similarity index 100%
rename from src/PTM/ptm_graph_tools.cpp
rename to src/USER-PTM/ptm_graph_tools.cpp
diff --git a/src/PTM/ptm_graph_tools.h b/src/USER-PTM/ptm_graph_tools.h
similarity index 100%
rename from src/PTM/ptm_graph_tools.h
rename to src/USER-PTM/ptm_graph_tools.h
diff --git a/src/PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
similarity index 100%
rename from src/PTM/ptm_index.cpp
rename to src/USER-PTM/ptm_index.cpp
diff --git a/src/PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
similarity index 100%
rename from src/PTM/ptm_initialize_data.cpp
rename to src/USER-PTM/ptm_initialize_data.cpp
diff --git a/src/PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h
similarity index 100%
rename from src/PTM/ptm_initialize_data.h
rename to src/USER-PTM/ptm_initialize_data.h
diff --git a/src/PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp
similarity index 100%
rename from src/PTM/ptm_neighbour_ordering.cpp
rename to src/USER-PTM/ptm_neighbour_ordering.cpp
diff --git a/src/PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h
similarity index 100%
rename from src/PTM/ptm_neighbour_ordering.h
rename to src/USER-PTM/ptm_neighbour_ordering.h
diff --git a/src/PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp
similarity index 100%
rename from src/PTM/ptm_normalize_vertices.cpp
rename to src/USER-PTM/ptm_normalize_vertices.cpp
diff --git a/src/PTM/ptm_normalize_vertices.h b/src/USER-PTM/ptm_normalize_vertices.h
similarity index 100%
rename from src/PTM/ptm_normalize_vertices.h
rename to src/USER-PTM/ptm_normalize_vertices.h
diff --git a/src/PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp
similarity index 100%
rename from src/PTM/ptm_polar.cpp
rename to src/USER-PTM/ptm_polar.cpp
diff --git a/src/PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h
similarity index 100%
rename from src/PTM/ptm_polar.h
rename to src/USER-PTM/ptm_polar.h
diff --git a/src/PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp
similarity index 100%
rename from src/PTM/ptm_quat.cpp
rename to src/USER-PTM/ptm_quat.cpp
diff --git a/src/PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h
similarity index 100%
rename from src/PTM/ptm_quat.h
rename to src/USER-PTM/ptm_quat.h
diff --git a/src/PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp
similarity index 100%
rename from src/PTM/ptm_structure_matcher.cpp
rename to src/USER-PTM/ptm_structure_matcher.cpp
diff --git a/src/PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h
similarity index 100%
rename from src/PTM/ptm_structure_matcher.h
rename to src/USER-PTM/ptm_structure_matcher.h
diff --git a/src/PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
similarity index 100%
rename from src/PTM/ptm_voronoi_cell.cpp
rename to src/USER-PTM/ptm_voronoi_cell.cpp
diff --git a/src/PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h
similarity index 100%
rename from src/PTM/ptm_voronoi_cell.h
rename to src/USER-PTM/ptm_voronoi_cell.h
diff --git a/src/PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h
similarity index 100%
rename from src/PTM/ptm_voronoi_config.h
rename to src/USER-PTM/ptm_voronoi_config.h
diff --git a/src/USER-PTM/quat.cpp b/src/USER-PTM/quat.cpp
deleted file mode 100644
index f55aff3d2b..0000000000
--- a/src/USER-PTM/quat.cpp
+++ /dev/null
@@ -1,396 +0,0 @@
-#include <string.h>
-#include <cmath>
-#include <cfloat>
-
-
-#define SIGN(x) (x >= 0 ? 1 : -1)
-#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
-#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
-
-
-#define SQRT_2 1.4142135623730951454746218587388284504414
-#define HALF_SQRT_2 0.7071067811865474617150084668537601828575
-
-#define PHI 1.6180339887498949025257388711906969547272
-#define HALF_PHI 0.8090169943749474512628694355953484773636
-
-#define INV_PHI 0.6180339887498947915034364086750429123640
-#define HALF_INV_PHI 0.3090169943749473957517182043375214561820
-
-#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089
-#define SQRT_2_3 0.8164965809277260344600790631375275552273
-#define SQRT_1_6 0.4082482904638630172300395315687637776136
-
-
-double generator_cubic[24][4] = { {1, 0, 0, 0 },
- {0, 1, 0, 0 },
- {0, 0, 1, 0 },
- {0, 0, 0, 1 },
- {0.5, 0.5, 0.5, 0.5 },
- {0.5, 0.5, -0.5, 0.5 },
- {0.5, -0.5, 0.5, 0.5 },
- {0.5, -0.5, -0.5, 0.5 },
- {-0.5, 0.5, 0.5, 0.5 },
- {-0.5, 0.5, -0.5, 0.5 },
- {-0.5, -0.5, 0.5, 0.5 },
- {-0.5, -0.5, -0.5, 0.5 },
- {HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
- {HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
- {HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
- {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 },
- {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 },
- {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 },
- {0, HALF_SQRT_2, HALF_SQRT_2, 0 },
- {0, HALF_SQRT_2, 0, HALF_SQRT_2 },
- {0, 0, HALF_SQRT_2, HALF_SQRT_2 },
- {0, -HALF_SQRT_2, HALF_SQRT_2, 0 },
- {0, -HALF_SQRT_2, 0, HALF_SQRT_2 },
- {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } };
-
-double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 },
- {0, 1, 0, 0 },
- {0, 0, 1, 0 },
- {0, 0, 0, 1 },
- {0.5, 0.5, 0.5, 0.5 },
- {0.5, 0.5, -0.5, 0.5 },
- {0.5, -0.5, 0.5, 0.5 },
- {0.5, -0.5, -0.5, 0.5 },
- {-0.5, 0.5, 0.5, 0.5 },
- {-0.5, 0.5, -0.5, 0.5 },
- {-0.5, -0.5, 0.5, 0.5 },
- {-0.5, -0.5, -0.5, 0.5 } };
-
-double generator_hcp[6][4] = { {1, 0, 0, 0},
- {0.5, 0.5, 0.5, 0.5},
- {0.5, -0.5, -0.5, -0.5},
- {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6},
- {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6},
- {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} };
-
-double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0},
- {0.5, 0.5, 0.5, 0.5},
- {0.5, -0.5, -0.5, -0.5} };
-
-double generator_icosahedral[60][4] = { {1, 0, 0, 0},
- {HALF_PHI, -HALF_INV_PHI, -0.5, 0},
- {HALF_PHI, 0, -HALF_INV_PHI, -0.5},
- {HALF_PHI, -0.5, 0, -HALF_INV_PHI},
- {HALF_PHI, HALF_INV_PHI, -0.5, 0},
- {HALF_PHI, 0, HALF_INV_PHI, -0.5},
- {HALF_PHI, -0.5, 0, HALF_INV_PHI},
- {HALF_PHI, 0.5, 0, -HALF_INV_PHI},
- {HALF_PHI, 0, -HALF_INV_PHI, 0.5},
- {HALF_PHI, -HALF_INV_PHI, 0.5, 0},
- {HALF_PHI, 0, HALF_INV_PHI, 0.5},
- {HALF_PHI, HALF_INV_PHI, 0.5, 0},
- {HALF_PHI, 0.5, 0, HALF_INV_PHI},
- {0.5, HALF_PHI, -HALF_INV_PHI, 0},
- {0.5, HALF_PHI, HALF_INV_PHI, 0},
- {0.5, 0.5, 0.5, 0.5},
- {0.5, 0.5, 0.5, -0.5},
- {0.5, 0.5, -0.5, 0.5},
- {0.5, 0.5, -0.5, -0.5},
- {0.5, HALF_INV_PHI, 0, HALF_PHI},
- {0.5, HALF_INV_PHI, 0, -HALF_PHI},
- {0.5, 0, HALF_PHI, -HALF_INV_PHI},
- {0.5, 0, HALF_PHI, HALF_INV_PHI},
- {0.5, 0, -HALF_PHI, -HALF_INV_PHI},
- {0.5, 0, -HALF_PHI, HALF_INV_PHI},
- {0.5, -HALF_INV_PHI, 0, HALF_PHI},
- {0.5, -HALF_INV_PHI, 0, -HALF_PHI},
- {0.5, -0.5, 0.5, 0.5},
- {0.5, -0.5, 0.5, -0.5},
- {0.5, -0.5, -0.5, 0.5},
- {0.5, -0.5, -0.5, -0.5},
- {0.5, -HALF_PHI, -HALF_INV_PHI, 0},
- {0.5, -HALF_PHI, HALF_INV_PHI, 0},
- {HALF_INV_PHI, -HALF_PHI, 0, -0.5},
- {HALF_INV_PHI, 0, -0.5, -HALF_PHI},
- {HALF_INV_PHI, -0.5, -HALF_PHI, 0},
- {HALF_INV_PHI, 0, 0.5, -HALF_PHI},
- {HALF_INV_PHI, -HALF_PHI, 0, 0.5},
- {HALF_INV_PHI, 0.5, -HALF_PHI, 0},
- {HALF_INV_PHI, HALF_PHI, 0, -0.5},
- {HALF_INV_PHI, -0.5, HALF_PHI, 0},
- {HALF_INV_PHI, 0, -0.5, HALF_PHI},
- {HALF_INV_PHI, HALF_PHI, 0, 0.5},
- {HALF_INV_PHI, 0, 0.5, HALF_PHI},
- {HALF_INV_PHI, 0.5, HALF_PHI, 0},
- {0, 1, 0, 0},
- {0, HALF_PHI, -0.5, HALF_INV_PHI},
- {0, HALF_PHI, -0.5, -HALF_INV_PHI},
- {0, HALF_PHI, 0.5, HALF_INV_PHI},
- {0, HALF_PHI, 0.5, -HALF_INV_PHI},
- {0, 0.5, HALF_INV_PHI, -HALF_PHI},
- {0, 0.5, HALF_INV_PHI, HALF_PHI},
- {0, 0.5, -HALF_INV_PHI, -HALF_PHI},
- {0, 0.5, -HALF_INV_PHI, HALF_PHI},
- {0, HALF_INV_PHI, -HALF_PHI, 0.5},
- {0, HALF_INV_PHI, -HALF_PHI, -0.5},
- {0, HALF_INV_PHI, HALF_PHI, 0.5},
- {0, HALF_INV_PHI, HALF_PHI, -0.5},
- {0, 0, 1, 0},
- {0, 0, 0, 1} };
-
-static void quat_rot(double* r, double* a, double* b)
-{
- b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]);
- b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]);
- b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]);
- b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]);
-}
-
-static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q)
-{
- double max = 0.0;
- int i = 0, bi = -1;
- for (i=0;i<num_generators;i++)
- {
- double* g = generator[i];
- double t = fabs(q[0] * g[0] - q[1] * g[1] - q[2] * g[2] - q[3] * g[3]);
- if (t > max)
- {
- max = t;
- bi = i;
- }
- }
-
- double f[4];
- quat_rot(q, generator[bi], f);
- memcpy(q, &f, 4 * sizeof(double));
- if (q[0] < 0)
- {
- q[0] = -q[0];
- q[1] = -q[1];
- q[2] = -q[2];
- q[3] = -q[3];
- }
-
- return bi;
-}
-
-int rotate_quaternion_into_cubic_fundamental_zone(double* q)
-{
- return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q);
-}
-
-int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q)
-{
- return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q);
-}
-
-int rotate_quaternion_into_icosahedral_fundamental_zone(double* q)
-{
- return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q);
-}
-
-int rotate_quaternion_into_hcp_fundamental_zone(double* q)
-{
- return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q);
-}
-
-int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q)
-{
- return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q);
-}
-
-double quat_dot(double* a, double* b)
-{
- return a[0] * b[0]
- + a[1] * b[1]
- + a[2] * b[2]
- + a[3] * b[3];
-}
-
-double quat_size(double* q)
-{
- return sqrt(quat_dot(q, q));
-}
-
-void normalize_quaternion(double* q)
-{
- double size = quat_size(q);
-
- q[0] /= size;
- q[1] /= size;
- q[2] /= size;
- q[3] /= size;
-}
-
-void rotation_matrix_to_quaternion(double* u, double* q)
-{
- double r11 = u[0];
- double r12 = u[1];
- double r13 = u[2];
- double r21 = u[3];
- double r22 = u[4];
- double r23 = u[5];
- double r31 = u[6];
- double r32 = u[7];
- double r33 = u[8];
-
- q[0] = (1.0 + r11 + r22 + r33) / 4.0;
- q[1] = (1.0 + r11 - r22 - r33) / 4.0;
- q[2] = (1.0 - r11 + r22 - r33) / 4.0;
- q[3] = (1.0 - r11 - r22 + r33) / 4.0;
-
- q[0] = sqrt(MAX(0, q[0]));
- q[1] = sqrt(MAX(0, q[1]));
- q[2] = sqrt(MAX(0, q[2]));
- q[3] = sqrt(MAX(0, q[3]));
-
- double m0 = MAX(q[0], q[1]);
- double m1 = MAX(q[2], q[3]);
- double max = MAX(m0, m1);
-
- int i = 0;
- for (i=0;i<4;i++)
- if (q[i] == max)
- break;
-
- if (i == 0)
- {
- q[1] *= SIGN(r32 - r23);
- q[2] *= SIGN(r13 - r31);
- q[3] *= SIGN(r21 - r12);
- }
- else if (i == 1)
- {
- q[0] *= SIGN(r32 - r23);
- q[2] *= SIGN(r21 + r12);
- q[3] *= SIGN(r13 + r31);
- }
- else if (i == 2)
- {
- q[0] *= SIGN(r13 - r31);
- q[1] *= SIGN(r21 + r12);
- q[3] *= SIGN(r32 + r23);
- }
- else if (i == 3)
- {
- q[0] *= SIGN(r21 - r12);
- q[1] *= SIGN(r31 + r13);
- q[2] *= SIGN(r32 + r23);
- }
-
- normalize_quaternion(q);
-}
-
-void quaternion_to_rotation_matrix(double* q, double* u)
-{
- double a = q[0];
- double b = q[1];
- double c = q[2];
- double d = q[3];
-
- u[0] = a*a + b*b - c*c - d*d;
- u[1] = 2*b*c - 2*a*d;
- u[2] = 2*b*d + 2*a*c;
-
- u[3] = 2*b*c + 2*a*d;
- u[4] = a*a - b*b + c*c - d*d;
- u[5] = 2*c*d - 2*a*b;
-
- u[6] = 2*b*d - 2*a*c;
- u[7] = 2*c*d + 2*a*b;
- u[8] = a*a - b*b - c*c + d*d;
-}
-
-double quat_quick_misorientation(double* q1, double* q2)
-{
- double t = quat_dot(q1, q2);
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_misorientation(double* q1, double* q2)
-{
- return acos(quat_quick_misorientation(q1, q2));
-}
-
-
-double quat_quick_disorientation_cubic(double* q0, double* q1)
-{
- double qrot[4];
- double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
- quat_rot(qinv, q1, qrot);
-
- rotate_quaternion_into_cubic_fundamental_zone(qrot);
- double t = qrot[0];
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_disorientation_cubic(double* q0, double* q1)
-{
- return acos(quat_quick_disorientation_cubic(q0, q1));
-}
-
-double quat_quick_disorientation_diamond_cubic(double* q0, double* q1)
-{
- double qrot[4];
- double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
- quat_rot(qinv, q1, qrot);
-
- rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot);
- double t = qrot[0];
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_disorientation_diamond_cubic(double* q0, double* q1)
-{
- return acos(quat_quick_disorientation_diamond_cubic(q0, q1));
-}
-
-double quat_quick_disorientation_hcp(double* q0, double* q1)
-{
- double qrot[4];
- double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
- quat_rot(qinv, q1, qrot);
-
- rotate_quaternion_into_hcp_fundamental_zone(qrot);
- double t = qrot[0];
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_disorientation_hcp(double* q0, double* q1)
-{
- return acos(quat_quick_disorientation_hcp(q0, q1));
-}
-
-double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1)
-{
- double qrot[4];
- double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
- quat_rot(qinv, q1, qrot);
-
- rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot);
- double t = qrot[0];
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_disorientation_diamond_hexagonal(double* q0, double* q1)
-{
- return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1));
-}
-
-double quat_quick_disorientation_icosahedral(double* q0, double* q1)
-{
- double qrot[4];
- double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]};
- quat_rot(qinv, q1, qrot);
-
- rotate_quaternion_into_icosahedral_fundamental_zone(qrot);
- double t = qrot[0];
- t = MIN(1, MAX(-1, t));
- return 2 * t * t - 1;
-}
-
-double quat_disorientation_icosahedral(double* q0, double* q1)
-{
- return acos(quat_quick_disorientation_icosahedral(q0, q1));
-}
-
diff --git a/src/USER-PTM/quat.h b/src/USER-PTM/quat.h
deleted file mode 100644
index 725086322c..0000000000
--- a/src/USER-PTM/quat.h
+++ /dev/null
@@ -1,32 +0,0 @@
-#ifndef QUAT_H
-#define QUAT_H
-
-int rotate_quaternion_into_cubic_fundamental_zone(double* q);
-int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
-int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
-int rotate_quaternion_into_hcp_fundamental_zone(double* q);
-int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q);
-
-void normalize_quaternion(double* q);
-void quaternion_to_rotation_matrix(double* q, double* U);
-void rotation_matrix_to_quaternion(double* u, double* q);
-double quat_dot(double* a, double* b);
-double quat_quick_misorientation(double* q1, double* q2);
-double quat_misorientation(double* q1, double* q2);
-
-double quat_quick_disorientation_cubic(double* q0, double* q1);
-double quat_disorientation_cubic(double* q0, double* q1);
-double quat_quick_disorientation_diamond_cubic(double* q0, double* q1);
-double quat_disorientation_diamond_cubic(double* q0, double* q1);
-double quat_quick_disorientation_hcp(double* q0, double* q1);
-double quat_disorientation_hcp(double* q0, double* q1);
-double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1);
-double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
-double quat_quick_disorientation_icosahedral(double* q0, double* q1);
-double quat_disorientation_icosahedral(double* q0, double* q1);
-
-#endif
-
-
-
-
diff --git a/src/USER-PTM/structure_matcher.cpp b/src/USER-PTM/structure_matcher.cpp
deleted file mode 100644
index dad8e3599a..0000000000
--- a/src/USER-PTM/structure_matcher.cpp
+++ /dev/null
@@ -1,294 +0,0 @@
-#include <cstdio>
-#include <cstdlib>
-#include <string.h>
-#include <cmath>
-#include <cfloat>
-#include <cassert>
-#include <algorithm>
-#include "convex_hull_incremental.h"
-#include "canonical_coloured.h"
-#include "graph_data.h"
-#include "graph_tools.h"
-#include "normalize_vertices.h"
-#include "polar.h"
-#include "structure_matcher.h"
-#include "ptm_constants.h"
-
-
-static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
- double G1, double G2, double E0, double* q, double* p_scale)
-{
- double A0[9];
- InnerProduct(A0, num_points, ideal_points, normalized, mapping);
-
- double nrmsdsq, rot[9];
- FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot);
-
- double k0 = 0;
- for (int i=0;i<num_points;i++)
- {
- for (int j=0;j<3;j++)
- {
- double v = 0.0;
- for (int k=0;k<3;k++)
- v += rot[j*3+k] * ideal_points[i][k];
-
- k0 += v * normalized[mapping[i]][j];
- }
- }
-
- double scale = k0 / G2;
- *p_scale = scale;
- return sqrt(fabs(G1 - scale*k0) / num_points);
-}
-
-static void check_graphs( const refdata_t* s,
- uint64_t hash,
- int8_t* canonical_labelling,
- double (*normalized)[3],
- result_t* res)
-{
- int num_points = s->num_nbrs + 1;
- const double (*ideal_points)[3] = s->points;
- int8_t inverse_labelling[PTM_MAX_POINTS];
- int8_t mapping[PTM_MAX_POINTS];
-
- for (int i=0; i<num_points; i++)
- inverse_labelling[ canonical_labelling[i] ] = i;
-
- double G1 = 0, G2 = 0;
- for (int i=0;i<num_points;i++)
- {
- double x1 = ideal_points[i][0];
- double y1 = ideal_points[i][1];
- double z1 = ideal_points[i][2];
-
- double x2 = normalized[i][0];
- double y2 = normalized[i][1];
- double z2 = normalized[i][2];
-
- G1 += x1 * x1 + y1 * y1 + z1 * z1;
- G2 += x2 * x2 + y2 * y2 + z2 * z2;
- }
- double E0 = (G1 + G2) / 2;
-
- for (int i = 0;i<s->num_graphs;i++)
- {
- if (hash != s->graphs[i].hash)
- continue;
-
- graph_t* gref = &s->graphs[i];
- for (int j = 0;j<gref->num_automorphisms;j++)
- {
- for (int k=0;k<num_points;k++)
- mapping[automorphisms[gref->automorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ];
-
- double q[4], scale = 0;
- double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale);
- if (rmsd < res->rmsd)
- {
- res->rmsd = rmsd;
- res->scale = scale;
- res->ref_struct = s;
- memcpy(res->q, q, 4 * sizeof(double));
- memcpy(res->mapping, mapping, sizeof(int8_t) * num_points);
- }
- }
- }
-}
-
-int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res)
-{
- int8_t degree[PTM_MAX_NBRS];
- int8_t facets[PTM_MAX_FACETS][3];
-
- int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
- ch->ok = ret >= 0;
- if (ret != 0)
- return PTM_NO_ERROR;
-
- if (ch->num_facets != s->num_facets)
- return PTM_NO_ERROR; //incorrect number of facets in convex hull
-
- int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree);
- if (max_degree > s->max_degree)
- return PTM_NO_ERROR;
-
- if (s->type == PTM_MATCH_SC)
- for (int i = 0;i<s->num_nbrs;i++)
- if (degree[i] != 4)
- return PTM_NO_ERROR;
-
- double normalized[PTM_MAX_POINTS][3];
- subtract_barycentre(s->num_nbrs + 1, points, normalized);
-
- int8_t code[2 * PTM_MAX_EDGES];
- int8_t colours[PTM_MAX_POINTS] = {0};
- int8_t canonical_labelling[PTM_MAX_POINTS];
- uint64_t hash = 0;
- ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
- if (ret != PTM_NO_ERROR)
- return ret;
-
- check_graphs(s, hash, canonical_labelling, normalized, res);
- return PTM_NO_ERROR;
-}
-
-int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
-{
- int num_nbrs = structure_fcc.num_nbrs;
- int num_facets = structure_fcc.num_facets;
- int max_degree = structure_fcc.max_degree;
-
- int8_t degree[PTM_MAX_NBRS];
- int8_t facets[PTM_MAX_FACETS][3];
-
- int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
- ch->ok = ret >= 0;
- if (ret != 0)
- return PTM_NO_ERROR;
-
- if (ch->num_facets != num_facets)
- return PTM_NO_ERROR; //incorrect number of facets in convex hull
-
- int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
- if (_max_degree > max_degree)
- return PTM_NO_ERROR;
-
- double normalized[PTM_MAX_POINTS][3];
- subtract_barycentre(num_nbrs + 1, points, normalized);
-
- int8_t code[2 * PTM_MAX_EDGES];
- int8_t colours[PTM_MAX_POINTS] = {0};
- int8_t canonical_labelling[PTM_MAX_POINTS];
- uint64_t hash = 0;
- ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
- if (ret != PTM_NO_ERROR)
- return ret;
-
- if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res);
- if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res);
- if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res);
- return PTM_NO_ERROR;
-}
-
-int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res)
-{
- int num_nbrs = structure_dcub.num_nbrs;
- int num_facets = structure_fcc.num_facets;
- int max_degree = structure_dcub.max_degree;
-
-
- int8_t facets[PTM_MAX_FACETS][3];
- int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets);
- ch->ok = ret >= 0;
- if (ret != 0)
- return PTM_NO_ERROR;
-
- //check for facets with multiple inner atoms
- bool inverted[4] = {false, false, false, false};
- for (int i=0;i<ch->num_facets;i++)
- {
- int n = 0;
- for (int j=0;j<3;j++)
- {
- if (facets[i][j] <= 3)
- {
- inverted[facets[i][j]] = true;
- n++;
- }
- }
- if (n > 1)
- return PTM_NO_ERROR;
- }
-
- int num_inverted = 0;
- for (int i=0;i<4;i++)
- num_inverted += inverted[i] ? 1 : 0;
-
- if (ch->num_facets != num_facets + 2 * num_inverted)
- return PTM_NO_ERROR; //incorrect number of facets in convex hull
-
- int8_t degree[PTM_MAX_NBRS];
- int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree);
- if (_max_degree > max_degree)
- return PTM_NO_ERROR;
-
- int num_found = 0;
- int8_t toadd[4][3];
- for (int i=0;i<ch->num_facets;i++)
- {
- int a = facets[i][0];
- int b = facets[i][1];
- int c = facets[i][2];
- if (a <= 3 || b <= 3 || c <= 3)
- continue;
-
- int i0 = (a - 4) / 3;
- int i1 = (b - 4) / 3;
- int i2 = (c - 4) / 3;
-
- if (i0 == i1 && i0 == i2)
- {
- if (num_found + num_inverted >= 4)
- return PTM_NO_ERROR;
-
- toadd[num_found][0] = a;
- toadd[num_found][1] = b;
- toadd[num_found][2] = c;
- num_found++;
-
- memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t));
- ch->num_facets--;
- i--;
- }
- }
-
- if (num_found + num_inverted != 4)
- return PTM_NO_ERROR;
-
- for (int i=0;i<num_found;i++)
- {
- int a = toadd[i][0];
- int b = toadd[i][1];
- int c = toadd[i][2];
-
- int i0 = (a - 4) / 3;
-
- facets[ch->num_facets][0] = i0;
- facets[ch->num_facets][1] = b;
- facets[ch->num_facets][2] = c;
- ch->num_facets++;
-
- facets[ch->num_facets][0] = a;
- facets[ch->num_facets][1] = i0;
- facets[ch->num_facets][2] = c;
- ch->num_facets++;
-
- facets[ch->num_facets][0] = a;
- facets[ch->num_facets][1] = b;
- facets[ch->num_facets][2] = i0;
- ch->num_facets++;
- }
-
- _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree);
- if (_max_degree > max_degree)
- return PTM_NO_ERROR;
-
- double normalized[PTM_MAX_POINTS][3];
- subtract_barycentre(num_nbrs + 1, points, normalized);
-
- int8_t code[2 * PTM_MAX_EDGES];
- int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
- int8_t canonical_labelling[PTM_MAX_POINTS];
- uint64_t hash = 0;
- ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash);
- if (ret != PTM_NO_ERROR)
- return ret;
-
- if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res);
- if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res);
-
- return PTM_NO_ERROR;
-}
-
diff --git a/src/USER-PTM/structure_matcher.h b/src/USER-PTM/structure_matcher.h
deleted file mode 100644
index 25e80a94e1..0000000000
--- a/src/USER-PTM/structure_matcher.h
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef STRUCTURE_MATCHER_H
-#define STRUCTURE_MATCHER_H
-
-#include "initialize_data.h"
-#include "ptm_constants.h"
-
-typedef struct
-{
- double rmsd;
- double scale;
- double q[4]; //rotation in quaternion form (rigid body transformation)
- int8_t mapping[PTM_MAX_POINTS];
- const refdata_t* ref_struct;
-} result_t;
-
-int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res);
-int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
-int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
-
-#endif
-
--
GitLab
From 5aeba421bb8a150f109dc5ad5510e9686cd1dbb9 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Thu, 20 Sep 2018 09:15:43 -0400
Subject: [PATCH 275/332] Add compute_pressure_cylinder .cpp and .h files
---
src/USER-MISC/compute_pressure_cylinder.cpp | 493 ++++++++++++++++++++
src/USER-MISC/compute_pressure_cylinder.h | 74 +++
2 files changed, 567 insertions(+)
create mode 100644 src/USER-MISC/compute_pressure_cylinder.cpp
create mode 100644 src/USER-MISC/compute_pressure_cylinder.h
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
new file mode 100644
index 0000000000..bae6398691
--- /dev/null
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -0,0 +1,493 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "string.h"
+#include "stdlib.h"
+#include "compute_pressure_cylinder.h"
+#include "atom.h"
+#include "update.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "neigh_request.h"
+#include "neigh_list.h"
+#include "group.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_compute_pressure_cylinder[] =
+ "compute pressure/cylinder:\n\n"
+ "@Article{Addington,\n"
+ " author = {C. K. Addington, Y. Long, K. E. Gubbins},\n"
+ " title = {The pressure in interfaces having cylindrical geometry},\n"
+ " journal = {J.~Chem.~Phys.},\n"
+ " year = 2018,\n"
+ " volume = 149,\n"
+ " pages = {084109}\n"
+ "}\n\n";
+
+if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
+
+/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Calculate the configurational components of the pressure tensor in
+ cylindrical geometry, according to the formulation of Addington et al. (2018)
+ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+
+ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command");
+
+ zlo=force->numeric(FLERR,arg[3]);
+ zhi=force->numeric(FLERR,arg[4]);
+ Rmax=force->numeric(FLERR,arg[5]);
+ bin_width=force->numeric(FLERR,arg[6]);
+
+ nbins=(int)(Rmax/bin_width);
+
+ nzbins=(int)((zhi-zlo)/bin_width);
+
+ array_flag=1;
+ vector_flag=0;
+ extarray=0;
+ size_array_cols = 5; // r, number density, Pr, Pphi, Pz
+ size_array_rows = nbins;
+
+ Pr_temp = new double[nbins];
+ Pr_all = new double[nbins];
+ Pz_temp = new double[nbins];
+ Pz_all = new double[nbins];
+ Pphi_temp = new double[nbins];
+ Pphi_all = new double[nbins];
+ R = new double[nbins];
+ R2 = new double[nbins];
+ PrAinv = new double[nbins];
+ PzAinv = new double[nbins];
+ Rinv = new double[nbins];
+ binz = new double[nzbins];
+
+ R2kin = new double[nbins];
+ density_temp = new double[nbins];
+ invVbin = new double[nbins];
+ density_all = new double[nbins];
+
+ memory->create(array,nbins,5,"PN:array");
+
+ nphi=360;
+ tangent = new double[nphi];
+ ephi_x = new double[nphi];
+ ephi_y = new double[nphi];
+
+ nktv2p = force->nktv2p;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePressureCyl::~ComputePressureCyl()
+{
+ // count all of these for memory usage
+ memory->destroy(array);
+ delete [] R;
+ delete [] Rinv;
+ delete [] R2;
+ delete [] R2kin;
+ delete [] invVbin;
+ delete [] density_temp;
+ delete [] density_all;
+ delete [] tangent;
+ delete [] ephi_x;
+ delete [] ephi_y;
+ delete [] Pr_temp;
+ delete [] Pr_all;
+ delete [] Pz_temp;
+ delete [] Pz_all;
+ delete [] Pphi_temp;
+ delete [] Pphi_all;
+ delete [] PrAinv;
+ delete [] PzAinv;
+ delete [] binz;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureCyl::init()
+{
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute pressure/cylinder");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute pressure/cylinder");
+
+ double phi;
+
+ for (int iphi=0;iphi<nphi;iphi++)
+ {
+ phi=((double)iphi)*3.14159/180.0;
+ tangent[iphi]=tan(phi);
+ ephi_x[iphi]=-sin(phi);
+ ephi_y[iphi]=cos(phi);
+ }
+
+ for (int iq=0;iq<nbins;iq++)
+ {
+ R[iq]=((double)iq+0.5)*bin_width;
+ Rinv[iq]=1.0/R[iq];
+ R2[iq]=R[iq]*R[iq];
+ R2kin[iq]=(((double)iq)+1.0)*bin_width;
+ R2kin[iq]*=R2kin[iq];
+ PrAinv[iq]=1.0/(2.0*3.14159*(zhi-zlo)*R[iq]);
+ }
+ PphiAinv=1.0/((zhi-zlo)*bin_width*2.0*(double)nphi);
+
+ invVbin[0]=1.0/((zhi-zlo)*3.14159*R2kin[0]);
+ PzAinv[0]=1.0/(3.14159*R2kin[0]*((double)nzbins));
+ for (int jq=1;jq<nbins;jq++)
+ {
+ invVbin[jq]=1.0/((zhi-zlo)*3.14159*(R2kin[jq]-R2kin[jq-1]));
+ PzAinv[jq]=1.0/(3.14159*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
+ }
+
+ // need an occasional half neighbor list
+ int irequest = neighbor->request(this,instance_me);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
+ for (int zzz=0;zzz<nzbins;zzz++) binz[zzz]=(((double)zzz)+0.5)*bin_width+zlo;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureCyl::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+
+/* ----------------------------------------------------------------------
+ count pairs and compute pair info on this proc
+ only count pair once if newton_pair is off
+ both atom I,J must be in group
+ if flag is set, compute requested info about pair
+------------------------------------------------------------------------- */
+
+void ComputePressureCyl::compute_array()
+{
+ invoked_array = update->ntimestep;
+
+ int ibin;
+
+ // clear pressures
+ for (ibin=0;ibin<nbins;ibin++)
+ {
+ density_temp[ibin]=0.0;
+ density_all[ibin]=0.0;
+ Pr_temp[ibin]=0.0;
+ Pr_all[ibin]=0.0;
+ Pphi_temp[ibin]=0.0;
+ Pphi_all[ibin]=0.0;
+ Pz_temp[ibin]=0.0;
+ Pz_all[ibin]=0.0;
+ }
+
+ // what processor am I?
+ int me;
+ MPI_Comm_rank(world,&me);
+
+ int i,j,n,ii,jj,inum,jnum,itype,jtype;
+ tagint itag,jtag;
+ double xtmp,ytmp,ztmp,delx,dely,delz;
+ double rsq,eng,fpair,factor_coul,factor_lj;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+
+ // invoke half neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // calculate number density (by radius)
+ double temp_R2;
+ for (i=0;i<nlocal;i++) if (x[i][2]<zhi && x[i][2]>zlo)
+ {
+ temp_R2=x[i][0]*x[i][0]+x[i][1]*x[i][1];
+ if (temp_R2>R2kin[nbins-1]) continue; // outside of Rmax
+
+ for (j=0;j<nbins;j++) if (temp_R2<R2kin[j]) break;
+
+ density_temp[j]+=invVbin[j];
+ }
+ MPI_Allreduce(density_temp,density_all,nbins,MPI_DOUBLE,MPI_SUM,world);
+ for (i=0;i<nbins;i++) array[i][1]=density_all[i]; // NEW
+
+ // loop over neighbors of my atoms
+ // skip if I or J are not in group
+ // for newton = 0 and J = ghost atom,
+ // need to insure I,J pair is only output by one proc
+ // use same itag,jtag logic as in Neighbor::neigh_half_nsq()
+ // for flag = 0, just count pair interactions within force cutoff
+ // for flag = 1, calculate requested output fields
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ double r1=0.0;
+ double r2=0.0;
+ double risq,rjsq;
+ double ri,rj,rij,fij;
+ double A,B,C,Bsq,A2inv,A4,D;
+ double alpha1,alpha2,aij;
+ double xi,yi,zi,dx,dy,dz;
+ double m,xR,yR,zR,fn;
+ double alpha,xL,yL,zL,L2,ftphi,ftz;
+ double sqrtD;
+ double lower_z,upper_z;
+
+ for (ii = 0; ii < inum; ii++)
+ {
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itag = tag[i];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ r1=x[i][0]*x[i][0]+x[i][1]*x[i][1];
+
+ for (jj = 0; jj < jnum; jj++)
+ {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbit)) continue;
+
+ // itag = jtag is possible for long cutoffs that include images of self
+ // do calculation only on appropriate processor
+ if (newton_pair == 0 && j >= nlocal)
+ {
+ jtag = tag[j];
+ if (itag > jtag)
+ {
+ if ((itag+jtag) % 2 == 0) continue;
+ }
+ else if (itag < jtag)
+ {
+ if ((itag+jtag) % 2 == 1) continue;
+ }
+ else
+ {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp)
+ {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+
+ r2=x[j][0]*x[j][0]+x[j][1]*x[j][1];
+
+ // ri is smaller of r1 and r2
+ if (r2<r1)
+ {
+ risq=r2;
+ rjsq=r1;
+ xi=x[j][0];
+ yi=x[j][1];
+ zi=x[j][2];
+ dx=x[i][0]-x[j][0];
+ dy=x[i][1]-x[j][1];
+ dz=x[i][2]-x[j][2];
+ }
+ else
+ {
+ risq=r1;
+ rjsq=r2;
+ xi=x[i][0];
+ yi=x[i][1];
+ zi=x[i][2];
+ dx=x[j][0]-x[i][0];
+ dy=x[j][1]-x[i][1];
+ dz=x[j][2]-x[i][2];
+ }
+
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+ if (rsq >= cutsq[itype][jtype]) continue;
+
+ eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+
+ A=dx*dx+dy*dy;
+ B=2.0*(xi*dx+yi*dy);
+
+ // normal pressure contribution P_rhorho
+ for (ibin=0;ibin<nbins;ibin++)
+ {
+ // completely inside of R
+ if (rjsq<R2[ibin]) continue;
+
+ C=risq-R2[ibin];
+ D=B*B-4.0*A*C;
+
+ // completely outside of R
+ if (D<0.0) continue;
+
+ sqrtD=sqrt(D);
+ alpha1=0.5*(-B+sqrtD)/A;
+ alpha2=0.5*(-B-sqrtD)/A;
+
+ if (alpha1>0.0 && alpha1<1.0)
+ {
+ zR=zi+alpha1*dz;
+ if (zR<zhi && zR>zlo)
+ {
+ xR=xi+alpha1*dx;
+ yR=yi+alpha1*dy;
+ fn=fpair*fabs(xR*dx+yR*dy);
+
+ Pr_temp[ibin]+=fn;
+ }
+ }
+ if (alpha2>0.0 && alpha2<1.0)
+ {
+ zR=zi+alpha2*dz;
+ if (zR<zhi && zR>zlo)
+ {
+ xR=xi+alpha2*dx;
+ yR=yi+alpha2*dy;
+ fn=fpair*fabs(xR*dx+yR*dy);
+
+ Pr_temp[ibin]+=fn;
+ }
+ }
+ }
+
+ // azimuthal pressure contribution (P_phiphi)
+ for (int iphi=0;iphi<nphi;iphi++)
+ {
+ alpha=(yi-xi*tangent[iphi])/(dx*tangent[iphi]-dy);
+
+ // no intersection with phi surface
+ if (alpha>=1.0 || alpha<=0.0) continue;
+
+ // no contribution (outside of averaging region)
+ zL=zi+alpha*dz;
+ if (zL>zhi || zL<zlo) continue;
+
+ xL=xi+alpha*dx;
+ yL=yi+alpha*dy;
+
+ L2=xL*xL+yL*yL;
+
+ // no intersection (outside of Rmax)
+ if (L2>R2kin[nbins-1]) continue;
+
+ ftphi=fabs(dx*ephi_x[iphi]+dy*ephi_y[iphi])*fpair;
+
+ // add to appropriate bin
+ for (ibin=0;ibin<nbins;ibin++) if (L2<R2kin[ibin])
+ {
+ Pphi_temp[ibin]+=ftphi;
+ break;
+ }
+ }
+
+ // z pressure contribution (P_zz)
+ for (int zbin=0;zbin<nzbins;zbin++)
+ {
+ // check if interaction contributes
+ if (x[i][2]>binz[zbin] && x[j][2]>binz[zbin]) continue;
+ if (x[i][2]<binz[zbin] && x[j][2]<binz[zbin]) continue;
+
+ alpha=(binz[zbin]-zi)/dz;
+
+ xL=xi+alpha*dx;
+ yL=yi+alpha*dy;
+
+ L2=xL*xL+yL*yL;
+
+ if (L2>R2kin[nbins-1]) continue;
+
+ ftz=fabs(dz)*fpair;
+
+ // add to appropriate bin
+ for (ibin=0;ibin<nbins;ibin++) if (L2<R2kin[ibin])
+ {
+ Pz_temp[ibin]+=ftz;
+ break;
+ }
+ }
+ }
+ }
+
+ // calculate pressure (force over area)
+ for (ibin=0;ibin<nbins;ibin++)
+ {
+ Pr_temp[ibin]*=PrAinv[ibin]*Rinv[ibin];
+ Pphi_temp[ibin]*=PphiAinv;
+ Pz_temp[ibin]*=PzAinv[ibin];
+ }
+
+ // communicate these values across processors
+ MPI_Allreduce(Pr_temp,Pr_all,nbins,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(Pphi_temp,Pphi_all,nbins,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(Pz_temp,Pz_all,nbins,MPI_DOUBLE,MPI_SUM,world);
+
+ // populate array
+ for (ibin=0;ibin<nbins;ibin++)
+ {
+ array[ibin][0]=R[ibin];
+ array[ibin][2]=Pr_all[ibin]*nktv2p;
+ array[ibin][3]=Pphi_all[ibin]*nktv2p;
+ array[ibin][4]=Pz_all[ibin]*nktv2p;
+ }
+
+}
+
+/* ----------------------------------------------------------------------
+memory usage of data
+------------------------------------------------------------------------- */
+
+double ComputePressureCyl::memory_usage()
+{
+ double bytes =
+ (3.0*(double)nphi + 16.0*(double)nbins+5.0*(double)nbins) * sizeof(double);
+ return bytes;
+}
diff --git a/src/USER-MISC/compute_pressure_cylinder.h b/src/USER-MISC/compute_pressure_cylinder.h
new file mode 100644
index 0000000000..7151cca6ce
--- /dev/null
+++ b/src/USER-MISC/compute_pressure_cylinder.h
@@ -0,0 +1,74 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(pressure/cylinder,ComputePressureCyl)
+
+#else
+
+#ifndef LMP_COMPUTE_PRESSURE_CYLINDER
+#define LMP_COMPUTE_PRESSURE_CYLINDER
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePressureCyl : public Compute {
+ public:
+ ComputePressureCyl(class LAMMPS *, int, char **);
+ ~ComputePressureCyl();
+ void init();
+ void init_list(int, class NeighList *);
+ void compute_array();
+ double memory_usage();
+
+ private:
+ int nbins,nphi,nzbins;
+ double *Pr_temp,*Pr_all,*Pz_temp,*Pz_all,*Pphi_temp,*Pphi_all;
+ double *R,*Rinv,*R2,*PrAinv,*PzAinv,PphiAinv;
+ double Rmax,bin_width,nktv2p;
+ double *R2kin,*density_temp,*invVbin,*density_all;
+ double *tangent,*ephi_x,*ephi_y;
+ double *binz;
+
+ double zlo,zhi;
+
+ class NeighList *list;
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: No pair style is defined for compute pressure/cylinder
+
+Self-explanatory.
+
+E: Pair style does not support compute pressure/cylinder
+
+The pair style does not have a single() function, so it can
+not be invoked by compute pressure/cylinder.
+
+*/
+
--
GitLab
From dd39bc44ee2c69cf05d829fb3e05fb893b46a46b Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Thu, 20 Sep 2018 09:16:58 -0400
Subject: [PATCH 276/332] Add compute_pressure_cylinder documentation
---
doc/src/compute_pressure_cylinder.txt | 64 +++++++++++++++++++++++++++
1 file changed, 64 insertions(+)
create mode 100644 doc/src/compute_pressure_cylinder.txt
diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt
new file mode 100644
index 0000000000..c6d97e7958
--- /dev/null
+++ b/doc/src/compute_pressure_cylinder.txt
@@ -0,0 +1,64 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pressure/cylinder command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/cylinder = style name of this compute command
+zlo = minimum z-boundary for cylinder
+zhi = maximum z-boundary for cylinder
+Rmax = maximum radius to perform calculation to
+bin_width = width of radial bins to use for calculation :ul
+
+[Examples:]
+
+compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre
+
+[Description:]
+
+Define a computation that calculates the pressure tensor of a
+system in cylindrical coordinates, as discussed in "(Addington)"_#Addington1.
+This is useful for systems with a single axis of rotational symmetry,
+such as cylindrical micelles or carbon nanotubes. The compute splits
+the system into radial, cylindrical-shell-type bins of width bin_width, centered at x=0,y=0,
+and calculates the radial (P_rhorho), azimuthal (P_phiphi), and axial (P_zz) components of the configurational pressure
+tensor. The local density is also calculated for each bin, so that
+the true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf.
+The output is a global array with 5 columns; one each for bin radius,
+local number density, P_rhorho, P_phiphi, and P_zz. The number of
+rows is governed by the values of Rmax and bin_width. Pressure
+tensor values are output in pressure units.
+
+[Output info:]
+
+This compute calculates a global array with 5 columns and Rmax/bin_width
+rows.
+
+The values calculated by this compute are
+"intensive". The pressure values will be in pressure
+"units"_units.html. The number density values will be in
+inverse volume "units"_units.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute temp"_compute_temp.html, "compute
+stress/atom"_compute_stress_atom.html,
+"thermo_style"_thermo_style.html,
+
+[Default:] none
+
+:line
+
+:link(Addington1)
+[(Addington)] Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).
--
GitLab
From 6e546ef5af0c734da053d752fe1f25e29d34ffce Mon Sep 17 00:00:00 2001
From: pmla <pete.mahler.larsen@gmail.com>
Date: Thu, 20 Sep 2018 14:20:58 -0400
Subject: [PATCH 277/332] added ptm namespace
---
src/USER-PTM/ptm_alloy_types.cpp | 3 ++
src/USER-PTM/ptm_alloy_types.h | 4 ++
src/USER-PTM/ptm_canonical_coloured.cpp | 3 ++
src/USER-PTM/ptm_canonical_coloured.h | 3 ++
src/USER-PTM/ptm_convex_hull_incremental.cpp | 3 ++
src/USER-PTM/ptm_convex_hull_incremental.h | 3 ++
src/USER-PTM/ptm_deformation_gradient.cpp | 3 ++
src/USER-PTM/ptm_deformation_gradient.h | 4 ++
src/USER-PTM/ptm_fundamental_mappings.h | 3 ++
src/USER-PTM/ptm_graph_data.cpp | 4 ++
src/USER-PTM/ptm_graph_data.h | 3 ++
src/USER-PTM/ptm_graph_tools.cpp | 4 ++
src/USER-PTM/ptm_graph_tools.h | 4 ++
src/USER-PTM/ptm_index.cpp | 44 ++++++++++----------
src/USER-PTM/ptm_initialize_data.cpp | 26 ++++++------
src/USER-PTM/ptm_initialize_data.h | 3 ++
src/USER-PTM/ptm_neighbour_ordering.cpp | 12 +++---
src/USER-PTM/ptm_neighbour_ordering.h | 4 ++
src/USER-PTM/ptm_normalize_vertices.cpp | 3 ++
src/USER-PTM/ptm_normalize_vertices.h | 4 ++
src/USER-PTM/ptm_polar.cpp | 4 ++
src/USER-PTM/ptm_polar.h | 4 ++
src/USER-PTM/ptm_quat.cpp | 4 ++
src/USER-PTM/ptm_quat.h | 7 ++--
src/USER-PTM/ptm_structure_matcher.cpp | 4 ++
src/USER-PTM/ptm_structure_matcher.h | 5 +++
src/USER-PTM/ptm_voronoi_cell.cpp | 2 +-
src/USER-PTM/ptm_voronoi_cell.h | 2 +-
src/USER-PTM/ptm_voronoi_config.h | 2 +-
29 files changed, 128 insertions(+), 46 deletions(-)
diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp
index e14d06db99..151de3e5b8 100644
--- a/src/USER-PTM/ptm_alloy_types.cpp
+++ b/src/USER-PTM/ptm_alloy_types.cpp
@@ -2,6 +2,7 @@
#include "ptm_constants.h"
#include "ptm_initialize_data.h"
+namespace ptm {
#define NUM_ALLOY_TYPES 3
static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
@@ -99,3 +100,5 @@ int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
return PTM_ALLOY_NONE;
}
+}
+
diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h
index 6ea6ed1b8a..559e0a7490 100644
--- a/src/USER-PTM/ptm_alloy_types.h
+++ b/src/USER-PTM/ptm_alloy_types.h
@@ -3,7 +3,11 @@
#include "ptm_initialize_data.h"
+namespace ptm {
+
int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp
index 551f52d7e4..ade8f23b15 100644
--- a/src/USER-PTM/ptm_canonical_coloured.cpp
+++ b/src/USER-PTM/ptm_canonical_coloured.cpp
@@ -4,6 +4,7 @@
#include "ptm_graph_tools.h"
#include "ptm_constants.h"
+namespace ptm {
static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
{
@@ -165,3 +166,5 @@ int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, i
return PTM_NO_ERROR;
}
+}
+
diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h
index e71bb08bfc..f8e2a7af5d 100644
--- a/src/USER-PTM/ptm_canonical_coloured.h
+++ b/src/USER-PTM/ptm_canonical_coloured.h
@@ -3,7 +3,10 @@
#include <stdint.h>
+namespace ptm {
+
int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
+}
#endif
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp
index c996b17b58..7c79fd371a 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.cpp
+++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp
@@ -6,6 +6,7 @@
#include "ptm_convex_hull_incremental.h"
#include "ptm_constants.h"
+namespace ptm {
#define VISIBLE 1
#define INVISIBLE 2
@@ -361,3 +362,5 @@ int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch,
return ret;
}
+}
+
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h
index 563a0c436a..6474723907 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.h
+++ b/src/USER-PTM/ptm_convex_hull_incremental.h
@@ -6,6 +6,7 @@
#include <stdbool.h>
#include "ptm_constants.h"
+namespace ptm {
typedef struct
{
@@ -23,5 +24,7 @@ typedef struct
void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp
index d566d5ca11..fc851920a6 100644
--- a/src/USER-PTM/ptm_deformation_gradient.cpp
+++ b/src/USER-PTM/ptm_deformation_gradient.cpp
@@ -1,5 +1,6 @@
#include "ptm_deformation_gradient.h"
+namespace ptm {
void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
{
@@ -35,3 +36,5 @@ void calculate_deformation_gradient(int num_points, const double (*ideal_points)
}
}
+}
+
diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h
index 7decab4b76..32836da44d 100644
--- a/src/USER-PTM/ptm_deformation_gradient.h
+++ b/src/USER-PTM/ptm_deformation_gradient.h
@@ -4,6 +4,8 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
+
void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
//sc
@@ -137,6 +139,8 @@ const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 2 * kdcub, -2 * kdcub },
{ 2 * kdcub, 0, -2 * kdcub },
};
+}
+
#endif
diff --git a/src/USER-PTM/ptm_fundamental_mappings.h b/src/USER-PTM/ptm_fundamental_mappings.h
index 3dd7c39cbb..35fae7f088 100644
--- a/src/USER-PTM/ptm_fundamental_mappings.h
+++ b/src/USER-PTM/ptm_fundamental_mappings.h
@@ -3,6 +3,8 @@
#include <stdint.h>
+namespace ptm {
+
#define NUM_CUBIC_MAPPINGS 24
#define NUM_ICO_MAPPINGS 60
#define NUM_HEX_MAPPINGS 6
@@ -175,6 +177,7 @@ const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
{0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
+}
#endif
diff --git a/src/USER-PTM/ptm_graph_data.cpp b/src/USER-PTM/ptm_graph_data.cpp
index a591dbf993..a742c8b339 100644
--- a/src/USER-PTM/ptm_graph_data.cpp
+++ b/src/USER-PTM/ptm_graph_data.cpp
@@ -1,6 +1,8 @@
#include "ptm_graph_data.h"
+namespace ptm {
+
int8_t automorphisms[65][17] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
@@ -2057,3 +2059,5 @@ graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
};
+}
+
diff --git a/src/USER-PTM/ptm_graph_data.h b/src/USER-PTM/ptm_graph_data.h
index 11f46a471f..251c82d2f5 100644
--- a/src/USER-PTM/ptm_graph_data.h
+++ b/src/USER-PTM/ptm_graph_data.h
@@ -4,6 +4,7 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
typedef struct
{
@@ -33,5 +34,7 @@ extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
+}
+
#endif
diff --git a/src/USER-PTM/ptm_graph_tools.cpp b/src/USER-PTM/ptm_graph_tools.cpp
index 89d07fc87a..f6fd34d097 100644
--- a/src/USER-PTM/ptm_graph_tools.cpp
+++ b/src/USER-PTM/ptm_graph_tools.cpp
@@ -4,6 +4,8 @@
#include "ptm_constants.h"
+namespace ptm {
+
bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
{
memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
@@ -50,3 +52,5 @@ int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degr
return max_degree;
}
+}
+
diff --git a/src/USER-PTM/ptm_graph_tools.h b/src/USER-PTM/ptm_graph_tools.h
index 78934e87c1..7befad526b 100644
--- a/src/USER-PTM/ptm_graph_tools.h
+++ b/src/USER-PTM/ptm_graph_tools.h
@@ -4,8 +4,12 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
+
bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
index 7b6618848e..24998dadd0 100644
--- a/src/USER-PTM/ptm_index.cpp
+++ b/src/USER-PTM/ptm_index.cpp
@@ -36,13 +36,13 @@ static double calculate_lattice_constant(int type, double interatomic_distance)
static int rotate_into_fundamental_zone(int type, double* q)
{
- if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
- if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
- if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
+ if (type == PTM_MATCH_SC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_FCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_BCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_ICO) return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q);
+ if (type == PTM_MATCH_HCP) return ptm::rotate_quaternion_into_hcp_fundamental_zone(q);
+ if (type == PTM_MATCH_DCUB) return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_DHEX) return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
return -1;
}
@@ -52,8 +52,8 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double
if (topological_ordering)
{
double normalized_points[PTM_MAX_INPUT_POINTS][3];
- normalize_vertices(num_points, unpermuted_points, normalized_points);
- int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
+ ptm::normalize_vertices(num_points, unpermuted_points, normalized_points);
+ int ret = ptm::calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
if (ret != 0)
topological_ordering = false;
}
@@ -71,7 +71,7 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double
}
}
-static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
+static void output_data(ptm::result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res,
double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
{
@@ -82,13 +82,13 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe
if (mapping != NULL)
memset(mapping, -1, num_points * sizeof(int8_t));
- const refdata_t* ref = res->ref_struct;
+ const ptm::refdata_t* ref = res->ref_struct;
if (ref == NULL)
return;
*p_type = ref->type;
if (p_alloy_type != NULL && unpermuted_numbers != NULL)
- *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
+ *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers);
int bi = rotate_into_fundamental_zone(ref->type, res->q);
int8_t temp[PTM_MAX_POINTS];
@@ -101,17 +101,17 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe
{
double scaled_points[PTM_MAX_INPUT_POINTS][3];
- subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
+ ptm::subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
for (int i = 0;i<ref->num_nbrs + 1;i++)
{
scaled_points[i][0] *= res->scale;
scaled_points[i][1] *= res->scale;
scaled_points[i][2] *= res->scale;
}
- calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
+ ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
if (P != NULL && U != NULL)
- polar_decomposition_3x3(F, false, U, P);
+ ptm::polar_decomposition_3x3(F, false, U, P);
}
if (mapping != NULL)
@@ -156,7 +156,7 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
assert(num_points >= PTM_NUM_POINTS_DCUB);
int ret = 0;
- result_t res;
+ ptm::result_t res;
res.ref_struct = NULL;
res.rmsd = INFINITY;
@@ -168,32 +168,32 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
double dpoints[PTM_MAX_POINTS][3];
int32_t dnumbers[PTM_MAX_POINTS];
- convexhull_t ch;
+ ptm::convexhull_t ch;
double ch_points[PTM_MAX_INPUT_POINTS][3];
if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
{
int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
- normalize_vertices(num_lpoints, points, ch_points);
+ ptm::normalize_vertices(num_lpoints, points, ch_points);
ch.ok = false;
if (flags & PTM_CHECK_SC)
- ret = match_general(&structure_sc, ch_points, points, &ch, &res);
+ ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res);
if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);
if (flags & PTM_CHECK_BCC)
- ret = match_general(&structure_bcc, ch_points, points, &ch, &res);
+ ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res);
}
if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
{
- ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
+ ret = ptm::calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
if (ret == 0)
{
- normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
+ ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
ch.ok = false;
ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
index 6157ff862f..8d96e2a2b7 100644
--- a/src/USER-PTM/ptm_initialize_data.cpp
+++ b/src/USER-PTM/ptm_initialize_data.cpp
@@ -14,20 +14,20 @@ static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const dou
double origin[3] = {0, 0, 0};
for (int i = 0;i<num_facets;i++)
- add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
+ ptm::add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
}
-static int initialize_graphs(const refdata_t* s, int8_t* colours)
+static int initialize_graphs(const ptm::refdata_t* s, int8_t* colours)
{
for (int i = 0;i<s->num_graphs;i++)
{
int8_t code[2 * PTM_MAX_EDGES];
int8_t degree[PTM_MAX_NBRS];
- int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
+ int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
assert(_max_degree <= s->max_degree);
make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
- int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
+ int ret = ptm::canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
if (ret != 0)
return ret;
}
@@ -44,13 +44,13 @@ int ptm_initialize_global()
int8_t colours[PTM_MAX_POINTS] = {0};
int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
- int ret = initialize_graphs(&structure_sc, colours);
- ret |= initialize_graphs(&structure_fcc, colours);
- ret |= initialize_graphs(&structure_hcp, colours);
- ret |= initialize_graphs(&structure_ico, colours);
- ret |= initialize_graphs(&structure_bcc, colours);
- ret |= initialize_graphs(&structure_dcub, dcolours);
- ret |= initialize_graphs(&structure_dhex, dcolours);
+ int ret = initialize_graphs(&ptm::structure_sc, colours);
+ ret |= initialize_graphs(&ptm::structure_fcc, colours);
+ ret |= initialize_graphs(&ptm::structure_hcp, colours);
+ ret |= initialize_graphs(&ptm::structure_ico, colours);
+ ret |= initialize_graphs(&ptm::structure_bcc, colours);
+ ret |= initialize_graphs(&ptm::structure_dcub, dcolours);
+ ret |= initialize_graphs(&ptm::structure_dhex, dcolours);
if (ret == PTM_NO_ERROR)
ptm_initialized = true;
@@ -61,11 +61,11 @@ int ptm_initialize_global()
ptm_local_handle_t ptm_initialize_local()
{
assert(ptm_initialized);
- return (ptm_local_handle_t)voronoi_initialize_local();
+ return (ptm_local_handle_t)ptm::voronoi_initialize_local();
}
void ptm_uninitialize_local(ptm_local_handle_t ptr)
{
- voronoi_uninitialize_local(ptr);
+ ptm::voronoi_uninitialize_local(ptr);
}
diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h
index f381dd864b..5374fbf7d0 100644
--- a/src/USER-PTM/ptm_initialize_data.h
+++ b/src/USER-PTM/ptm_initialize_data.h
@@ -11,6 +11,8 @@
#include "ptm_convex_hull_incremental.h"
+namespace ptm {
+
typedef struct
{
int type;
@@ -35,6 +37,7 @@ const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, N
const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
+}
#ifdef __cplusplus
extern "C" {
diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp
index 6b5ac9601a..c77a779c68 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.cpp
+++ b/src/USER-PTM/ptm_neighbour_ordering.cpp
@@ -5,9 +5,9 @@
#include <algorithm>
#include "ptm_constants.h"
#include "ptm_voronoi_cell.h"
-using namespace voro;
+namespace ptm {
typedef struct
{
@@ -31,7 +31,7 @@ static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
}
//todo: change voronoi code to return errors rather than exiting
-static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
+static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
{
const double k = 1000 * max_norm; //todo: reduce this constant
v->init(-k,k,-k,k,-k,k);
@@ -53,7 +53,7 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do
{
assert(num_points <= PTM_MAX_INPUT_POINTS);
- voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
+ ptm_voro::voronoicell_neighbor* voronoi_handle = (ptm_voro::voronoicell_neighbor*)_voronoi_handle;
double max_norm = 0;
double points[PTM_MAX_INPUT_POINTS][3];
@@ -116,13 +116,13 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do
void* voronoi_initialize_local()
{
- voronoicell_neighbor* ptr = new voronoicell_neighbor;
+ ptm_voro::voronoicell_neighbor* ptr = new ptm_voro::voronoicell_neighbor;
return (void*)ptr;
}
void voronoi_uninitialize_local(void* _ptr)
{
- voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
+ ptm_voro::voronoicell_neighbor* ptr = (ptm_voro::voronoicell_neighbor*)_ptr;
delete ptr;
}
@@ -201,3 +201,5 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po
return 0;
}
+}
+
diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h
index ce4dfca2c0..e43ced9fd5 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.h
+++ b/src/USER-PTM/ptm_neighbour_ordering.h
@@ -1,6 +1,8 @@
#ifndef PTM_NEIGHBOUR_ORDERING_H
#define PTM_NEIGHBOUR_ORDERING_H
+namespace ptm {
+
int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
@@ -9,5 +11,7 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po
void* voronoi_initialize_local();
void voronoi_uninitialize_local(void* ptr);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp
index 61dca5006f..22e3c1e670 100644
--- a/src/USER-PTM/ptm_normalize_vertices.cpp
+++ b/src/USER-PTM/ptm_normalize_vertices.cpp
@@ -1,5 +1,6 @@
#include <cmath>
+namespace ptm {
void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
{
@@ -53,3 +54,5 @@ double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
return scale;
}
+}
+
diff --git a/src/USER-PTM/ptm_normalize_vertices.h b/src/USER-PTM/ptm_normalize_vertices.h
index 2c7b722752..dc93db94a3 100644
--- a/src/USER-PTM/ptm_normalize_vertices.h
+++ b/src/USER-PTM/ptm_normalize_vertices.h
@@ -1,8 +1,12 @@
#ifndef PTM_NORMALIZE_VERTICES_H
#define PTM_NORMALIZE_VERTICES_H
+namespace ptm {
+
void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp
index 9089b327b9..fa199ca656 100644
--- a/src/USER-PTM/ptm_polar.cpp
+++ b/src/USER-PTM/ptm_polar.cpp
@@ -91,6 +91,8 @@
#include "ptm_quat.h"
+namespace ptm {
+
static void matmul_3x3(double* A, double* x, double* b)
{
b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
@@ -335,3 +337,5 @@ int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q,
return 0;
}
+}
+
diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h
index d5aa3d9540..15d1f185b7 100644
--- a/src/USER-PTM/ptm_polar.h
+++ b/src/USER-PTM/ptm_polar.h
@@ -4,9 +4,13 @@
#include <stdint.h>
#include <stdbool.h>
+namespace ptm {
+
int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp
index f55aff3d2b..376cc74901 100644
--- a/src/USER-PTM/ptm_quat.cpp
+++ b/src/USER-PTM/ptm_quat.cpp
@@ -3,6 +3,8 @@
#include <cfloat>
+namespace ptm {
+
#define SIGN(x) (x >= 0 ? 1 : -1)
#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
@@ -394,3 +396,5 @@ double quat_disorientation_icosahedral(double* q0, double* q1)
return acos(quat_quick_disorientation_icosahedral(q0, q1));
}
+}
+
diff --git a/src/USER-PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h
index 381c3ce876..74caa2c62c 100644
--- a/src/USER-PTM/ptm_quat.h
+++ b/src/USER-PTM/ptm_quat.h
@@ -1,6 +1,8 @@
#ifndef PTM_QUAT_H
#define PTM_QUAT_H
+namespace ptm {
+
int rotate_quaternion_into_cubic_fundamental_zone(double* q);
int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
@@ -25,8 +27,7 @@ double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
double quat_quick_disorientation_icosahedral(double* q0, double* q1);
double quat_disorientation_icosahedral(double* q0, double* q1);
-#endif
-
-
+}
+#endif
diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp
index 7eb0a44143..a86b3670ce 100644
--- a/src/USER-PTM/ptm_structure_matcher.cpp
+++ b/src/USER-PTM/ptm_structure_matcher.cpp
@@ -15,6 +15,8 @@
#include "ptm_constants.h"
+namespace ptm {
+
static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
double G1, double G2, double E0, double* q, double* p_scale)
{
@@ -292,3 +294,5 @@ int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags,
return PTM_NO_ERROR;
}
+}
+
diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h
index 4b6f969597..ffaed78e82 100644
--- a/src/USER-PTM/ptm_structure_matcher.h
+++ b/src/USER-PTM/ptm_structure_matcher.h
@@ -4,6 +4,9 @@
#include "ptm_initialize_data.h"
#include "ptm_constants.h"
+
+namespace ptm {
+
typedef struct
{
double rmsd;
@@ -17,5 +20,7 @@ int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3
int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
index 6503ea16c6..ffd7a95ea2 100644
--- a/src/USER-PTM/ptm_voronoi_cell.cpp
+++ b/src/USER-PTM/ptm_voronoi_cell.cpp
@@ -15,7 +15,7 @@
#include "ptm_voronoi_config.h"
#include "ptm_voronoi_cell.h"
-namespace voro {
+namespace ptm_voro {
inline void voro_fatal_error(const char *p,int status) {
fprintf(stderr,"voro++: %s\n",p);
diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h
index 80a0501b3c..e0284bc56f 100644
--- a/src/USER-PTM/ptm_voronoi_cell.h
+++ b/src/USER-PTM/ptm_voronoi_cell.h
@@ -17,7 +17,7 @@
#include "ptm_voronoi_config.h"
-namespace voro {
+namespace ptm_voro {
/** \brief A class representing a single Voronoi cell.
*
diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h
index 86257e60cc..46c5a4b915 100644
--- a/src/USER-PTM/ptm_voronoi_config.h
+++ b/src/USER-PTM/ptm_voronoi_config.h
@@ -12,7 +12,7 @@
#ifndef PTM_VOROPP_CONFIG_HH
#define PTM_VOROPP_CONFIG_HH
-namespace voro {
+namespace ptm_voro {
// These constants set the initial memory allocation for the Voronoi cell
/** The initial memory allocation for the number of vertices. */
--
GitLab
From 36c5fb2ec62554996193c6351449feba4e230b33 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 24 Sep 2018 10:33:26 -0400
Subject: [PATCH 278/332] update formatting
---
doc/src/pair_coul_shield.txt | 3 ++-
doc/src/pair_ilp_graphene_hbn.txt | 22 +++++++++++++---------
doc/src/pair_kolmogorov_crespi_full.txt | 22 ++++++++++++----------
3 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 8b88d07ece..df04e76de9 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -38,7 +38,8 @@ charge and molecule ID information is included.
Where Tap(r_ij) is the taper function which provides a continuous cutoff
(up to third derivative) for inter-atomic separations larger than r_c
-"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
+"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1.
+Here {lambda} is the shielding parameter that
eliminates the short-range singularity of the classical mono-polar
electrostatic interaction expression "(Maaravi)"_#Maaravi1.
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index b7d1c2cdb1..f048b16ccf 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -25,14 +25,15 @@ pair_coeff * * rebo CH.airebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
-pair_coeff 1 2 coul/shield 0.69498201415576216335
+pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69 :pre
[Description:]
The {ilp/graphene/hbn} style computes the registry-dependent interlayer
-potential (ILP) potential as described in "(Leven1)"_#Leven1, "(Leven2)"_#Leven2 and
-"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
+potential (ILP) potential as described in "(Leven1)"_#Leven1,
+"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2.
+The normals are calculated in the way as described
in "(Kolmogorov)"_#Kolmogorov2.
:c,image(Eqs/pair_ilp_graphene_hbn.jpg)
@@ -62,12 +63,15 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
-NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials are presented in "(Ouyang)"_#Ouyang.
-These parameters provide a good description in both short- and long-range interaction regimes.
-While the old ILP parameters published in "(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2 are
-only suitable for long-range interaction regime. This feature is essential for simulations
-in high pressure regime (i.e., the interlayer distance is smaller than the equilibrium distance).
-The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang.
+NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
+Materials are presented in "(Ouyang)"_#Ouyang. These parameters provide
+a good description in both short- and long-range interaction regimes.
+While the old ILP parameters published in "(Leven2)"_#Leven2 and
+"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction
+regime. This feature is essential for simulations in high pressure
+regime (i.e., the interlayer distance is smaller than the equilibrium
+distance). The benchmark tests and comparison of these parameters can
+be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 1fe87dd7ee..df9a9696be 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -53,15 +53,17 @@ and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
-NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC (without the taper function)
-and CH_taper.KC (with the taper function) are presented in "(Ouyang)"_#Ouyang1.
-The energy for the KC potential with the taper function goes continuously to zero at the cutoff.
-The parameters in both CH.KC and CH_taper.KC provide a good description in
-both short- and long-range interaction regimes. While the original parameters (CC.KC)
-published in "(Kolmogorov)"_#Kolmogorov1 are only suitable for long-range interaction regime.
-This feature is essential for simulations in high pressure regime
-(i.e., the interlayer distance is smaller than the equilibrium distance).
-The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
+NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC
+(without the taper function) and CH_taper.KC (with the taper function)
+are presented in "(Ouyang)"_#Ouyang1. The energy for the KC potential
+with the taper function goes continuously to zero at the cutoff. The
+parameters in both CH.KC and CH_taper.KC provide a good description in
+both short- and long-range interaction regimes. While the original
+parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only
+suitable for long-range interaction regime. This feature is essential
+for simulations in high pressure regime (i.e., the interlayer distance
+is smaller than the equilibrium distance). The benchmark tests and
+comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
@@ -109,4 +111,4 @@ units.
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
:link(Ouyang1)
-[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
\ No newline at end of file
+[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
--
GitLab
From aefdcd0f94820a2f41bee0df44bfaeaf0ce5ce43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Tue, 25 Sep 2018 11:14:42 +0200
Subject: [PATCH 279/332] Silence some warnings
---
src/USER-MEAMC/meam_dens_init.cpp | 5 ++---
src/USER-MEAMC/meam_funcs.cpp | 2 +-
src/USER-MEAMC/pair_meamc.cpp | 9 +++++----
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index 4bbaa42596..0aa71125c8 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -101,7 +101,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
double xjtmp, yjtmp, zjtmp, delxik, delyik, delzik, rik2 /*,rik*/;
double xktmp, yktmp, zktmp, delxjk, delyjk, delzjk, rjk2 /*,rjk*/;
double xik, xjk, sij, fcij, sfcij, dfcij, sikj, dfikj, cikj;
- double Cmin, Cmax, delc, /*ebound,*/ rbound, a, coef1, coef2;
+ double Cmin, Cmax, delc, /*ebound,*/ a, coef1, coef2;
double dCikj;
double rnorm, fc, dfc, drinv;
@@ -129,6 +129,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
rij2 = delxij * delxij + delyij * delyij + delzij * delzij;
rij = sqrt(rij2);
+ const double rbound = this->ebound_meam[elti][eltj] * rij2;
if (rij > this->rc_meam) {
fcij = 0.0;
dfcij = 0.0;
@@ -138,7 +139,6 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
sij = 1.0;
// if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse
- const double rbound = this->ebound_meam[elti][eltj] * rij2;
for (kn = 0; kn < numneigh_full; kn++) {
k = firstneigh_full[kn];
eltk = fmap[type[k]];
@@ -193,7 +193,6 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
if (iszero(sfcij) || iszero(sfcij - 1.0))
goto LABEL_100;
- rbound = this->ebound_meam[elti][eltj] * rij2;
for (kn = 0; kn < numneigh_full; kn++) {
k = firstneigh_full[kn];
if (k == j) continue;
diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp
index 29db27fc4b..1d47dcc1f6 100644
--- a/src/USER-MEAMC/meam_funcs.cpp
+++ b/src/USER-MEAMC/meam_funcs.cpp
@@ -87,7 +87,7 @@ MEAM::dG_gam(const double gamma, const int ibar, double& dG) const
// e.g. gsmooth_factor is 99, {:
// gsmooth_switchpoint = -0.99
// G = 0.01*(-0.99/gamma)**99
- double G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor);
+ G = 1 / (gsmooth_factor + 1) * pow((gsmooth_switchpoint / gamma), gsmooth_factor);
G = sqrt(G);
dG = -gsmooth_factor * G / (2.0 * gamma);
return G;
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index ff2a1180b5..b74416a46d 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -206,7 +206,7 @@ void PairMEAMC::settings(int narg, char **/*arg*/)
void PairMEAMC::coeff(int narg, char **arg)
{
- int i,j,m,n;
+ int m,n;
if (!allocated) allocate();
@@ -222,7 +222,7 @@ void PairMEAMC::coeff(int narg, char **arg)
// elements = list of unique element names
if (nelements) {
- for (i = 0; i < nelements; i++) delete [] elements[i];
+ for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
}
@@ -231,7 +231,7 @@ void PairMEAMC::coeff(int narg, char **arg)
elements = new char*[nelements];
mass = new double[nelements];
- for (i = 0; i < nelements; i++) {
+ for (int i = 0; i < nelements; i++) {
n = strlen(arg[i+3]) + 1;
elements[i] = new char[n];
strcpy(elements[i],arg[i+3]);
@@ -247,8 +247,9 @@ void PairMEAMC::coeff(int narg, char **arg)
// read args that map atom types to MEAM elements
// map[i] = which element the Ith atom type is, -1 if not mapped
- for (i = 4 + nelements; i < narg; i++) {
+ for (int i = 4 + nelements; i < narg; i++) {
m = i - (4+nelements) + 1;
+ int j;
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
if (j < nelements) map[m] = j;
--
GitLab
From e5ddc909adc491cfb52fe4d7a8d78979918da22b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= <sebastian.huetter@ovgu.de>
Date: Tue, 25 Sep 2018 14:19:26 +0200
Subject: [PATCH 280/332] Fully zero-init MEAM data structure
---
src/USER-MEAMC/meam_impl.cpp | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp
index 25c53785e4..d4a47a4f48 100644
--- a/src/USER-MEAMC/meam_impl.cpp
+++ b/src/USER-MEAMC/meam_impl.cpp
@@ -34,6 +34,19 @@ MEAM::MEAM(Memory* mem)
maxneigh = 0;
scrfcn = dscrfcn = fcpair = NULL;
+
+ neltypes = 0;
+ for (int i = 0; i < maxelt; i++) {
+ Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] =
+ beta1_meam[i]= beta2_meam[i] = beta3_meam[i] =
+ t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] =
+ rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0;
+ for (int j = 0; j < maxelt; j++) {
+ lattce_meam[i][j] = FCC;
+ Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0;
+ nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0;
+ }
+ }
}
MEAM::~MEAM()
--
GitLab
From 93e56c113af8b274ea4504a9e3b284058498b5de Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 25 Sep 2018 09:18:11 -0400
Subject: [PATCH 281/332] add USER-PTM to build system
---
cmake/CMakeLists.txt | 13 +++++++------
src/Makefile | 2 +-
2 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index ce8de0b501..610fb5b57c 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -164,12 +164,13 @@ set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
- SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
- USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
- USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
- USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS
- USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+ KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+ SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
+ USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
+ USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
+ USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
+ USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
+ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
diff --git a/src/Makefile b/src/Makefile
index 2ee7885562..eefc64b274 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -61,7 +61,7 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
user-mgpt user-misc user-mofff user-molfile \
- user-netcdf user-omp user-phonon user-qmmm user-qtb \
+ user-netcdf user-omp user-phonon user-ptm user-qmmm user-qtb \
user-quip user-reaxc user-scafacos user-smd user-smtbq \
user-sph user-tally user-uef user-vtk
--
GitLab
From 37fe03c0ab7905e11cf3b8ed9dcb4fb0b42d074d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 25 Sep 2018 09:19:09 -0400
Subject: [PATCH 282/332] escape backslash in bibtex string for correct citeme
output
---
src/USER-PTM/compute_ptm_atom.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp
index b6b4a9786c..eb0138de26 100644
--- a/src/USER-PTM/compute_ptm_atom.cpp
+++ b/src/USER-PTM/compute_ptm_atom.cpp
@@ -46,7 +46,7 @@ using namespace LAMMPS_NS;
static const char cite_user_ptm_package[] =
"USER-PTM package:\n\n"
"@Article{larsen2016ptm,\n"
- " author={Larsen, Peter Mahler and Schmidt, S{\o}ren and Schi{\o}tz, "
+ " author={Larsen, Peter Mahler and Schmidt, S{\\o}ren and Schi{\\o}tz, "
"Jakob},\n"
" title={Robust structural identification via polyhedral template "
"matching},\n"
--
GitLab
From 5a6226caa5a4b6c347733b5d67ad33f33baf8bc7 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 25 Sep 2018 10:50:43 -0600
Subject: [PATCH 283/332] jive src headers with doc page entries and example
scripts
---
....txt => compute_smd_triangle_vertices.txt} | 6 +-
doc/src/compute_spin.txt | 13 ++---
doc/src/fix_msst.txt | 2 +-
doc/src/fix_nve_awpmd.txt | 56 +++++++++++++++++++
doc/src/fix_poems.txt | 2 +-
doc/src/pair_body_nparticle.txt | 2 +-
doc/src/pair_buck6d_coul_gauss.txt | 4 +-
doc/src/pair_lj_expand.txt | 23 ++++++--
doc/src/pair_meam_spline.txt | 4 +-
doc/src/pair_meam_sw_spline.txt | 4 +-
doc/src/pair_sdk.txt | 14 +++--
doc/src/pair_spin_magelec.txt | 8 +--
doc/src/pair_spin_neel.txt | 36 ++++++------
examples/SPIN/bfo/in.spin.bfo | 2 +-
examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc | 2 +-
examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp | 2 +-
examples/SPIN/iron/in.spin.iron | 2 +-
examples/SPIN/nickel/in.spin.nickel | 2 +-
examples/SPIN/read_restart/in.spin.read_data | 2 +-
examples/SPIN/read_restart/in.spin.restart | 2 +-
.../SPIN/read_restart/in.spin.write_restart | 2 +-
.../fluid_structure_interaction.lmp | 2 +-
src/PYTHON/fix_python_invoke.h | 2 +-
src/SPIN/compute_spin.h | 2 +-
src/SPIN/pair_spin.h | 7 ---
....cpp => compute_smd_triangle_vertices.cpp} | 0
...ices.h => compute_smd_triangle_vertices.h} | 0
src/USER-SMD/compute_smd_vol.h | 2 +-
src/USER-SMD/fix_smd_setvel.h | 6 +-
29 files changed, 140 insertions(+), 71 deletions(-)
rename doc/src/{compute_smd_triangle_mesh_vertices.txt => compute_smd_triangle_vertices.txt} (91%)
create mode 100644 doc/src/fix_nve_awpmd.txt
rename src/USER-SMD/{compute_smd_triangle_mesh_vertices.cpp => compute_smd_triangle_vertices.cpp} (100%)
rename src/USER-SMD/{compute_smd_triangle_mesh_vertices.h => compute_smd_triangle_vertices.h} (100%)
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_vertices.txt
similarity index 91%
rename from doc/src/compute_smd_triangle_mesh_vertices.txt
rename to doc/src/compute_smd_triangle_vertices.txt
index cd1f8fdd9b..487b1b590b 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_vertices.txt
@@ -6,14 +6,14 @@
:line
-compute smd/triangle/mesh/vertices :h3
+compute smd/triangle/vertices command :h3
[Syntax:]
-compute ID group-ID smd/triangle/mesh/vertices :pre
+compute ID group-ID smd/triangle/vertices :pre
ID, group-ID are documented in "compute"_compute.html command
-smd/triangle/mesh/vertices = style name of this compute command :ul
+smd/triangle/vertices = style name of this compute command :ul
[Examples:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index e6185a2dd8..4edecc2408 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -10,14 +10,14 @@ compute spin command :h3
[Syntax:]
-compute ID group-ID compute/spin :pre
+compute ID group-ID spin :pre
ID, group-ID are documented in "compute"_compute.html command
-compute/spin = style name of this compute command :ul
+spin = style name of this compute command :ul
[Examples:]
-compute out_mag all compute/spin :pre
+compute out_mag all spin :pre
[Description:]
@@ -26,7 +26,8 @@ of atoms having spins.
This compute calculates 6 magnetic quantities.
-The three first quantities are the x,y and z coordinates of the total magnetization.
+The three first quantities are the x,y and z coordinates of the total
+magnetization.
The fourth quantity is the norm of the total magnetization.
@@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation
is to define some of the quantities as variables, and to use the thermo and
thermo_style commands, for example:
-compute out_mag all compute/spin :pre
+compute out_mag all spin :pre
variable mag_z equal c_out_mag\[3\]
variable mag_norm equal c_out_mag\[4\]
@@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
-
[Output info:]
The array values are "intensive". The array values will be in
@@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid.
[Related commands:] none
-
[Default:] none
:line
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index e31f61e5f7..7f0e5512ae 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -6,7 +6,7 @@
:line
- fix msst command :h3
+fix msst command :h3
[Syntax:]
diff --git a/doc/src/fix_nve_awpmd.txt b/doc/src/fix_nve_awpmd.txt
new file mode 100644
index 0000000000..c266d46eee
--- /dev/null
+++ b/doc/src/fix_nve_awpmd.txt
@@ -0,0 +1,56 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix nve/awpmd command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/awpmd :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nve/awpmd = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nve/awpmd :pre
+
+[Description:]
+
+Perform constant NVE integration to update position and velocity for
+nuclei and electrons in the group for the "Antisymmetrized Wave Packet
+Molecular Dynamics"_pair_awpmd.html model. V is volume; E is energy.
+This creates a system trajectory consistent with the microcanonical
+ensemble.
+
+The operation of this fix is exactly like that described by the "fix
+nve"_fix_nve.html command, except that the width and width-velocity of
+the electron wavefunctions are also updated.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-AWPMD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html
+
+[Default:] none
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 52ab0ca44d..8fe793ce7f 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -6,7 +6,7 @@
:line
-fix poems :h3
+fix poems command :h3
Syntax:
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 158eb68ca8..7d841119ca 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -6,7 +6,7 @@
:line
-pair_style body command :h3
+pair_style body/nparticle command :h3
[Syntax:]
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index d9780e0320..21de3330f4 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -6,8 +6,8 @@
:line
-pair_style buck6d/coul/gauss/dsf :h3
-pair_style buck6d/coul/gauss/long :h3
+pair_style buck6d/coul/gauss/dsf command :h3
+pair_style buck6d/coul/gauss/long command :h3
[Syntax:]
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index d26c88e4f7..f37cb0fb83 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -9,6 +9,8 @@
pair_style lj/expand command :h3
pair_style lj/expand/gpu command :h3
pair_style lj/expand/omp command :h3
+pair_style lj/expand/coul/long command :h3
+pair_style lj/expand/coul/long/gpu command :h3
[Syntax:]
@@ -22,6 +24,11 @@ pair_style lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre
+pair_style lj/expand/coul/long 2.5
+pair_style lj/expand/coul/long 2.5 4.0
+pair_coeff * * 1.0 1.0 0.5
+pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre
+
[Description:]
Style {lj/expand} computes a LJ interaction with a distance shifted by
@@ -34,11 +41,12 @@ formula:
Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands, or by mixing as described below:
+For all of the {lj/expand} pair styles, the following coefficients must
+be defined for each pair of atoms types via the
+"pair_coeff"_pair_coeff.html command as in the examples above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands, or by mixing as
+described below:
epsilon (energy units)
sigma (distance units)
@@ -48,6 +56,11 @@ cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
+For {lj/expand/coul/long} only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index df5db81264..74adba2432 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -6,8 +6,8 @@
:line
-pair_style meam/spline :h3
-pair_style meam/spline/omp :h3
+pair_style meam/spline command :h3
+pair_style meam/spline/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index 2e8c26658a..8281315031 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -6,8 +6,8 @@
:line
-pair_style meam/sw/spline :h3
-pair_style meam/sw/spline/omp :h3
+pair_style meam/sw/spline command :h3
+pair_style meam/sw/spline/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index b977aefe88..06a0a42d5a 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -13,6 +13,8 @@ pair_style lj/sdk/omp command :h3
pair_style lj/sdk/coul/long command :h3
pair_style lj/sdk/coul/long/gpu command :h3
pair_style lj/sdk/coul/long/omp command :h3
+pair_style lj/sdk/coul/msm command :h3
+pair_style lj/sdk/coul/msm/omp command :h3
[Syntax:]
@@ -35,6 +37,10 @@ pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
+pair_style lj/sdk/coul/msm 10.0
+pair_style lj/sdk/coul/msm 10.0 12.0
+pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
+
[Description:]
The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
@@ -75,10 +81,10 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
-For {lj/sdk/coul/long} only the LJ cutoff can be specified since a
-Coulombic cutoff cannot be specified for an individual I,J type pair.
-All type pairs use the same global Coulombic cutoff specified in the
-pair_style command.
+For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff can be
+specified since a Coulombic cutoff cannot be specified for an
+individual I,J type pair. All type pairs use the same global
+Coulombic cutoff specified in the pair_style command.
:line
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index f552c56a4b..360f440792 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -6,11 +6,11 @@
:line
-pair_style spin/me command :h3
+pair_style spin/magelec command :h3
[Syntax:]
-pair_style spin/me cutoff :pre
+pair_style spin/magelec cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
@@ -18,8 +18,8 @@ cutoff = global cutoff pair (distance in metal units) :ulb,l
[Examples:]
-pair_style spin/me 4.5
-pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
+pair_style spin/magelec 4.5
+pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre
[Description:]
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index fe3bb1ad14..7af71021a0 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -29,34 +29,36 @@ between pairs of magnetic spins:
:c,image(Eqs/pair_spin_neel_interaction.jpg)
-where si and sj are two neighboring magnetic spins of two particles,
+where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
-eij = (ri - rj)/|ri-rj| is their normalized separation vector
-and g1, q1 and q2 are three functions defining the intensity of the
-dipolar and quadrupolar contributions, with:
+eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
+q1 and q2 are three functions defining the intensity of the dipolar
+and quadrupolar contributions, with:
:c,image(Eqs/pair_spin_neel_functions.jpg)
-With the functions g(rij) and q(rij) defined and fitted according to the same
-Bethe-Slater function used to fit the exchange interaction:
+With the functions g(rij) and q(rij) defined and fitted according to
+the same Bethe-Slater function used to fit the exchange interaction:
:c,image(Eqs/pair_spin_exchange_function.jpg)
-where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command.
+where a, b and d are the three constant coefficients defined in the
+associated "pair_coeff" command.
-The coefficients a, b, and d need to be fitted so that the function above matches with
-the values of the magneto-elastic constant of the materials at stake.
+The coefficients a, b, and d need to be fitted so that the function
+above matches with the values of the magneto-elastic constant of the
+materials at stake.
-Examples and more explanations about this function and its parametrization are reported
-in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in
-future work.
+Examples and more explanations about this function and its
+parametrization are reported in "(Tranchida)"_#Tranchida6. More
+examples of parametrization will be provided in future work.
-From this DM interaction, each spin i will be submitted to a magnetic torque
-omega and its associated atom to a force F (for spin-lattice calculations only).
+From this DM interaction, each spin i will be submitted to a magnetic
+torque omega and its associated atom to a force F (for spin-lattice
+calculations only).
-More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida6.
+More details about the derivation of these torques/forces are reported
+in "(Tranchida)"_#Tranchida6.
:line
diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo
index de23ba87ba..e3c88b0f06 100644
--- a/examples/SPIN/bfo/in.spin.bfo
+++ b/examples/SPIN/bfo/in.spin.bfo
@@ -36,7 +36,7 @@ fix 3 all nve/spin lattice no
timestep 0.0002
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
index fd6833727b..ea98eeba94 100644
--- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
+++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc
@@ -40,7 +40,7 @@ timestep 0.0001
# compute and output options
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
index 35aa1df86c..3ff0b1cadf 100644
--- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
+++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp
@@ -40,7 +40,7 @@ fix 3 all nve/spin lattice yes
timestep 0.0001
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron
index c2d5082cb6..1db5007dff 100644
--- a/examples/SPIN/iron/in.spin.iron
+++ b/examples/SPIN/iron/in.spin.iron
@@ -37,7 +37,7 @@ timestep 0.0001
# compute and output options
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel
index ba447b077f..0ed2fac410 100644
--- a/examples/SPIN/nickel/in.spin.nickel
+++ b/examples/SPIN/nickel/in.spin.nickel
@@ -38,7 +38,7 @@ timestep 0.0001
# compute and output options
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data
index 80de036661..17343994b5 100644
--- a/examples/SPIN/read_restart/in.spin.read_data
+++ b/examples/SPIN/read_restart/in.spin.read_data
@@ -25,7 +25,7 @@ timestep 0.0001
# define outputs and computes
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart
index a1198ccf93..39157fdac4 100644
--- a/examples/SPIN/read_restart/in.spin.restart
+++ b/examples/SPIN/read_restart/in.spin.restart
@@ -29,7 +29,7 @@ timestep 0.0001
# define outputs
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart
index 84fea24611..42f07fd316 100644
--- a/examples/SPIN/read_restart/in.spin.write_restart
+++ b/examples/SPIN/read_restart/in.spin.write_restart
@@ -34,7 +34,7 @@ timestep 0.0001
# compute and output options
-compute out_mag all compute/spin
+compute out_mag all spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
diff --git a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
index 5100a52d84..0f7d726e21 100644
--- a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
+++ b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
@@ -129,7 +129,7 @@ compute contact_radius all smd/contact/radius
compute S solids smd/tlsph/stress
compute nn water smd/ulsph/num/neighs
compute epl solids smd/plastic/strain
-compute vol all smd/volume
+compute vol all smd/vol
compute rho all smd/rho
dump dump_id all custom 100 dump.LAMMPS id type x y &
diff --git a/src/PYTHON/fix_python_invoke.h b/src/PYTHON/fix_python_invoke.h
index c277e295a1..89310eeded 100644
--- a/src/PYTHON/fix_python_invoke.h
+++ b/src/PYTHON/fix_python_invoke.h
@@ -13,8 +13,8 @@
#ifdef FIX_CLASS
-FixStyle(python,FixPythonInvoke)
FixStyle(python/invoke,FixPythonInvoke)
+FixStyle(python,FixPythonInvoke)
#else
diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h
index b57876b7a0..c5d55b84cb 100644
--- a/src/SPIN/compute_spin.h
+++ b/src/SPIN/compute_spin.h
@@ -13,7 +13,7 @@
#ifdef COMPUTE_CLASS
-ComputeStyle(compute/spin,ComputeSpin)
+ComputeStyle(spin,ComputeSpin)
#else
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
index 100eec1732..1be8550c65 100644
--- a/src/SPIN/pair_spin.h
+++ b/src/SPIN/pair_spin.h
@@ -11,12 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef PAIR_CLASS
-
-PairStyle(pair/spin,PairSpin)
-
-#else
-
#ifndef LMP_PAIR_SPIN_H
#define LMP_PAIR_SPIN_H
@@ -46,7 +40,6 @@ friend class FixNVESpin;
}
-#endif
#endif
/* ERROR/WARNING messages:
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp
similarity index 100%
rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
rename to src/USER-SMD/compute_smd_triangle_vertices.cpp
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_vertices.h
similarity index 100%
rename from src/USER-SMD/compute_smd_triangle_mesh_vertices.h
rename to src/USER-SMD/compute_smd_triangle_vertices.h
diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h
index 5525ce57cb..08ad150627 100644
--- a/src/USER-SMD/compute_smd_vol.h
+++ b/src/USER-SMD/compute_smd_vol.h
@@ -25,7 +25,7 @@
#ifdef COMPUTE_CLASS
-ComputeStyle(smd/volume,ComputeSMDVol)
+ComputeStyle(smd/vol,ComputeSMDVol)
#else
diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h
index a3e650e682..f5fc34b4ea 100644
--- a/src/USER-SMD/fix_smd_setvel.h
+++ b/src/USER-SMD/fix_smd_setvel.h
@@ -24,12 +24,12 @@
#ifdef FIX_CLASS
-FixStyle(smd/setvelocity,FixSMDSetVel)
+FixStyle(smd/setvel,FixSMDSetVel)
#else
-#ifndef LMP_FIX_SMD_SET_VELOCITY_H
-#define LMP_FIX_SMD_SET_VELOCITY_H
+#ifndef LMP_FIX_SMD_SETVEL_H
+#define LMP_FIX_SMD_SETVEL_H
#include "fix.h"
--
GitLab
From a9b8a6521d15cbcf97fff4348ff15b1266f17178 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Tue, 25 Sep 2018 13:18:54 -0600
Subject: [PATCH 284/332] more mis-matches between doc pages and src files
---
doc/src/Commands_bond.txt | 2 +-
doc/src/Commands_fix.txt | 2 +-
doc/src/Commands_pair.txt | 2 +-
doc/src/angle_sdk.txt | 25 ++++++++++++++++++++++++
doc/src/fix_property_atom.txt | 24 +++++++++++++++++++++++
doc/src/fix_surface_global.txt | 19 ------------------
doc/src/fix_wall_gran.txt | 23 ++++++++++++++++++++++
doc/src/pair_born.txt | 19 ++----------------
doc/src/pair_buck.txt | 14 +++-----------
doc/src/pair_charmm.txt | 3 +++
doc/src/pair_cs.txt | 34 +++++++++++++++++++++++++++++++++
doc/src/pair_dipole.txt | 1 +
doc/src/pair_edip.txt | 1 +
doc/src/pair_gran.txt | 2 +-
doc/src/pair_gromacs.txt | 2 ++
doc/src/pair_hybrid.txt | 3 +--
doc/src/pair_lj.txt | 2 ++
doc/src/pair_lj_expand.txt | 1 +
doc/src/pair_lj_long.txt | 1 +
doc/src/pair_meam_sw_spline.txt | 1 -
doc/src/pair_tersoff.txt | 8 ++++----
21 files changed, 131 insertions(+), 58 deletions(-)
delete mode 100644 doc/src/fix_surface_global.txt
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 0cf433d53a..773202f126 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -70,7 +70,7 @@ OPT.
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html,
+"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index e002c11770..838bcbe7a6 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -216,7 +216,7 @@ OPT.
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
+"wall/gran (o)"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 33890df1fe..3b6a5f48fa 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -26,7 +26,7 @@ OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
+"hybrid (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
"adp (o)"_pair_adp.html,
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 4de1a6755d..22238880fe 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -7,6 +7,7 @@
:line
angle_style sdk command :h3
+angle_style sdk/omp command :h3
[Syntax:]
@@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
The also required {lj/sdk} parameters will be extracted automatically
from the pair_style.
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 8a70cd8213..19e3b0ca40 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -7,6 +7,7 @@
:line
fix property/atom command :h3
+fix property/atom/kk command :h3
[Syntax:]
@@ -201,6 +202,7 @@ added classes.
:line
:link(isotopes)
+
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
@@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
:line
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
deleted file mode 100644
index 2ee045141a..0000000000
--- a/doc/src/fix_surface_global.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-fix wall/surface/global command :h3
-
-[Description:]
-
-This feature is not yet implemented.
-
-[Related commands:]
-
-"dump image"_dump_image.html
-
-
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 0ea5b194eb..871ee2e5d1 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -7,6 +7,7 @@
:line
fix wall/gran command :h3
+fix wall/gran/omp command :h3
[Syntax:]
@@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index 195d3e6669..9cbfcffea0 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -11,19 +11,14 @@ pair_style born command :h3
pair_style born/omp command :h3
pair_style born/gpu command :h3
pair_style born/coul/long command :h3
-pair_style born/coul/long/cs command :h3
-pair_style born/coul/long/cs/gpu command :h3
pair_style born/coul/long/gpu command :h3
pair_style born/coul/long/omp command :h3
pair_style born/coul/msm command :h3
pair_style born/coul/msm/omp command :h3
pair_style born/coul/wolf command :h3
-pair_style born/coul/wolf/cs command :h3
-pair_style born/coul/wolf/cs/gpu command :h3
pair_style born/coul/wolf/gpu command :h3
pair_style born/coul/wolf/omp command :h3
pair_style born/coul/dsf command :h3
-pair_style born/coul/dsf/cs command :h3
[Syntax:]
@@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
+pair_style born/coul/long 10.0 8.
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
-pair_style born/coul/wolf/cs 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
@@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
-Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-The same correction is introduced for the {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}. And likewise for
-{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
-
Note that these potentials are related to the "Buckingham
potential"_pair_buck.html.
@@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
The {born/coul/long} pair style supports the
-"pair_modify"_pair_modify.html table option ti tabulate the
+"pair_modify"_pair_modify.html table option to tabulate the
short-range portion of the long-range Coulombic interaction.
These styles support the pair_modify tail option for adding long-range
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index 5b1688e868..ec83e6b339 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
pair_style buck/coul/cut/kk command :h3
pair_style buck/coul/cut/omp command :h3
pair_style buck/coul/long command :h3
-pair_style buck/coul/long/cs command :h3
pair_style buck/coul/long/gpu command :h3
pair_style buck/coul/long/intel command :h3
pair_style buck/coul/long/kk command :h3
@@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
pair_style style args :pre
-style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
+style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
args = list of arguments for a particular style :ul
{buck} args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
{buck/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
- {buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
+ {buck/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/msm} args = cutoff (cutoff2)
@@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
@@ -92,10 +89,6 @@ A,C and Coulombic terms. If two cutoffs are specified, the first is
used as the cutoff for the A,C terms, and the second is the cutoff for
the Coulombic term.
-Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
@@ -184,8 +177,7 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
-The {buck/coul/long} style is part of the KSPACE package. The
-{buck/coul/long/cs} style is part of the CORESHELL package. They are
+The {buck/coul/long} style is part of the KSPACE package. They are
only enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index dfc87e1bce..131e289227 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -8,12 +8,15 @@
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/intel command :h3
+pair_style lj/charmm/coul/charmm/kk command :h3
pair_style lj/charmm/coul/charmm/omp command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
+pair_style lj/charmm/coul/charmm/implicit/kk command :h3
pair_style lj/charmm/coul/charmm/implicit/omp command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/intel command :h3
+pair_style lj/charmm/coul/long/kk command :h3
pair_style lj/charmm/coul/long/opt command :h3
pair_style lj/charmm/coul/long/omp command :h3
pair_style lj/charmm/coul/msm command :h3
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 8bd4abed68..faaea42f15 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -7,9 +7,11 @@
:line
pair_style born/coul/long/cs command :h3
+pair_style born/coul/long/cs/gpu command :h3
pair_style buck/coul/long/cs command :h3
pair_style born/coul/dsf/cs command :h3
pair_style born/coul/wolf/cs command :h3
+pair_style born/coul/wolf/cs/gpu command :h3
[Syntax:]
@@ -97,6 +99,38 @@ a long-range solver, thus the only correction is the addition of a
minimal distance to avoid the possible r = 0.0 case for a
core/shell pair.
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page. The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+See the corresponding doc pages for pair styles without the "cs"
+suffix to see how mixing, shifting, tabulation, tail correction,
+restarting, and rRESPA are handled by theses pair styles.
+
+:line
+
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index dcb2448949..bdf37983b6 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
pair_style lj/sf/dipole/sf/gpu command :h3
pair_style lj/sf/dipole/sf/omp command :h3
pair_style lj/cut/dipole/long command :h3
+pair_style lj/cut/dipole/long/gpu command :h3
pair_style lj/long/dipole/long command :h3
[Syntax:]
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index 053d43b2ba..e0e8fbb27e 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -7,6 +7,7 @@
:line
pair_style edip command :h3
+pair_style edip/omp command :h3
pair_style edip/multi command :h3
[Syntax:]
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index e06d410084..5beaf30e06 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -7,7 +7,7 @@
:line
pair_style gran/hooke command :h3
-pair_style gran/omp command :h3
+pair_style gran/hooke/omp command :h3
pair_style gran/hooke/history command :h3
pair_style gran/hooke/history/omp command :h3
pair_style gran/hertz/history command :h3
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 6a36a036c9..e50a21588c 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -8,8 +8,10 @@
pair_style lj/gromacs command :h3
pair_style lj/gromacs/gpu command :h3
+pair_style lj/gromacs/kk command :h3
pair_style lj/gromacs/omp command :h3
pair_style lj/gromacs/coul/gromacs command :h3
+pair_style lj/gromacs/coul/gromacs/kk command :h3
pair_style lj/gromacs/coul/gromacs/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 6e68e820a8..97a5972bfb 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -7,9 +7,8 @@
:line
pair_style hybrid command :h3
-pair_style hybrid/omp command :h3
+pair_style hybrid/kk command :h3
pair_style hybrid/overlay command :h3
-pair_style hybrid/overlay/omp command :h3
pair_style hybrid/overlay/kk command :h3
[Syntax:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index b5a5726182..4939f505bb 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3
pair_style lj/cut/omp command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/cut/gpu command :h3
+pair_style lj/cut/coul/cut/kk command :h3
pair_style lj/cut/coul/cut/omp command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/debye/gpu command :h3
@@ -26,6 +27,7 @@ pair_style lj/cut/coul/dsf/omp command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/cs command :h3
pair_style lj/cut/coul/long/gpu command :h3
+pair_style lj/cut/coul/long/kk command :h3
pair_style lj/cut/coul/long/intel command :h3
pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index f37cb0fb83..178ba8d1a8 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -8,6 +8,7 @@
pair_style lj/expand command :h3
pair_style lj/expand/gpu command :h3
+pair_style lj/expand/kk command :h3
pair_style lj/expand/omp command :h3
pair_style lj/expand/coul/long command :h3
pair_style lj/expand/coul/long/gpu command :h3
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 2bc2b656ac..47a554ef4f 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3
pair_style lj/long/coul/long/omp command :h3
pair_style lj/long/coul/long/opt command :h3
pair_style lj/long/tip4p/long command :h3
+pair_style lj/long/tip4p/long/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index 8281315031..77322953cf 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -7,7 +7,6 @@
:line
pair_style meam/sw/spline command :h3
-pair_style meam/sw/spline/omp command :h3
[Syntax:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 20744bc2a9..4b7bb0d93d 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -8,10 +8,10 @@
pair_style tersoff command :h3
pair_style tersoff/table command :h3
-pair_style tersoff/gpu :h3
-pair_style tersoff/intel :h3
-pair_style tersoff/kk :h3
-pair_style tersoff/omp :h3
+pair_style tersoff/gpu command :h3
+pair_style tersoff/intel command :h3
+pair_style tersoff/kk command :h3
+pair_style tersoff/omp command :h3
pair_style tersoff/table/omp command :h3
[Syntax:]
--
GitLab
From b07adbf98c637579bba0a4c0da89abc2c9f94c07 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 05:49:43 -0400
Subject: [PATCH 285/332] Update installing/running LAMMPS on ubuntu for daily
binary
---
doc/src/Install_linux.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt
index cc15ac0ae0..2eeeb6602c 100644
--- a/doc/src/Install_linux.txt
+++ b/doc/src/Install_linux.txt
@@ -60,10 +60,10 @@ To install LAMMPS do the following once:
sudo apt-get install lammps-daily :pre
-This downloads an executable named "lammps-daily" to your box, which
+This downloads an executable named "lmp_daily" to your box, which
can then be used in the usual way to run input scripts:
-lammps-daily < in.lj :pre
+lmp_daily -in in.lj :pre
To update LAMMPS to the most current version, do the following:
--
GitLab
From 7987f3319ee7876f13dae302f9c949c387730e93 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 06:05:26 -0400
Subject: [PATCH 286/332] remove outdated references to linux rpms on
rpm.lammps.org
---
doc/src/Install_linux.txt | 28 +---------------------------
1 file changed, 1 insertion(+), 27 deletions(-)
diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt
index 2eeeb6602c..d44ff2b1c7 100644
--- a/doc/src/Install_linux.txt
+++ b/doc/src/Install_linux.txt
@@ -9,39 +9,13 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Download an executable for Linux :h3
-Binaries are available for many different versions of Linux:
+Binaries are available for different versions of Linux:
-"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
"Pre-built Ubuntu Linux executables"_#ubuntu
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
:line
-Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
-
-Pre-built LAMMPS executables for various Linux distributions
-can be downloaded as binary RPM files from this site:
-
-"http://rpm.lammps.org"_http://rpm.lammps.org
-
-There are multiple package variants supporting serial, parallel and
-Python wrapper versions. The LAMMPS binaries contain all optional
-packages included in the source distribution except: GPU, KIM, REAX,
-and USER-INTEL.
-
-Installation instructions for the various versions are here:
-
-"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
-
-The instructions show how to enable the repository in the respective
-system's package management system. Installing and updating are then
-straightforward and automatic.
-
-Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
-up this RPM capability.
-
-:line
-
Pre-built Ubuntu Linux executables :h4,link(ubuntu)
A pre-built LAMMPS executable suitable for running on the latest
--
GitLab
From 8e7ddff6dcd0ecf6d66f93d8e82f9cbf782ce0c5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 06:15:03 -0400
Subject: [PATCH 287/332] reverse order in which pdf files are created.
Creating Developer.pdf first and Manual.pdf later makes
any warnings from the latter step, e.g. about missing
files in doc/src/lammps.book more visible.
---
doc/Makefile | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/doc/Makefile b/doc/Makefile
index 9069fa1d60..e4ba2fe6a1 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML doc pages in html dir"
- @echo " pdf create Manual.pdf and Developer.pdf in this dir"
+ @echo " pdf create Developer.pdf and Manual.pdf in this dir"
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@@ -116,17 +116,17 @@ mobi: epub
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \
- cd src; \
+ cd src/Developer; \
+ pdflatex developer; \
+ pdflatex developer; \
+ mv developer.pdf ../../Developer.pdf; \
+ cd ..; \
../utils/txt2html/txt2html.exe -b *.txt; \
htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
do grep -q $$s lammps.book || \
echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \
- cd Developer; \
- pdflatex developer; \
- pdflatex developer; \
- mv developer.pdf ../../Developer.pdf; \
)
old: utils/txt2html/txt2html.exe
--
GitLab
From cf0f3b6b618e1f12456c3c41def8c48bbd1c235f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 06:23:59 -0400
Subject: [PATCH 288/332] Update manual for renamed or removed files
---
doc/src/Commands_compute.txt | 2 +-
doc/src/computes.txt | 2 +-
doc/src/dump_image.txt | 7 +------
doc/src/fix_smd_move_triangulated_surface.txt | 2 +-
doc/src/fix_smd_wall_surface.txt | 2 +-
doc/src/fixes.txt | 2 +-
doc/src/lammps.book | 4 ++--
7 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 6185634187..724eeef98e 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -117,7 +117,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index a6a194ac24..e2d55605d3 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -91,7 +91,7 @@ Computes :h1
compute_smd_tlsph_strain
compute_smd_tlsph_strain_rate
compute_smd_tlsph_stress
- compute_smd_triangle_mesh_vertices
+ compute_smd_triangle_vertices
compute_smd_ulsph_num_neighs
compute_smd_ulsph_strain
compute_smd_ulsph_strain_rate
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 9b56dd95a6..df1ff324c1 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -384,12 +384,7 @@ change this via the "dump_modify"_dump_modify.html command.
:line
The {fix} keyword can be used with a "fix"_fix.html that produces
-objects to be drawn. An example is the "fix
-surface/global"_fix_surface_global.html command which can draw lines
-or triangles for 2d/3d simulations.
-
-NOTE: Aug 2016 - The fix surface/global command is not yet added to
-LAMMPS.
+objects to be drawn.
The {fflag1} and {fflag2} settings are numerical values which are
passed to the fix to affect how the drawing of its objects is done.
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index 2a998ba8c6..fca21b78f7 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -73,7 +73,7 @@ package"_Build_package.html doc page for more info.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index dc3625e95e..47527363a2 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -64,7 +64,7 @@ multiple objects in one file.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index f2f257b134..7b4fdc429b 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -92,6 +92,7 @@ Fixes :h1
fix_nve
fix_nve_asphere
fix_nve_asphere_noforce
+ fix_nve_awpmd
fix_nve_body
fix_nve_dot
fix_nve_dotc_langevin
@@ -154,7 +155,6 @@ Fixes :h1
fix_srd
fix_store_force
fix_store_state
- fix_surface_global
fix_temp_berendsen
fix_temp_csvr
fix_temp_rescale
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0e5ceae861..972b026fde 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -311,6 +311,7 @@ fix_npt_sphere.html
fix_nve.html
fix_nve_asphere.html
fix_nve_asphere_noforce.html
+fix_nve_awpmd.html
fix_nve_body.html
fix_nve_dot.html
fix_nve_dotc_langevin.html
@@ -374,7 +375,6 @@ fix_spring_self.html
fix_srd.html
fix_store_force.html
fix_store_state.html
-fix_surface_global.html
fix_temp_berendsen.html
fix_temp_csvr.html
fix_temp_rescale.html
@@ -488,7 +488,7 @@ compute_smd_tlsph_shape.html
compute_smd_tlsph_strain.html
compute_smd_tlsph_strain_rate.html
compute_smd_tlsph_stress.html
-compute_smd_triangle_mesh_vertices.html
+compute_smd_triangle_vertices.html
compute_smd_ulsph_num_neighs.html
compute_smd_ulsph_strain.html
compute_smd_ulsph_strain_rate.html
--
GitLab
From 91286ddb0ebff3f652a33a7c1655110563e66e0d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 06:51:30 -0400
Subject: [PATCH 289/332] remove references to fix ave/spatial and
ave/spatial/sphere
---
doc/src/Errors_messages.txt | 62 -------------------------------------
doc/src/Errors_warnings.txt | 18 -----------
2 files changed, 80 deletions(-)
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index a74182967c..695b949f7e 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -1092,11 +1092,6 @@ correct. :dd
The specified file cannot be opened. Check that the path and name are
correct. :dd
-{Cannot open fix ave/spatial file %s} :dt
-
-The specified file cannot be opened. Check that the path and name are
-correct. :dd
-
{Cannot open fix ave/time file %s} :dt
The specified file cannot be opened. Check that the path and name are
@@ -1677,10 +1672,6 @@ provided by an atom map. An atom map does not exist (by default) for
non-molecular problems. Using the atom_modify map command will force
an atom map to be created. :dd
-{Cannot use fix ave/spatial z for 2 dimensional model} :dt
-
-Self-explanatory. :dd
-
{Cannot use fix bond/break with non-molecular systems} :dt
Only systems with bonds that can be changed can be used. Atom_style
@@ -2425,10 +2416,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Compute ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
{Compute ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@@ -4074,10 +4061,6 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Fix ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
{Fix ID for fix ave/time does not exist} :dt
Self-explanatory. :dd
@@ -4379,51 +4362,6 @@ same style. :dd
Self-explanatory. :dd
-{Fix ave/spatial compute does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial compute does not calculate a per-atom vector} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute does not calculate per-atom values} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom vector} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix does not calculate per-atom values} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial for triclinic boxes requires units reduced} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial settings invalid with changing box size} :dt
-
-If the box size changes, only the units reduced option can be
-used. :dd
-
-{Fix ave/spatial variable is not atom-style variable} :dt
-
-A variable used by fix ave/spatial must generate per-atom values. :dd
-
{Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
One of more of the vector inputs has individual elements which are
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 98b66f2aa5..0980120a10 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -291,24 +291,6 @@ This may cause accuracy problems. :dd
This may cause accuracy problems. :dd
-{Fix thermal/conductivity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that fix
-thermal/conductivity comes first. If you are using fix ave/spatial to
-measure the temperature profile induced by fix viscosity, then this
-may cause a glitch in the profile since you are averaging immediately
-after swaps have occurred. Flipping the order of the 2 fixes
-typically helps. :dd
-
-{Fix viscosity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that
-fix viscosity comes first. If you are using fix ave/spatial
-to measure the velocity profile induced by fix viscosity, then
-this may cause a glitch in the profile since you are averaging
-immediately after swaps have occurred. Flipping the order
-of the 2 fixes typically helps. :dd
-
{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
This is current restriction with Kokkos. :dd
--
GitLab
From 5481e99331f126baca35f1cdb14aec8bbb896dbf Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 06:52:20 -0400
Subject: [PATCH 290/332] remove broken USER-OMP pair style
---
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 170 ------------------------
src/USER-OMP/pair_nb3b_harmonic_omp.h | 49 -------
2 files changed, 219 deletions(-)
delete mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.cpp
delete mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.h
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
deleted file mode 100644
index 2ab96c43a0..0000000000
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
+++ /dev/null
@@ -1,170 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- This software is distributed under the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Axel Kohlmeyer (Temple U)
-------------------------------------------------------------------------- */
-
-#include <cmath>
-#include "pair_nb3b_harmonic_omp.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-
-#include "suffix.h"
-using namespace LAMMPS_NS;
-
-/* ---------------------------------------------------------------------- */
-
-PairNb3bHarmonicOMP::PairNb3bHarmonicOMP(LAMMPS *lmp) :
- PairNb3bHarmonic(lmp), ThrOMP(lmp, THR_PAIR)
-{
- suffix_flag |= Suffix::OMP;
- respa_enable = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairNb3bHarmonicOMP::compute(int eflag, int vflag)
-{
- if (eflag || vflag) {
- ev_setup(eflag,vflag);
- } else evflag = vflag_fdotr = 0;
-
- const int nall = atom->nlocal + atom->nghost;
- const int nthreads = comm->nthreads;
- const int inum = list->inum;
-
-#if defined(_OPENMP)
-#pragma omp parallel default(none) shared(eflag,vflag)
-#endif
- {
- int ifrom, ito, tid;
-
- loop_setup_thr(ifrom, ito, tid, inum, nthreads);
- ThrData *thr = fix->get_thr(tid);
- thr->timer(Timer::START);
- ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
-
- if (evflag) {
- if (eflag) {
- eval<1,1>(ifrom, ito, thr);
- } else {
- eval<1,0>(ifrom, ito, thr);
- }
- } else eval<0,0>(ifrom, ito, thr);
-
- thr->timer(Timer::PAIR);
- reduce_thr(this, eflag, vflag, thr);
- } // end of omp parallel region
-}
-
-template <int EVFLAG, int EFLAG>
-void PairNb3bHarmonicOMP::eval(int iifrom, int iito, ThrData * const thr)
-{
- int i,j,k,ii,jj,kk,jnum,jnumm1;
- int itype,jtype,ktype,ijparam,ikparam,ijkparam;
- double xtmp,ytmp,ztmp,evdwl;
- double rsq1,rsq2;
- double delr1[3],delr2[3],fj[3],fk[3];
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- evdwl = 0.0;
-
- const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
- dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
- const int * _noalias const type = atom->type;
-
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- double fxtmp,fytmp,fztmp;
-
- // loop over full neighbor list of my atoms
-
- for (ii = iifrom; ii < iito; ++ii) {
-
- i = ilist[ii];
- itype = map[type[i]];
- xtmp = x[i].x;
- ytmp = x[i].y;
- ztmp = x[i].z;
- fxtmp = fytmp = fztmp = 0.0;
-
- // two-body interactions, skip half of them
-
- jlist = firstneigh[i];
- jnum = numneigh[i];
- jnumm1 = jnum - 1;
-
- for (jj = 0; jj < jnumm1; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
- jtype = map[type[j]];
- ijparam = elem2param[itype][jtype][jtype];
- delr1[0] = x[j].x - xtmp;
- delr1[1] = x[j].y - ytmp;
- delr1[2] = x[j].z - ztmp;
- rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
- if (rsq1 > params[ijparam].cutsq) continue;
-
- double fjxtmp,fjytmp,fjztmp;
- fjxtmp = fjytmp = fjztmp = 0.0;
-
- for (kk = jj+1; kk < jnum; kk++) {
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k].x - xtmp;
- delr2[1] = x[k].y - ytmp;
- delr2[2] = x[k].z - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[ikparam].cutsq) continue;
-
- threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
- rsq1,rsq2,delr1,delr2,fj,fk,EFLAG,evdwl);
-
- fxtmp -= fj[0] + fk[0];
- fytmp -= fj[1] + fk[1];
- fztmp -= fj[2] + fk[2];
- fjxtmp += fj[0];
- fjytmp += fj[1];
- fjztmp += fj[2];
- f[k].x += fk[0];
- f[k].y += fk[1];
- f[k].z += fk[2];
-
- if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
- }
- f[j].x += fjxtmp;
- f[j].y += fjytmp;
- f[j].z += fjztmp;
- }
- f[i].x += fxtmp;
- f[i].y += fytmp;
- f[i].z += fztmp;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairNb3bHarmonicOMP::memory_usage()
-{
- double bytes = memory_usage_thr();
- bytes += PairNb3bHarmonic::memory_usage();
-
- return bytes;
-}
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.h b/src/USER-OMP/pair_nb3b_harmonic_omp.h
deleted file mode 100644
index 6b8fbd8897..0000000000
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Axel Kohlmeyer (Temple U)
-------------------------------------------------------------------------- */
-
-#ifdef PAIR_CLASS
-
-//PairStyle(nb3b/harmonic/omp,PairNb3bHarmonicOMP)
-PairStyle(disabled,PairNb3bHarmonicOMP)
-
-#else
-
-#ifndef LMP_PAIR_NB3BHARMONIC_OMP_H
-#define LMP_PAIR_NB3BHARMONIC_OMP_H
-
-#include "pair_nb3b_harmonic.h"
-#include "thr_omp.h"
-
-namespace LAMMPS_NS {
-
-class PairNb3bHarmonicOMP : public PairNb3bHarmonic, public ThrOMP {
-
- public:
- PairNb3bHarmonicOMP(class LAMMPS *);
-
- virtual void compute(int, int);
- virtual double memory_usage();
-
- private:
- template <int EVFLAG, int EFLAG>
- void eval(int ifrom, int ito, ThrData * const thr);
-};
-
-}
-
-#endif
-#endif
--
GitLab
From e1627caf04eb20d6fcf2282964f025c866b3aad9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 07:20:03 -0400
Subject: [PATCH 291/332] integrate compute ptm/atom and USER-PTM into the docs
---
doc/src/Commands_compute.txt | 1 +
doc/src/Packages_details.txt | 20 ++++++++++++++++++++
doc/src/Packages_user.txt | 1 +
doc/src/compute_ptm_atom.txt | 6 +++++-
doc/src/computes.txt | 1 +
doc/src/lammps.book | 1 +
6 files changed, 29 insertions(+), 1 deletion(-)
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 028e274c9b..a89f3adf5d 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -95,6 +95,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
+"ptm/atom"_compute_ptm_atom.html
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 494f393a16..73345a2940 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -89,6 +89,7 @@ as contained in the file name.
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
"USER-PHONON"_#PKG-USER-PHONON,
+"USER-PTM"_#PKG-USER-PTM,
"USER-QMMM"_#PKG-USER-QMMM,
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
@@ -1744,6 +1745,25 @@ examples/USER/phonon :ul
:line
+USER-PTM package :link(PKG-USER-PTM),h4
+
+[Contents:]
+
+A "compute ptm/atom"_compute_ptm.html command that calculates
+local structure characterization using the Polyhedral Template
+Matching methodology.
+
+[Author:] Peter Mahler Larsen (MIT).
+
+[Supporting info:]
+
+src/USER-PHONON: filenames -> commands
+src/USER-PHONON/README
+"fix phonon"_fix_phonon.html
+examples/USER/phonon :ul
+
+:line
+
USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 70ac6022b6..6d3a8f754a 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
index c668eb7726..6fe4d012f5 100644
--- a/doc/src/compute_ptm_atom.txt
+++ b/doc/src/compute_ptm_atom.txt
@@ -101,7 +101,11 @@ The (qw,qx,qy,qz) parameters represent the orientation of the local structure
in quaternion form. The reference coordinates for each template (from which the
orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
-[Restrictions:] none
+[Restrictions:]
+
+This fix is part of the USER-PTM package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 46dd30f757..aa6cf5bb64 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -70,6 +70,7 @@ Computes :h1
compute_property_atom
compute_property_chunk
compute_property_local
+ compute_ptm_atom
compute_rdf
compute_reduce
compute_rigid_local
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 828863ae67..ae58e66efd 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -467,6 +467,7 @@ compute_pressure_uef.html
compute_property_atom.html
compute_property_chunk.html
compute_property_local.html
+compute_ptm_atom.html
compute_rdf.html
compute_reduce.html
compute_rigid_local.html
--
GitLab
From f23b638d471e3e76f23b82a229cb9a62a8638cf3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 07:23:38 -0400
Subject: [PATCH 292/332] include USER-PTM into git management
---
.github/CODEOWNERS | 1 +
src/.gitignore | 5 +++++
2 files changed, 6 insertions(+)
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 4f561a4c19..164bc05d60 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -30,6 +30,7 @@ src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PHONON/* @lingtikong
+src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
diff --git a/src/.gitignore b/src/.gitignore
index df3a22a5cd..13a8622fe1 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -41,6 +41,11 @@
/pair_meamc.cpp
/pair_meamc.h
+/ptm_*.cpp
+/ptm_*.h
+/compute_ptm.cpp
+/compute_ptm.h
+
/fix_qeq*.cpp
/fix_qeq*.h
--
GitLab
From 9ae6cb5c4fde9ad598aa7eecd8d2a92937b1a0c9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 07:28:44 -0400
Subject: [PATCH 293/332] add recently renamed file to purge list
---
src/Purge.list | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/Purge.list b/src/Purge.list
index c70392c935..6cfc580c25 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -24,6 +24,9 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
+# renamed on 25 September 2018
+compute_smd_triangle_mesh_vertices.h
+compute_smd_triangle_mesh_vertices.cpp
# renamed on 6 September 2018
pair_cdeam_omp.h
pair_cdeam_omp.cpp
--
GitLab
From f58aa05e02129c0d125b1acb9700d0756ab73c42 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 07:44:54 -0400
Subject: [PATCH 294/332] remove references to USER-OMP version of pair style
nb3b/harmonic
---
doc/src/Commands_pair.txt | 2 +-
doc/src/pair_nb3b_harmonic.txt | 23 -----------------------
2 files changed, 1 insertion(+), 24 deletions(-)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 3b6a5f48fa..ae115dd904 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -167,7 +167,7 @@ OPT.
"morse/soft"_pair_morse.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 6a119d74e1..2b2152a873 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -7,7 +7,6 @@
:line
pair_style nb3b/harmonic command :h3
-pair_style nb3b/harmonic/omp command :h3
[Syntax:]
@@ -89,28 +88,6 @@ a particular simulation; LAMMPS ignores those entries.
:line
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page. The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
[Restrictions:]
This pair style can only be used if LAMMPS was built with the MANYBODY
--
GitLab
From 21c59d4cf0762bceefaab1e96284ce8a244a6ec6 Mon Sep 17 00:00:00 2001
From: dilkins <wilkinsd@outlook.com>
Date: Fri, 28 Sep 2018 12:46:11 +0200
Subject: [PATCH 295/332] Fast-forward Langevin functionality included
---
doc/src/fix_ffl.txt | 129 ++++++++++
src/USER-MISC/README | 1 +
src/USER-MISC/fix_ffl.cpp | 527 ++++++++++++++++++++++++++++++++++++++
src/USER-MISC/fix_ffl.h | 67 +++++
4 files changed, 724 insertions(+)
create mode 100644 doc/src/fix_ffl.txt
create mode 100644 src/USER-MISC/fix_ffl.cpp
create mode 100644 src/USER-MISC/fix_ffl.h
diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt
new file mode 100644
index 0000000000..8d6b243142
--- /dev/null
+++ b/doc/src/fix_ffl.txt
@@ -0,0 +1,129 @@
+<script type="text/javascript"
+ src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix ffl command :h3
+
+[Syntax:]
+
+fix ID id-group ffl tau Tstart Tstop seed \[flip-type\] :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+ffl = style name of this fix command :l
+tau = thermostat parameter (positive real) :l
+Tstart, Tstop = temperature ramp during the run :l
+seed = random number seed to use for generating noise (positive integer) :l
+one more value may be appended :l
+ flip-type = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default :pre
+:ule
+
+[Examples:]
+
+fix 3 boundary ffl 10 300 300 31415
+fix 1 all ffl 100 500 500 9265 soft :pre
+
+[Description:]
+
+Apply a Fast-Forward Langevin Equation (FFL) thermostat as described
+in "(Hijazi)"_#Hijazi. Contrary to
+"fix langevin"_fix_langevin.html, this fix performs both
+thermostatting and evolution of the Hamiltonian equations of motion, so it
+should not be used together with "fix nve"_fix_nve.html -- at least not
+on the same atom groups.
+
+The time-evolution of a single particle undergoing Langevin dynamics is described
+by the equations
+
+\begin\{equation\} \frac \{dq\}\{dt\} = \frac\{p\}\{m\}, \end\{equation\}
+
+\begin\{equation\} \frac \{dp\}\{dt\} = -\gamma p + W + F, \end\{equation\}
+
+where \(F\) is the physical force, \(\gamma\) is the friction coefficient, and \(W\) is a
+Gaussian random force.
+
+The friction coefficient is the inverse of the thermostat parameter : \(\gamma = 1/\tau\), with \(\tau\) the thermostat parameter {tau}.
+The thermostat parameter is given in the time units, \(\gamma\) is in inverse time units.
+
+Equilibrium sampling a temperature T is obtained by specifying the
+target value as the {Tstart} and {Tstop} arguments, so that the internal
+constants depending on the temperature are computed automatically.
+
+The random number {seed} must be a positive integer. A Marsaglia random
+number generator is used. Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+The flipping type {flip-type} can be chosen between 4 types described in
+"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting
+step and it flips the momenta of the atoms. If no_flip is chosen, no flip
+will be executed and the integration will be the same as a standard
+Langevin thermostat "(Bussi)"_#Bussi. The other flipping types are : rescale - hard - soft.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The instantaneous values of the extended variables are written to
+"binary restart files"_restart.html. Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+Note however that you should use a different seed each time you
+restart, otherwise the same sequence of random numbers will be used
+each time, which might lead to stochastic synchronization and
+subtle artefacts in the sampling.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command. See the
+"run"_run.html command for details of how to do this.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15. The scalar is the
+cumulative energy change due to this fix. The scalar value
+calculated by this fix is "extensive".
+
+[Restrictions:]
+
+The GLE thermostat in its current implementation should not be used
+with rigid bodies, SHAKE or RATTLE. It is expected that all the
+thermostatted degrees of freedom are fully flexible, and the sampled
+ensemble will not be correct otherwise.
+
+In order to perform constant-pressure simulations please use
+"fix press/berendsen"_fix_press_berendsen.html, rather than
+"fix npt"_fix_nh.html, to avoid duplicate integration of the
+equations of motion.
+
+This fix is part of the USER-MISC package. It is only enabled if LAMMPS
+was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
+viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
+dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html
+
+:line
+
+:link(Hijazi)
+[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
+:link(Bussi)
+[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
+
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index eb221c07db..b3c3e85948 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -44,6 +44,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
+fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
new file mode 100644
index 0000000000..54e5c03a62
--- /dev/null
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -0,0 +1,527 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Fast-forward Langevin thermostat, see
+ M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL),
+ Michele Ceriotti (EPFL)
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "fix_ffl.h"
+#include "math_extra.h"
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "force.h"
+#include "update.h"
+#include "modify.h"
+#include "compute.h"
+#include "domain.h"
+#include "region.h"
+#include "respa.h"
+#include "comm.h"
+#include "input.h"
+#include "variable.h"
+#include "random_mars.h"
+#include "memory.h"
+#include "error.h"
+#include "group.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum {NOBIAS,BIAS};
+enum {CONSTANT,EQUAL,ATOM};
+//#define FFL_DEBUG 1
+
+#define MAXLINE 1024
+
+/* syntax for fix_ffl:
+ * fix nfix id-group ffl tau Tstart Tstop seed [flip_type]
+ *
+ * */
+
+/* ---------------------------------------------------------------------- */
+
+
+FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+
+
+ if (narg < 7)
+ error->all(FLERR,"Illegal fix ffl command. Expecting: fix <fix-ID>"
+ " <group-ID> ffl <tau> <Tstart> <Tstop> <seed> ");
+
+ restart_peratom = 1;
+ time_integrate = 1;
+ scalar_flag = 1;
+
+ //gamma = 1/ time constant(tau)
+ if (force->numeric(FLERR,arg[3]) <= 0)
+ error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0");
+ gamma = 1.0/force->numeric(FLERR,arg[3]);
+ ffl_every=1;
+ ffl_step=0;
+
+ // start temperature (t ramp)
+ t_start = force->numeric(FLERR,arg[4]);
+
+ // final temperature (t ramp)
+ t_stop = force->numeric(FLERR,arg[5]);
+
+ // PRNG seed
+ int seed = force->inumeric(FLERR,arg[6]);
+
+ // Flip type used, uses rescale if no flip is given
+ if (narg == 8) strcpy(flip_type,arg[7]);
+ else strcpy(flip_type,"rescale");
+
+
+ // Tests if the flip type is valid
+ if ( strcmp(flip_type,"rescale") && strcmp(flip_type,"hard")
+ && strcmp(flip_type,"soft") && strcmp(flip_type,"no_flip") )
+ error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
+
+ if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0;
+ if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1;
+ if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2;
+ if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3;
+
+ t_target=t_start;
+ const double kT = t_target * force->boltz / force->mvv2e;
+
+
+ // initialize Marsaglia RNG with processor-unique seed
+ // NB: this means runs will not be the same with different numbers of processors
+ if (seed <= 0) error->all(FLERR,"Illegal fix ffl command");
+ random = new RanMars(lmp,seed + comm->me);
+
+ // allocate per-type arrays for mass-scaling
+ sqrt_m=NULL;
+ memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m");
+
+ // allocates space for temporaries
+ ffl_tmp1=ffl_tmp2=NULL;
+
+ grow_arrays(atom->nmax);
+
+ // add callbacks to enable restarts
+ atom->add_callback(0);
+ atom->add_callback(1);
+
+ energy = 0.0;
+}
+
+
+/* --- Frees up memory used by temporaries and buffers ------------------ */
+
+FixFFL::~FixFFL()
+{
+ delete random;
+
+ memory->destroy(sqrt_m);
+ memory->destroy(ffl_tmp1);
+ memory->destroy(ffl_tmp2);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixFFL::setmask()
+{
+ int mask = 0;
+
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ mask |= INITIAL_INTEGRATE_RESPA;
+ mask |= FINAL_INTEGRATE_RESPA;
+ mask |= THERMO_ENERGY;
+
+
+ return mask;
+}
+
+/* ------- Initializes one-time quantities for FFL ---------------------- */
+
+void FixFFL::init()
+{
+ doffl = 1;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+
+ // set force prefactors
+ if (!atom->rmass)
+ {
+ for (int i = 1; i <= atom->ntypes; i++)
+ {
+ sqrt_m[i] = sqrt(atom->mass[i]);
+ }
+ }
+
+ if (strstr(update->integrate_style,"respa"))
+ {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ step_respa = ((Respa *) update->integrate)->step;
+ }
+
+ init_ffl();
+}
+
+/* ------- Initializes constants for FFL (change with T and dt) ------- */
+
+void FixFFL::init_ffl()
+{
+ const double kT = t_target * force->boltz / force->mvv2e;
+
+ // compute constants for FFL
+
+ c1 = exp ( - gamma * 0.5 * dtv );
+ c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term
+
+
+}
+
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixFFL::setup(int vflag)
+{
+ if (strstr(update->integrate_style,"verlet"))
+ post_force(vflag);
+ else
+ {
+ ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+ post_force_respa(vflag,nlevels_respa-1,0);
+ ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+ }
+}
+
+void FixFFL::ffl_integrate()
+{
+ double **v = atom->v;
+ double *rmass = atom->rmass, smi, ismi;
+ double factor;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ // loads momentum data (mass-scaled) into the temporary vectors for the propagation
+ int nk=0;
+ double deltae=0.0;
+ for (int i = 0; i < nlocal; i++)
+ {
+ if (mask[i] & groupbit)
+ {
+ if (rmass) smi = sqrt(rmass[i]);
+ else smi = sqrt_m[type[i]];
+
+ for (int k = 0; k<3; k++)
+ {
+ // first loads velocities and accumulates conserved quantity
+ ffl_tmp2[nk] = v[i][k] * smi;
+ deltae += ffl_tmp2[nk] * ffl_tmp2[nk];
+ nk++;
+ }
+ }
+ }
+
+ //fills up a vector of random numbers
+ for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian();
+
+
+ // unloads momentum data (mass-scaled) from the temporary vectors
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
+ {
+ if (rmass) ismi = 1.0 / sqrt(rmass[i]);
+ else ismi = 1.0/ sqrt_m[type[i]];
+
+ for (int k = 0; k<3; k++)
+ {
+ // fetches new velocities and completes computation of the conserved quantity change
+ v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi;
+
+ deltae-= v[i][k]*v[i][k] /ismi /ismi;
+
+ //flips the sign of the momentum (HARD FLIP)
+ if ( flip_int == 2)
+ {
+ if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k];
+ }
+
+ nk++;
+ }
+ }
+
+ //rescale operation (RESCALE FLIP)
+ if (flip_int == 1)
+ {
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
+ {
+ factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) /
+ (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
+ + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]));
+
+ for (int k = 0; k<3; k++)
+ {
+ v[i][k]= factor * ffl_tmp2[nk];
+ nk++;
+ }
+ }
+ }
+
+
+ //soft flip operation (SOFT FLIP)
+ if (flip_int == 3)
+ {
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
+ {
+ factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2];
+ if (factor < 0)
+ {
+ factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
+ + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]);
+
+ for (int k = 0; k<3; k++)
+ {
+ v[i][k] -= 2.0 * factor * ffl_tmp2[nk];
+ nk++;
+ }
+ }
+ else
+ nk += 3;
+ }
+ }
+
+ energy += deltae*0.5*force->mvv2e;
+
+}
+
+void FixFFL::initial_integrate(int vflag)
+{
+ double dtfm;
+
+ // update v and x of atoms in group
+ double **x = atom->x;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ ffl_step--;
+ if (doffl && ffl_step<1) ffl_integrate();
+
+ if (rmass)
+ {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+
+ }
+ else
+ {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+}
+
+void FixFFL::final_integrate()
+{
+ double dtfm;
+
+ // update v of atoms in group
+
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (rmass)
+ {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ }
+
+ }
+ else
+ {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ }
+ }
+
+ if (doffl && ffl_step<1)
+ {
+ ffl_integrate();
+ ffl_step = ffl_every;
+ }
+
+ // Change the temperature for the next step
+ double delta = update->ntimestep - update->beginstep;
+ delta /= update->endstep - update->beginstep;
+ t_target = t_start + delta * (t_stop - t_start);
+ if (t_stop != t_start)
+ {
+ // only updates if it is really necessary
+ init_ffl();
+ }
+
+}
+/* ---------------------------------------------------------------------- */
+
+void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+
+ // innermost level - NVE update of v and x
+ // all other levels - NVE update of v
+
+ if (ilevel==nlevels_respa-1) ffl_integrate();
+ doffl=0;
+ if (ilevel == 0) initial_integrate(vflag);
+ else
+ {
+ final_integrate();
+ }
+}
+
+void FixFFL::final_integrate_respa(int ilevel, int iloop)
+{
+
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ doffl=0;
+ final_integrate();
+ if (ilevel==nlevels_respa-1) ffl_integrate();
+}
+
+
+double FixFFL::compute_scalar()
+{
+
+ double energy_me = energy;
+ double energy_all;
+ MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
+
+ return energy_all;
+}
+
+/* ----------------------------------------------------------------------
+ extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixFFL::extract(const char *str, int &dim)
+{
+ dim = 0;
+ if (strcmp(str,"t_target") == 0)
+ {
+ return &t_target;
+ }
+ return NULL;
+}
+
+
+/* ----------------------------------------------------------------------
+ Called when a change to the target temperature is requested mid-run
+------------------------------------------------------------------------- */
+
+void FixFFL::reset_target(double t_new)
+{
+
+ t_target = t_start = t_stop = t_new;
+}
+
+/* ----------------------------------------------------------------------
+ Called when a change to the timestep is requested mid-run
+------------------------------------------------------------------------- */
+
+void FixFFL::reset_dt()
+{
+ // set the time integration constants
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * (force->ftm2v);
+ init_ffl();
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double FixFFL::memory_usage()
+{
+ double bytes = atom->nmax*(3*2)*sizeof(double);
+ return bytes;
+}
+
+
+/* ----------------------------------------------------------------------
+ allocate local atom-based arrays
+------------------------------------------------------------------------- */
+
+void FixFFL::grow_arrays(int nmax)
+{
+ memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1");
+ memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2");
+ //zeroes out temporary buffers
+ for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0;
+ for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0;
+}
+
+
diff --git a/src/USER-MISC/fix_ffl.h b/src/USER-MISC/fix_ffl.h
new file mode 100644
index 0000000000..1225d25989
--- /dev/null
+++ b/src/USER-MISC/fix_ffl.h
@@ -0,0 +1,67 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(ffl,FixFFL)
+
+#else
+
+#ifndef LMP_FIX_FFL_H
+#define LMP_FIX_FFL_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixFFL : public Fix {
+ public:
+ FixFFL(class LAMMPS *, int, char **);
+ virtual ~FixFFL();
+ int setmask();
+ void init();
+ void setup(int);
+ void ffl_integrate();
+ void initial_integrate_respa(int vflag, int ilevel, int iloop);
+ void final_integrate_respa(int ilevel, int iloop);
+ void initial_integrate(int vflag);
+ void final_integrate();
+ double compute_scalar();
+ void reset_target(double);
+ virtual void reset_dt();
+ double memory_usage();
+ void grow_arrays(int);
+
+ virtual void *extract(const char *, int &);
+
+ void init_ffl();
+ protected:
+ double *ffl_tmp1, *ffl_tmp2;
+ double t_start, t_stop, t_target;
+ double dtv, dtf, c1, c2, gamma;
+ char flip_type[10];
+
+ int doffl, ffl_every, ffl_step, flip_int;
+ class RanMars *random;
+ double *sqrt_m;
+ double *step_respa;
+ double energy;
+ int nlevels_respa;
+
+ double **vaux;
+};
+
+}
+
+#endif
+#endif
--
GitLab
From 497af2ebb959acf56a71ceea08969760c1fb3d8c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 28 Sep 2018 13:44:42 +0200
Subject: [PATCH 296/332] document eam/cd/old
---
doc/src/Commands_pair.txt | 1 +
doc/src/pair_eam.txt | 10 ++++++++--
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index ae115dd904..5715c0123b 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -81,6 +81,7 @@ OPT.
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,
+"eam/cd/old (o)"_pair_eam.html,
"eam/fs (gikot)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"edip/multi"_pair_edip.html,
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 6c3793cb61..ed1378b6fd 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -20,6 +20,8 @@ pair_style eam/alloy/omp command :h3
pair_style eam/alloy/opt command :h3
pair_style eam/cd command :h3
pair_style eam/cd/omp command :h3
+pair_style eam/cd/old command :h3
+pair_style eam/cd/old/omp command :h3
pair_style eam/fs command :h3
pair_style eam/fs/gpu command :h3
pair_style eam/fs/intel command :h3
@@ -31,7 +33,7 @@ pair_style eam/fs/opt command :h3
pair_style style :pre
-style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
+style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul
[Examples:]
@@ -268,7 +270,8 @@ Style {eam/cd} is similar to the {eam/alloy} style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
-"(Stukowski)"_#Stukowski.
+"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly
+different and slower two-site formulation of the model "(Caro)"_#Caro.
The pair_coeff command is specified the same as for the {eam/alloy}
style. However the DYNAMO {setfl} file must has two
@@ -442,3 +445,6 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Stukowski)
[(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
+
+:link(Caro)
+[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
--
GitLab
From 12d2dd201a149b9ecd862af47b6134699095a85b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 28 Sep 2018 15:47:56 +0200
Subject: [PATCH 297/332] update description of RPM based LAMMPS packages with
info from @junghans
this fixes #1135
---
doc/src/Install_linux.txt | 77 +++++++++++++++++++++++++++++++++++++++
1 file changed, 77 insertions(+)
diff --git a/doc/src/Install_linux.txt b/doc/src/Install_linux.txt
index d44ff2b1c7..bd22de057c 100644
--- a/doc/src/Install_linux.txt
+++ b/doc/src/Install_linux.txt
@@ -12,6 +12,9 @@ Download an executable for Linux :h3
Binaries are available for different versions of Linux:
"Pre-built Ubuntu Linux executables"_#ubuntu
+"Pre-built Fedora Linux executables"_#fedora
+"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
+"Pre-built OpenSuse Linux executables"_#opensuse
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
:line
@@ -73,6 +76,80 @@ Ubuntu package capability.
:line
+Pre-built Fedora Linux executables :h4,link(fedora)
+
+Pre-built LAMMPS packages for stable releases are available
+in the Fedora Linux distribution as of version 28. The packages
+can be installed via the dnf package manager. There are 3 basic
+varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+lammps-openmpi = OpenMPI MPI library) and for each support for
+linking to the C library interface (lammps-devel, lammps-mpich-devel,
+lammps-openmpi-devel), the header for compiling programs using
+the C library interface (lammps-headers), and the LAMMPS python
+module for Python 3. All packages can be installed at the same
+time and the name of the LAMMPS executable is {lmp} in all 3 cases.
+By default, {lmp} will refer to the serial executable, unless
+one of the MPI environment modules is loaded
+("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
+Then the corresponding parallel LAMMPS executable is used.
+The same mechanism applies when loading the LAMMPS python module.
+
+To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
+
+dnf install lammps-openmpi
+module load mpi/openmpi-x86_64
+mpirun -np 2 lmp -in in.lj :pre
+
+The "dnf install" command is needed only once. In case of a new LAMMPS
+stable release, "dnf update" will automatically update to the newer
+version as soon at the RPM files are built and uploaded to the download
+mirrors. The "module load" command is needed once per (shell) session
+or shell terminal instance, unless it is automatically loaded from the
+shell profile.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
+
+:line
+
+Pre-built EPEL Linux executable :h4,link(epel)
+
+Pre-built LAMMPS packages for stable releases are available
+in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL
+for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
+and compatible Linux distributions. Names of packages, executable,
+and content are the same as described above for Fedora Linux.
+But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
+in Fedora 28.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
+
+:line
+
+Pre-built OpenSuse Linux executable :h4,link(opensuse)
+
+A pre-built LAMMPS package for stable releases is available
+in OpenSuse as of Leap 15.0. You can install the package with:
+
+zypper install lammps :pre
+
+This includes support for OpenMPI. The name of the LAMMPS executable
+is {lmp}. Thus to run an input in parallel on 2 CPUs you would do:
+
+mpirun -np 2 lmp -in in.lj :pre
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
+
+:line
+
Pre-built Gentoo Linux executable :h4,link(gentoo)
LAMMPS is part of Gentoo's main package tree and can be installed by
--
GitLab
From a333fdac307dce61d997adf44afe1f7ec2964930 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 28 Sep 2018 18:02:13 +0200
Subject: [PATCH 298/332] correct some documentation issues with the recently
added USER-PTM package
---
doc/src/Commands_compute.txt | 2 +-
doc/src/Packages_details.txt | 9 ++++-----
doc/src/Packages_user.txt | 2 +-
doc/src/compute_ptm_atom.txt | 4 ++--
4 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 99c46eed4a..81b618a6e2 100644
--- a/doc/src/Commands_compute.txt
+++ b/doc/src/Commands_compute.txt
@@ -96,7 +96,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
-"ptm/atom"_compute_ptm_atom.html
+"ptm/atom"_compute_ptm_atom.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.html,
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 73345a2940..6efcfd5f62 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -1749,7 +1749,7 @@ USER-PTM package :link(PKG-USER-PTM),h4
[Contents:]
-A "compute ptm/atom"_compute_ptm.html command that calculates
+A "compute ptm/atom"_compute_ptm_atom.html command that calculates
local structure characterization using the Polyhedral Template
Matching methodology.
@@ -1757,10 +1757,9 @@ Matching methodology.
[Supporting info:]
-src/USER-PHONON: filenames -> commands
-src/USER-PHONON/README
-"fix phonon"_fix_phonon.html
-examples/USER/phonon :ul
+src/USER-PTM: filename starting with ptm_ -> supporting code, other filenames -> commands
+src/USER-PTM/LICENSE
+"compute ptm/atom"_compute_ptm_atom.html :ul
:line
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 6d3a8f754a..6e363b28f7 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -62,7 +62,7 @@ Package, Description, Doc page, Example, Library
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
-"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no
+"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
index 6fe4d012f5..2e22e4e9fb 100644
--- a/doc/src/compute_ptm_atom.txt
+++ b/doc/src/compute_ptm_atom.txt
@@ -80,9 +80,9 @@ too frequently or to have multiple compute/dump commands, each with a
[Output info:]
-This compute calculates a per-atom array, which can be accessed by
+This compute calculates a per-atom arry, which can be accessed by
any command that uses per-atom values from a compute as input. See
-"Section 6.15"_Section_howto.html#howto_15 for an overview of
+the "Howto output"_Howto_output.html doc page for an overview of
LAMMPS output options.
Results are stored in the per-atom array in the following order:
--
GitLab
From 799ffc58d914d3335d4ebb18fb8f58dd670bfd71 Mon Sep 17 00:00:00 2001
From: dilkins <wilkinsd@outlook.com>
Date: Mon, 1 Oct 2018 17:13:56 +0200
Subject: [PATCH 299/332] C++ system headers included and enumeration of
flip_int used;documentation corrected
---
doc/src/fix_ffl.txt | 5 -----
src/USER-MISC/fix_ffl.cpp | 31 ++++++++++++++++++-------------
2 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt
index 8d6b243142..b8e745eddd 100644
--- a/doc/src/fix_ffl.txt
+++ b/doc/src/fix_ffl.txt
@@ -100,11 +100,6 @@ calculated by this fix is "extensive".
[Restrictions:]
-The GLE thermostat in its current implementation should not be used
-with rigid bodies, SHAKE or RATTLE. It is expected that all the
-thermostatted degrees of freedom are fully flexible, and the sampled
-ensemble will not be correct otherwise.
-
In order to perform constant-pressure simulations please use
"fix press/berendsen"_fix_press_berendsen.html, rather than
"fix npt"_fix_nh.html, to avoid duplicate integration of the
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
index 54e5c03a62..29fce9b8ff 100644
--- a/src/USER-MISC/fix_ffl.cpp
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -22,9 +22,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_ffl.h"
#include "math_extra.h"
#include "atom.h"
@@ -91,19 +91,24 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
int seed = force->inumeric(FLERR,arg[6]);
// Flip type used, uses rescale if no flip is given
- if (narg == 8) strcpy(flip_type,arg[7]);
- else strcpy(flip_type,"rescale");
+ if (narg == 8) {
+ if (strcmp(arg[7],"no_flip") == 0) {flip_int = 0;}
+ else if ((strcmp(arg[7],"rescale") == 0) {flip_int = 1;}
+ else if ((strcmp(arg[7],"hard") == 0) {flip_int = 2;}
+ else if ((strcmp(arg[7],"soft") == 0) {flip_int = 3;}
+ else {
+ error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
+ }
+ } else {
+ flip_int = 1;
+ }
- // Tests if the flip type is valid
- if ( strcmp(flip_type,"rescale") && strcmp(flip_type,"hard")
- && strcmp(flip_type,"soft") && strcmp(flip_type,"no_flip") )
- error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
- if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0;
- if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1;
- if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2;
- if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3;
+// if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0;
+ // if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1;
+ // if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2;
+ // if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3;
t_target=t_start;
const double kT = t_target * force->boltz / force->mvv2e;
--
GitLab
From 14251948f31eb678597c641b3fee51f1718fb61d Mon Sep 17 00:00:00 2001
From: dilkins <wilkinsd@outlook.com>
Date: Tue, 2 Oct 2018 10:18:40 +0200
Subject: [PATCH 300/332] LAMMPS coding conventions
---
src/USER-MISC/fix_ffl.cpp | 656 ++++++++++++++++++--------------------
1 file changed, 303 insertions(+), 353 deletions(-)
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
index 29fce9b8ff..f6cf1b268e 100644
--- a/src/USER-MISC/fix_ffl.cpp
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -17,7 +17,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL),
+ Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL),
Michele Ceriotti (EPFL)
------------------------------------------------------------------------- */
@@ -62,143 +62,132 @@ enum {CONSTANT,EQUAL,ATOM};
FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
-{
-
-
- if (narg < 7)
- error->all(FLERR,"Illegal fix ffl command. Expecting: fix <fix-ID>"
- " <group-ID> ffl <tau> <Tstart> <Tstop> <seed> ");
-
- restart_peratom = 1;
- time_integrate = 1;
- scalar_flag = 1;
-
- //gamma = 1/ time constant(tau)
- if (force->numeric(FLERR,arg[3]) <= 0)
- error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0");
- gamma = 1.0/force->numeric(FLERR,arg[3]);
- ffl_every=1;
- ffl_step=0;
-
- // start temperature (t ramp)
- t_start = force->numeric(FLERR,arg[4]);
-
- // final temperature (t ramp)
- t_stop = force->numeric(FLERR,arg[5]);
-
- // PRNG seed
- int seed = force->inumeric(FLERR,arg[6]);
-
- // Flip type used, uses rescale if no flip is given
- if (narg == 8) {
- if (strcmp(arg[7],"no_flip") == 0) {flip_int = 0;}
- else if ((strcmp(arg[7],"rescale") == 0) {flip_int = 1;}
- else if ((strcmp(arg[7],"hard") == 0) {flip_int = 2;}
- else if ((strcmp(arg[7],"soft") == 0) {flip_int = 3;}
- else {
- error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
- }
+ Fix(lmp, narg, arg) {
+
+
+ if (narg < 7)
+ error->all(FLERR,"Illegal fix ffl command. Expecting: fix <fix-ID>"
+ " <group-ID> ffl <tau> <Tstart> <Tstop> <seed> ");
+
+ restart_peratom = 1;
+ time_integrate = 1;
+ scalar_flag = 1;
+
+ //gamma = 1/ time constant(tau)
+ if (force->numeric(FLERR,arg[3]) <= 0)
+ error->all(FLERR,"Illegal fix ffl tau value, should be greater than 0");
+ gamma = 1.0/force->numeric(FLERR,arg[3]);
+ ffl_every=1;
+ ffl_step=0;
+
+ // start temperature (t ramp)
+ t_start = force->numeric(FLERR,arg[4]);
+
+ // final temperature (t ramp)
+ t_stop = force->numeric(FLERR,arg[5]);
+
+ // PRNG seed
+ int seed = force->inumeric(FLERR,arg[6]);
+
+ // Flip type used, uses rescale if no flip is given
+ if (narg == 8) {
+ if (strcmp(arg[7],"no_flip") == 0) {
+ flip_int = 0;
+ } else if (strcmp(arg[7],"rescale") == 0) {
+ flip_int = 1;
+ } else if (strcmp(arg[7],"hard") == 0) {
+ flip_int = 2;
+ } else if (strcmp(arg[7],"soft") == 0) {
+ flip_int = 3;
} else {
- flip_int = 1;
+ error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
}
+ } else {
+ flip_int = 1;
+ }
+ t_target=t_start;
+ const double kT = t_target * force->boltz / force->mvv2e;
-// if ( strcmp(flip_type,"no_flip") == 0 ) flip_int = 0;
- // if ( strcmp(flip_type,"rescale") == 0 ) flip_int = 1;
- // if ( strcmp(flip_type,"hard") == 0 ) flip_int = 2;
- // if ( strcmp(flip_type,"soft") == 0 ) flip_int = 3;
+ // initialize Marsaglia RNG with processor-unique seed
+ // NB: this means runs will not be the same with different numbers of processors
+ if (seed <= 0) error->all(FLERR,"Illegal fix ffl command");
+ random = new RanMars(lmp,seed + comm->me);
- t_target=t_start;
- const double kT = t_target * force->boltz / force->mvv2e;
+ // allocate per-type arrays for mass-scaling
+ sqrt_m=NULL;
+ memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m");
+ // allocates space for temporaries
+ ffl_tmp1=ffl_tmp2=NULL;
- // initialize Marsaglia RNG with processor-unique seed
- // NB: this means runs will not be the same with different numbers of processors
- if (seed <= 0) error->all(FLERR,"Illegal fix ffl command");
- random = new RanMars(lmp,seed + comm->me);
+ grow_arrays(atom->nmax);
- // allocate per-type arrays for mass-scaling
- sqrt_m=NULL;
- memory->grow(sqrt_m, atom->ntypes+1,"ffl:sqrt_m");
+ // add callbacks to enable restarts
+ atom->add_callback(0);
+ atom->add_callback(1);
- // allocates space for temporaries
- ffl_tmp1=ffl_tmp2=NULL;
-
- grow_arrays(atom->nmax);
-
- // add callbacks to enable restarts
- atom->add_callback(0);
- atom->add_callback(1);
-
- energy = 0.0;
+ energy = 0.0;
}
/* --- Frees up memory used by temporaries and buffers ------------------ */
-FixFFL::~FixFFL()
-{
- delete random;
+FixFFL::~FixFFL() {
+ delete random;
- memory->destroy(sqrt_m);
- memory->destroy(ffl_tmp1);
- memory->destroy(ffl_tmp2);
+ memory->destroy(sqrt_m);
+ memory->destroy(ffl_tmp1);
+ memory->destroy(ffl_tmp2);
}
/* ---------------------------------------------------------------------- */
-int FixFFL::setmask()
-{
- int mask = 0;
+int FixFFL::setmask() {
+ int mask = 0;
- mask |= INITIAL_INTEGRATE;
- mask |= FINAL_INTEGRATE;
- mask |= INITIAL_INTEGRATE_RESPA;
- mask |= FINAL_INTEGRATE_RESPA;
- mask |= THERMO_ENERGY;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ mask |= INITIAL_INTEGRATE_RESPA;
+ mask |= FINAL_INTEGRATE_RESPA;
+ mask |= THERMO_ENERGY;
- return mask;
+ return mask;
}
/* ------- Initializes one-time quantities for FFL ---------------------- */
-void FixFFL::init()
-{
- doffl = 1;
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
-
- // set force prefactors
- if (!atom->rmass)
- {
- for (int i = 1; i <= atom->ntypes; i++)
- {
- sqrt_m[i] = sqrt(atom->mass[i]);
- }
- }
+void FixFFL::init() {
+ doffl = 1;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
- if (strstr(update->integrate_style,"respa"))
- {
- nlevels_respa = ((Respa *) update->integrate)->nlevels;
- step_respa = ((Respa *) update->integrate)->step;
+ // set force prefactors
+ if (!atom->rmass) {
+ for (int i = 1; i <= atom->ntypes; i++) {
+ sqrt_m[i] = sqrt(atom->mass[i]);
}
+ }
- init_ffl();
+ if (strstr(update->integrate_style,"respa")) {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ step_respa = ((Respa *) update->integrate)->step;
+ }
+
+ init_ffl();
}
/* ------- Initializes constants for FFL (change with T and dt) ------- */
-void FixFFL::init_ffl()
-{
- const double kT = t_target * force->boltz / force->mvv2e;
+void FixFFL::init_ffl() {
+ const double kT = t_target * force->boltz / force->mvv2e;
- // compute constants for FFL
+ // compute constants for FFL
- c1 = exp ( - gamma * 0.5 * dtv );
- c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term
+ c1 = exp ( - gamma * 0.5 * dtv );
+ c2 = sqrt( (1.0 - c1*c1)* kT ); //without the mass term
}
@@ -207,279 +196,244 @@ void FixFFL::init_ffl()
/* ---------------------------------------------------------------------- */
-void FixFFL::setup(int vflag)
-{
- if (strstr(update->integrate_style,"verlet"))
- post_force(vflag);
- else
- {
- ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
- post_force_respa(vflag,nlevels_respa-1,0);
- ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
- }
+void FixFFL::setup(int vflag) {
+ if (strstr(update->integrate_style,"verlet"))
+ post_force(vflag);
+ else {
+ ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+ post_force_respa(vflag,nlevels_respa-1,0);
+ ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+ }
}
-void FixFFL::ffl_integrate()
-{
- double **v = atom->v;
- double *rmass = atom->rmass, smi, ismi;
- double factor;
- int *type = atom->type;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (igroup == atom->firstgroup) nlocal = atom->nfirst;
-
- // loads momentum data (mass-scaled) into the temporary vectors for the propagation
- int nk=0;
- double deltae=0.0;
- for (int i = 0; i < nlocal; i++)
- {
- if (mask[i] & groupbit)
- {
- if (rmass) smi = sqrt(rmass[i]);
- else smi = sqrt_m[type[i]];
-
- for (int k = 0; k<3; k++)
- {
- // first loads velocities and accumulates conserved quantity
- ffl_tmp2[nk] = v[i][k] * smi;
- deltae += ffl_tmp2[nk] * ffl_tmp2[nk];
- nk++;
- }
- }
+void FixFFL::ffl_integrate() {
+ double **v = atom->v;
+ double *rmass = atom->rmass, smi, ismi;
+ double factor;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ // loads momentum data (mass-scaled) into the temporary vectors for the propagation
+ int nk=0;
+ double deltae=0.0;
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ if (rmass) smi = sqrt(rmass[i]);
+ else smi = sqrt_m[type[i]];
+
+ for (int k = 0; k<3; k++) {
+ // first loads velocities and accumulates conserved quantity
+ ffl_tmp2[nk] = v[i][k] * smi;
+ deltae += ffl_tmp2[nk] * ffl_tmp2[nk];
+ nk++;
+ }
}
+ }
- //fills up a vector of random numbers
- for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian();
+ //fills up a vector of random numbers
+ for (int i = 0; i < nk; i++) ffl_tmp1[i] = random->gaussian();
- // unloads momentum data (mass-scaled) from the temporary vectors
- nk=0;
- for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
- {
- if (rmass) ismi = 1.0 / sqrt(rmass[i]);
- else ismi = 1.0/ sqrt_m[type[i]];
-
- for (int k = 0; k<3; k++)
- {
- // fetches new velocities and completes computation of the conserved quantity change
- v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi;
-
- deltae-= v[i][k]*v[i][k] /ismi /ismi;
-
- //flips the sign of the momentum (HARD FLIP)
- if ( flip_int == 2)
- {
- if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k];
- }
-
- nk++;
- }
+ // unloads momentum data (mass-scaled) from the temporary vectors
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
+ if (rmass) ismi = 1.0 / sqrt(rmass[i]);
+ else ismi = 1.0/ sqrt_m[type[i]];
+
+ for (int k = 0; k<3; k++) {
+ // fetches new velocities and completes computation of the conserved quantity change
+ v[i][k]= c1*v[i][k] + c2*ffl_tmp1[nk]*ismi;
+
+ deltae-= v[i][k]*v[i][k] /ismi /ismi;
+
+ //flips the sign of the momentum (HARD FLIP)
+ if ( flip_int == 2) {
+ if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k];
}
- //rescale operation (RESCALE FLIP)
- if (flip_int == 1)
- {
- nk=0;
- for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
- {
- factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) /
- (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
- + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]));
-
- for (int k = 0; k<3; k++)
- {
- v[i][k]= factor * ffl_tmp2[nk];
- nk++;
- }
- }
+ nk++;
+ }
}
+ //rescale operation (RESCALE FLIP)
+ if (flip_int == 1) {
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
+ factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) /
+ (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
+ + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]));
+
+ for (int k = 0; k<3; k++) {
+ v[i][k]= factor * ffl_tmp2[nk];
+ nk++;
+ }
+ }
+ }
+
- //soft flip operation (SOFT FLIP)
- if (flip_int == 3)
- {
- nk=0;
- for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit)
- {
- factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2];
- if (factor < 0)
- {
- factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
- + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]);
-
- for (int k = 0; k<3; k++)
- {
- v[i][k] -= 2.0 * factor * ffl_tmp2[nk];
- nk++;
- }
- }
- else
- nk += 3;
- }
+ //soft flip operation (SOFT FLIP)
+ if (flip_int == 3) {
+ nk=0;
+ for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
+ factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2];
+ if (factor < 0) {
+ factor = factor / (ffl_tmp2[nk]*ffl_tmp2[nk] + ffl_tmp2[nk+1]*ffl_tmp2[nk+1]
+ + ffl_tmp2[nk+2]*ffl_tmp2[nk+2]);
+
+ for (int k = 0; k<3; k++) {
+ v[i][k] -= 2.0 * factor * ffl_tmp2[nk];
+ nk++;
+ }
+ } else {
+ nk += 3;
+ }
}
- energy += deltae*0.5*force->mvv2e;
+ }
+
+ energy += deltae*0.5*force->mvv2e;
}
-void FixFFL::initial_integrate(int vflag)
-{
- double dtfm;
-
- // update v and x of atoms in group
- double **x = atom->x;
- double **v = atom->v;
- double **f = atom->f;
- double *rmass = atom->rmass;
- double *mass = atom->mass;
- int *type = atom->type;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (igroup == atom->firstgroup) nlocal = atom->nfirst;
-
- ffl_step--;
- if (doffl && ffl_step<1) ffl_integrate();
-
- if (rmass)
- {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- }
+void FixFFL::initial_integrate(int vflag) {
+ double dtfm;
- }
- else
- {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- }
- }
+ // update v and x of atoms in group
+ double **x = atom->x;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ ffl_step--;
+ if (doffl && ffl_step<1) ffl_integrate();
+
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+
+ } else {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
}
-void FixFFL::final_integrate()
-{
- double dtfm;
-
- // update v of atoms in group
-
- double **v = atom->v;
- double **f = atom->f;
- double *rmass = atom->rmass;
- double *mass = atom->mass;
- int *type = atom->type;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (igroup == atom->firstgroup) nlocal = atom->nfirst;
-
- if (rmass)
- {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- {
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- }
+void FixFFL::final_integrate() {
+ double dtfm;
- }
- else
- {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
- {
- dtfm = dtf / mass[type[i]];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
- }
- }
+ // update v of atoms in group
- if (doffl && ffl_step<1)
- {
- ffl_integrate();
- ffl_step = ffl_every;
- }
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
- // Change the temperature for the next step
- double delta = update->ntimestep - update->beginstep;
- delta /= update->endstep - update->beginstep;
- t_target = t_start + delta * (t_stop - t_start);
- if (t_stop != t_start)
- {
- // only updates if it is really necessary
- init_ffl();
- }
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ }
+
+ } else {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+ }
+ }
+
+ if (doffl && ffl_step<1) {
+ ffl_integrate();
+ ffl_step = ffl_every;
+ }
+
+ // Change the temperature for the next step
+ double delta = update->ntimestep - update->beginstep;
+ delta /= update->endstep - update->beginstep;
+ t_target = t_start + delta * (t_stop - t_start);
+ if (t_stop != t_start) {
+ // only updates if it is really necessary
+ init_ffl();
+ }
}
/* ---------------------------------------------------------------------- */
-void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop)
-{
- dtv = step_respa[ilevel];
- dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) {
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
- // innermost level - NVE update of v and x
- // all other levels - NVE update of v
+ // innermost level - NVE update of v and x
+ // all other levels - NVE update of v
- if (ilevel==nlevels_respa-1) ffl_integrate();
- doffl=0;
- if (ilevel == 0) initial_integrate(vflag);
- else
- {
- final_integrate();
- }
+ if (ilevel==nlevels_respa-1) ffl_integrate();
+ doffl=0;
+ if (ilevel == 0) initial_integrate(vflag);
+ else {
+ final_integrate();
+ }
}
-void FixFFL::final_integrate_respa(int ilevel, int iloop)
-{
+void FixFFL::final_integrate_respa(int ilevel, int iloop) {
- dtv = step_respa[ilevel];
- dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
- doffl=0;
- final_integrate();
- if (ilevel==nlevels_respa-1) ffl_integrate();
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ doffl=0;
+ final_integrate();
+ if (ilevel==nlevels_respa-1) ffl_integrate();
}
-double FixFFL::compute_scalar()
-{
+double FixFFL::compute_scalar() {
- double energy_me = energy;
- double energy_all;
- MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
+ double energy_me = energy;
+ double energy_all;
+ MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
- return energy_all;
+ return energy_all;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
-void *FixFFL::extract(const char *str, int &dim)
-{
- dim = 0;
- if (strcmp(str,"t_target") == 0)
- {
- return &t_target;
- }
- return NULL;
+void *FixFFL::extract(const char *str, int &dim) {
+ dim = 0;
+ if (strcmp(str,"t_target") == 0) {
+ return &t_target;
+ }
+ return NULL;
}
@@ -487,32 +441,29 @@ void *FixFFL::extract(const char *str, int &dim)
Called when a change to the target temperature is requested mid-run
------------------------------------------------------------------------- */
-void FixFFL::reset_target(double t_new)
-{
+void FixFFL::reset_target(double t_new) {
- t_target = t_start = t_stop = t_new;
+ t_target = t_start = t_stop = t_new;
}
/* ----------------------------------------------------------------------
Called when a change to the timestep is requested mid-run
------------------------------------------------------------------------- */
-void FixFFL::reset_dt()
-{
- // set the time integration constants
- dtv = update->dt;
- dtf = 0.5 * update->dt * (force->ftm2v);
- init_ffl();
+void FixFFL::reset_dt() {
+ // set the time integration constants
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * (force->ftm2v);
+ init_ffl();
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
-double FixFFL::memory_usage()
-{
- double bytes = atom->nmax*(3*2)*sizeof(double);
- return bytes;
+double FixFFL::memory_usage() {
+ double bytes = atom->nmax*(3*2)*sizeof(double);
+ return bytes;
}
@@ -520,13 +471,12 @@ double FixFFL::memory_usage()
allocate local atom-based arrays
------------------------------------------------------------------------- */
-void FixFFL::grow_arrays(int nmax)
-{
- memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1");
- memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2");
- //zeroes out temporary buffers
- for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0;
- for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0;
+void FixFFL::grow_arrays(int nmax) {
+ memory->grow(ffl_tmp1, nmax*3,"ffl:tmp1");
+ memory->grow(ffl_tmp2, nmax*3,"ffl:tmp2");
+ //zeroes out temporary buffers
+ for (int i=0; i< nmax*3; ++i) ffl_tmp1[i] = 0.0;
+ for (int i=0; i< nmax*3; ++i) ffl_tmp2[i] = 0.0;
}
--
GitLab
From d5e71e709913271d5d192c0904c216e2741b3323 Mon Sep 17 00:00:00 2001
From: dilkins <wilkinsd@outlook.com>
Date: Tue, 2 Oct 2018 10:41:55 +0200
Subject: [PATCH 301/332] enumeration of flip types
---
src/USER-MISC/fix_ffl.cpp | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
index f6cf1b268e..e2fb0166a2 100644
--- a/src/USER-MISC/fix_ffl.cpp
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -49,6 +49,7 @@ using namespace FixConst;
enum {NOBIAS,BIAS};
enum {CONSTANT,EQUAL,ATOM};
+enum {NO_FLIP, FLIP_RESCALE, FLIP_HARD, FLIP_SOFT};
//#define FFL_DEBUG 1
#define MAXLINE 1024
@@ -92,18 +93,18 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
// Flip type used, uses rescale if no flip is given
if (narg == 8) {
if (strcmp(arg[7],"no_flip") == 0) {
- flip_int = 0;
+ flip_int = NO_FLIP;
} else if (strcmp(arg[7],"rescale") == 0) {
- flip_int = 1;
+ flip_int = FLIP_RESCALE;
} else if (strcmp(arg[7],"hard") == 0) {
- flip_int = 2;
+ flip_int = FLIP_HARD;
} else if (strcmp(arg[7],"soft") == 0) {
- flip_int = 3;
+ flip_int = FLIP_SOFT;
} else {
error->all(FLERR,"Illegal fix ffl flip type, only accepts : rescale - hard - soft - no_flip");
}
} else {
- flip_int = 1;
+ flip_int = FLIP_RESCALE;
}
t_target=t_start;
@@ -249,7 +250,7 @@ void FixFFL::ffl_integrate() {
deltae-= v[i][k]*v[i][k] /ismi /ismi;
//flips the sign of the momentum (HARD FLIP)
- if ( flip_int == 2) {
+ if ( flip_int == FLIP_HARD) {
if (v[i][k]*ffl_tmp2[nk] < 0.0) v[i][k] = -v[i][k];
}
@@ -258,7 +259,7 @@ void FixFFL::ffl_integrate() {
}
//rescale operation (RESCALE FLIP)
- if (flip_int == 1) {
+ if (flip_int == FLIP_RESCALE) {
nk=0;
for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
factor = sqrt ((v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) /
@@ -274,7 +275,7 @@ void FixFFL::ffl_integrate() {
//soft flip operation (SOFT FLIP)
- if (flip_int == 3) {
+ if (flip_int == FLIP_SOFT) {
nk=0;
for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) {
factor = v[i][0]*ffl_tmp2[nk] + v[i][1]*ffl_tmp2[nk+1] + v[i][2]*ffl_tmp2[nk+2];
--
GitLab
From 990a93f9d98b78991d99e1aa340e551daf3c34bd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 10:58:28 +0200
Subject: [PATCH 302/332] fix typo in example input
---
doc/src/dihedral_nharmonic.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 7a8bf6cdb7..660bbb3f1f 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -16,7 +16,7 @@ dihedral_style nharmonic :pre
[Examples:]
dihedral_style nharmonic
-dihedral_coeff 3 10.0 20.0 30.0 :pre
+dihedral_coeff * 3 10.0 20.0 30.0 :pre
[Description:]
--
GitLab
From 66bfdd20d4275e09480f0429115c2e0546223a8b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 11:24:45 +0200
Subject: [PATCH 303/332] fully integrate fix ffl docs into the manual system
---
doc/src/Commands_fix.txt | 1 +
doc/src/fix_ffl.txt | 12 ++++++------
doc/src/fixes.txt | 1 +
doc/src/lammps.book | 1 +
4 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index e002c11770..2b6f4a3080 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -65,6 +65,7 @@ OPT.
"eos/table/rx (k)"_fix_eos_table_rx.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
+"ffl"_fix_ffl.html,
"filter/corotate"_fix_filter_corotate.html,
"flow/gauss"_fix_flow_gauss.html,
"freeze"_fix_freeze.html,
diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt
index b8e745eddd..8b874fb3b7 100644
--- a/doc/src/fix_ffl.txt
+++ b/doc/src/fix_ffl.txt
@@ -94,9 +94,9 @@ system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is the
-cumulative energy change due to this fix. The scalar value
-calculated by this fix is "extensive".
+"output commands"_Howto_output.html. The scalar is the cumulative
+energy change due to this fix. The scalar value calculated by this
+fix is "extensive".
[Restrictions:]
@@ -105,9 +105,9 @@ In order to perform constant-pressure simulations please use
"fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion.
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index f2f257b134..9ab299465b 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -46,6 +46,7 @@ Fixes :h1
fix_eos_table_rx
fix_evaporate
fix_external
+ fix_ffl
fix_filter_corotate
fix_flow_gauss
fix_freeze
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0e5ceae861..110ae3876c 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -266,6 +266,7 @@ fix_eos_table.html
fix_eos_table_rx.html
fix_evaporate.html
fix_external.html
+fix_ffl.html
fix_filter_corotate.html
fix_flow_gauss.html
fix_freeze.html
--
GitLab
From 4b4f7d6ee037013a448b2a0037a09dd7a12c4aa7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 11:25:12 +0200
Subject: [PATCH 304/332] implement conventions for unique links in docs
---
doc/src/fix_ffl.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt
index 8b874fb3b7..ea33dc432f 100644
--- a/doc/src/fix_ffl.txt
+++ b/doc/src/fix_ffl.txt
@@ -69,7 +69,7 @@ The flipping type {flip-type} can be chosen between 4 types described in
"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting
step and it flips the momenta of the atoms. If no_flip is chosen, no flip
will be executed and the integration will be the same as a standard
-Langevin thermostat "(Bussi)"_#Bussi. The other flipping types are : rescale - hard - soft.
+Langevin thermostat "(Bussi)"_#Bussi3. The other flipping types are : rescale - hard - soft.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -119,6 +119,6 @@ dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html
:link(Hijazi)
[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
-:link(Bussi)
+:link(Bussi3)
[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
--
GitLab
From ca3a64ea3e26c8a62db4f9b1b1faef7f722289d3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 11:25:39 +0200
Subject: [PATCH 305/332] fully integrate fix ffl in conventional build
processing
---
src/.gitignore | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/.gitignore b/src/.gitignore
index 3a6ba21426..d7cfae2ffb 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -424,6 +424,8 @@
/fix_eos_table.h
/fix_evaporate.cpp
/fix_evaporate.h
+/fix_ffl.cpp
+/fix_ffl.h
/fix_filter_corotate.cpp
/fix_filter_corotate.h
/fix_viscosity.cpp
--
GitLab
From 3a0cfc1d57869c51309e8828f48a2a7597357481 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 09:32:26 -0400
Subject: [PATCH 306/332] Modifying headers
---
src/USER-MISC/compute_pressure_cylinder.cpp | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index bae6398691..4c3b227842 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <cmath>
+#include <string.h>
+#include <stdlib.h>
#include "compute_pressure_cylinder.h"
#include "atom.h"
#include "update.h"
@@ -25,6 +25,7 @@
#include "group.h"
#include "memory.h"
#include "error.h"
+#include "citeme.h"
using namespace LAMMPS_NS;
--
GitLab
From 89c0655809998f498a172c4018f46337cb7d3087 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 09:46:53 -0400
Subject: [PATCH 307/332] Add input validation
---
src/USER-MISC/compute_pressure_cylinder.cpp | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index 4c3b227842..a40e105b5a 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -26,6 +26,7 @@
#include "memory.h"
#include "error.h"
#include "citeme.h"
+#include "domain.h"
using namespace LAMMPS_NS;
@@ -56,10 +57,19 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
zhi=force->numeric(FLERR,arg[4]);
Rmax=force->numeric(FLERR,arg[5]);
bin_width=force->numeric(FLERR,arg[6]);
+
+ if (bin_width<0.0 || bin_width<Rmax)
+ error->all(FLERR,"Illegal compute pressure/cylinder command");
+ if (zhi<zlo || (zhi-zlo)<bin_width)
+ error->all(FLERR,"Illegal compute pressure/cylinder command");
+ if (zhi>domain->boxhi[2] || zlo<domain->boxlo[2])
+ error->all(FLERR,"Illegal compute pressure/cylinder command");
nbins=(int)(Rmax/bin_width);
-
nzbins=(int)((zhi-zlo)/bin_width);
+
+ if (nbins<1 or nzbins<1)
+ error->all(FLERR,"Illegal compute pressure/cylinder command");
array_flag=1;
vector_flag=0;
--
GitLab
From af5ac6bcdf9b97e2eeeb124edd86426f423aa8a2 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 09:55:37 -0400
Subject: [PATCH 308/332] Add NULL pointers to constructor init
---
src/USER-MISC/compute_pressure_cylinder.cpp | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index a40e105b5a..cb8f841ac3 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -49,7 +49,11 @@ if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg)
+ Compute(lmp, narg, arg),
+ R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL),
+ density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL),
+ ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL),
+ Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL)
{
if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command");
--
GitLab
From 69c3ff560eb96c57b510b80f98962129954c0426 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 10:11:57 -0400
Subject: [PATCH 309/332] Clarify restrictions and output
---
doc/src/compute_pressure_cylinder.txt | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt
index c6d97e7958..e73ac5b53d 100644
--- a/doc/src/compute_pressure_cylinder.txt
+++ b/doc/src/compute_pressure_cylinder.txt
@@ -41,14 +41,23 @@ tensor values are output in pressure units.
[Output info:]
This compute calculates a global array with 5 columns and Rmax/bin_width
-rows.
+rows. The output columns are: R (distance units), number density (inverse
+volume units), configurational radial pressure (pressure units),
+configurational azimuthal pressure (pressure units), and configurational
+axial pressure (pressure units).
The values calculated by this compute are
"intensive". The pressure values will be in pressure
"units"_units.html. The number density values will be in
inverse volume "units"_units.html.
-[Restrictions:] none
+[Restrictions:] This compute currently calculates the pressure
+tensor contributions for pair styles only (i.e. no bond, dihedral, etc.)
+and requires pair force
+calculations not available for many manybody pair styles. K-space
+calculations are also excluded. Note that the pressure outputs
+are the configurational terms only; the kinetic contribution may
+be calculated from the number density output by P_kin=density*k*T.
[Related commands:]
--
GitLab
From b5a5270f4a858bdda3c733d51fb76d011c0f6464 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 16:29:18 +0200
Subject: [PATCH 310/332] fix typos in compute msd/chunk
as reported by @evoyiatzis the example is incorrect,
but also a mention of the compute a few lines above.
---
doc/src/compute_msd_chunk.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 264f38d5fd..7ff57c9844 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -90,12 +90,12 @@ This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.
-The simplest way to output the results of the compute com/msd
+The simplest way to output the results of the compute msd/chunk
calculation to a file is to use the "fix ave/time"_fix_ave_time.html
command, for example:
compute cc1 all chunk/atom molecule
-compute myChunk all com/msd cc1
+compute myChunk all msd/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
[Output info:]
--
GitLab
From ac658a17fc612c73267e9678139c4daf84d982d7 Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 10:34:08 -0400
Subject: [PATCH 311/332] Update compute_pressure_cylinder.cpp
---
src/USER-MISC/compute_pressure_cylinder.cpp | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index cb8f841ac3..cbef2941a8 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -40,9 +40,7 @@ static const char cite_compute_pressure_cylinder[] =
" volume = 149,\n"
" pages = {084109}\n"
"}\n\n";
-
-if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
-
+
/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Calculate the configurational components of the pressure tensor in
cylindrical geometry, according to the formulation of Addington et al. (2018)
@@ -55,6 +53,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL),
Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL)
{
+ if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command");
zlo=force->numeric(FLERR,arg[3]);
--
GitLab
From c7c0defa7715d7a0d8a1d3cbe0f99de609a8590c Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 10:45:43 -0400
Subject: [PATCH 312/332] Insert a comma
---
src/USER-MISC/compute_pressure_cylinder.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index cbef2941a8..ebe28d848a 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -51,7 +51,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL),
density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL),
ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL),
- Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL) PzAinv(NULL), binz(NULL)
+ Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command");
--
GitLab
From 57b2f605564bcb073d4a3aee2e35cec851cc260e Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Tue, 2 Oct 2018 09:45:13 -0600
Subject: [PATCH 313/332] Fix bug in Kokkos EAM
---
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 3 +++
src/KOKKOS/pair_eam_fs_kokkos.cpp | 3 +++
src/KOKKOS/pair_eam_kokkos.cpp | 3 +++
3 files changed, 9 insertions(+)
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 49e1313c26..e198ddb85a 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -165,6 +165,9 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_rho, dup_rho);
+
// communicate and sum densities (on the host)
if (newton_pair) {
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index ee0a799826..f5e4445db3 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -165,6 +165,9 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_rho, dup_rho);
+
// communicate and sum densities (on the host)
if (newton_pair) {
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index a1431334b4..6ef3d99ac3 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -159,6 +159,9 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
+ if (need_dup)
+ Kokkos::Experimental::contribute(d_rho, dup_rho);
+
// communicate and sum densities (on the host)
if (newton_pair) {
--
GitLab
From f81836d605e8516713d16dae62f8d1f3f28cb4f6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 11:51:23 -0400
Subject: [PATCH 314/332] reformat compute pressure/cylinder docs and integrate
it into the manual
---
doc/src/compute_pressure_cylinder.txt | 44 ++++++++++++++++-----------
doc/src/computes.txt | 1 +
doc/src/lammps.book | 1 +
3 files changed, 28 insertions(+), 18 deletions(-)
diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt
index e73ac5b53d..4865fe8a79 100644
--- a/doc/src/compute_pressure_cylinder.txt
+++ b/doc/src/compute_pressure_cylinder.txt
@@ -25,18 +25,19 @@ compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre
[Description:]
-Define a computation that calculates the pressure tensor of a
-system in cylindrical coordinates, as discussed in "(Addington)"_#Addington1.
+Define a computation that calculates the pressure tensor of a system in
+cylindrical coordinates, as discussed in "(Addington)"_#Addington1.
This is useful for systems with a single axis of rotational symmetry,
-such as cylindrical micelles or carbon nanotubes. The compute splits
-the system into radial, cylindrical-shell-type bins of width bin_width, centered at x=0,y=0,
-and calculates the radial (P_rhorho), azimuthal (P_phiphi), and axial (P_zz) components of the configurational pressure
-tensor. The local density is also calculated for each bin, so that
-the true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf.
-The output is a global array with 5 columns; one each for bin radius,
-local number density, P_rhorho, P_phiphi, and P_zz. The number of
-rows is governed by the values of Rmax and bin_width. Pressure
-tensor values are output in pressure units.
+such as cylindrical micelles or carbon nanotubes. The compute splits the
+system into radial, cylindrical-shell-type bins of width bin_width,
+centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal
+(P_phiphi), and axial (P_zz) components of the configurational pressure
+tensor. The local density is also calculated for each bin, so that the
+true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf. The
+output is a global array with 5 columns; one each for bin radius, local
+number density, P_rhorho, P_phiphi, and P_zz. The number of rows is
+governed by the values of Rmax and bin_width. Pressure tensor values are
+output in pressure units.
[Output info:]
@@ -51,13 +52,20 @@ The values calculated by this compute are
"units"_units.html. The number density values will be in
inverse volume "units"_units.html.
-[Restrictions:] This compute currently calculates the pressure
-tensor contributions for pair styles only (i.e. no bond, dihedral, etc.)
-and requires pair force
-calculations not available for many manybody pair styles. K-space
-calculations are also excluded. Note that the pressure outputs
-are the configurational terms only; the kinetic contribution may
-be calculated from the number density output by P_kin=density*k*T.
+[Restrictions:]
+
+This compute currently calculates the pressure tensor contributions
+for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
+and in the presence of bonded interactions, the result will be incorrect
+due to exclusions for special bonds) and requires pair-wise force
+calculations not available for most manybody pair styles. K-space
+calculations are also excluded. Note that this pressure compute outputs
+the configurational terms only; the kinetic contribution is not included
+and may be calculated from the number density output by P_kin=density*k*T.
+
+This compute is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index a6a194ac24..bdd6455541 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -67,6 +67,7 @@ Computes :h1
compute_pe_atom
compute_plasticity_atom
compute_pressure
+ compute_pressure_cylinder
compute_pressure_uef
compute_property_atom
compute_property_chunk
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0e5ceae861..4bb4394062 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -464,6 +464,7 @@ compute_pe.html
compute_pe_atom.html
compute_plasticity_atom.html
compute_pressure.html
+compute_pressure_cylinder.html
compute_pressure_uef.html
compute_property_atom.html
compute_property_chunk.html
--
GitLab
From 13d3903e8dc36a696c889b4835f55feb821c6f8a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 11:56:29 -0400
Subject: [PATCH 315/332] integrate compute pressure/cylinder into build and
README
---
src/.gitignore | 2 ++
src/USER-MISC/README | 1 +
2 files changed, 3 insertions(+)
diff --git a/src/.gitignore b/src/.gitignore
index 3a6ba21426..323b63693c 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -296,6 +296,8 @@
/compute_plasticity_atom.h
/compute_pressure_bocs.cpp
/compute_pressure_bocs.h
+/compute_pressure_cylinder.cpp
+/compute_pressure_cylinder.h
/compute_pressure_grem.cpp
/compute_pressure_grem.h
/compute_rigid_local.cpp
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index eb221c07db..30431a704b 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -30,6 +30,7 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
+compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
--
GitLab
From ff7449b29af0010cc124ef65f64b0856bbf37e07 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 12:27:05 -0400
Subject: [PATCH 316/332] ensure, that we have no division by zero and add an
upper limit for bins
---
src/USER-MISC/compute_pressure_cylinder.cpp | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index ebe28d848a..04767eb4c3 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -61,17 +61,20 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
Rmax=force->numeric(FLERR,arg[5]);
bin_width=force->numeric(FLERR,arg[6]);
- if (bin_width<0.0 || bin_width<Rmax)
+ if ((bin_width <= 0.0) || (bin_width < Rmax))
error->all(FLERR,"Illegal compute pressure/cylinder command");
- if (zhi<zlo || (zhi-zlo)<bin_width)
+ if ((zhi < zlo) || ((zhi-zlo) < bin_width))
error->all(FLERR,"Illegal compute pressure/cylinder command");
- if (zhi>domain->boxhi[2] || zlo<domain->boxlo[2])
+ if ((zhi > domain->boxhi[2]) || (zlo < domain->boxlo[2]))
error->all(FLERR,"Illegal compute pressure/cylinder command");
nbins=(int)(Rmax/bin_width);
nzbins=(int)((zhi-zlo)/bin_width);
-
- if (nbins<1 or nzbins<1)
+
+ // NOTE: at 2^22 = 4.2M bins, we will be close to exhausting allocatable
+ // memory on a 32-bit environment. so we use this as an upper limit.
+
+ if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22))
error->all(FLERR,"Illegal compute pressure/cylinder command");
array_flag=1;
--
GitLab
From e3b80e734a5e77c25d5a185460a4b4544fdced4d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 12:37:13 -0400
Subject: [PATCH 317/332] remove trailing whitespace
---
src/USER-MISC/compute_pressure_cylinder.cpp | 50 ++++++++++-----------
1 file changed, 25 insertions(+), 25 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index 04767eb4c3..03331a1b98 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -40,16 +40,16 @@ static const char cite_compute_pressure_cylinder[] =
" volume = 149,\n"
" pages = {084109}\n"
"}\n\n";
-
+
/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Calculate the configurational components of the pressure tensor in
+ Calculate the configurational components of the pressure tensor in
cylindrical geometry, according to the formulation of Addington et al. (2018)
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL),
- density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL),
+ density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL),
ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL),
Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL)
{
@@ -60,8 +60,8 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
zhi=force->numeric(FLERR,arg[4]);
Rmax=force->numeric(FLERR,arg[5]);
bin_width=force->numeric(FLERR,arg[6]);
-
- if ((bin_width <= 0.0) || (bin_width < Rmax))
+
+ if ((bin_width <= 0.0) || (bin_width < Rmax))
error->all(FLERR,"Illegal compute pressure/cylinder command");
if ((zhi < zlo) || ((zhi-zlo) < bin_width))
error->all(FLERR,"Illegal compute pressure/cylinder command");
@@ -73,8 +73,8 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
// NOTE: at 2^22 = 4.2M bins, we will be close to exhausting allocatable
// memory on a 32-bit environment. so we use this as an upper limit.
-
- if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22))
+
+ if ((nbins < 1) || (nzbins < 1) || (nbins > 2>>22) || (nbins > 2>>22))
error->all(FLERR,"Illegal compute pressure/cylinder command");
array_flag=1;
@@ -109,7 +109,7 @@ ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
ephi_y = new double[nphi];
nktv2p = force->nktv2p;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -170,8 +170,8 @@ void ComputePressureCyl::init()
PphiAinv=1.0/((zhi-zlo)*bin_width*2.0*(double)nphi);
invVbin[0]=1.0/((zhi-zlo)*3.14159*R2kin[0]);
- PzAinv[0]=1.0/(3.14159*R2kin[0]*((double)nzbins));
- for (int jq=1;jq<nbins;jq++)
+ PzAinv[0]=1.0/(3.14159*R2kin[0]*((double)nzbins));
+ for (int jq=1;jq<nbins;jq++)
{
invVbin[jq]=1.0/((zhi-zlo)*3.14159*(R2kin[jq]-R2kin[jq-1]));
PzAinv[jq]=1.0/(3.14159*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
@@ -206,12 +206,12 @@ void ComputePressureCyl::init_list(int id, NeighList *ptr)
void ComputePressureCyl::compute_array()
{
- invoked_array = update->ntimestep;
+ invoked_array = update->ntimestep;
int ibin;
// clear pressures
- for (ibin=0;ibin<nbins;ibin++)
+ for (ibin=0;ibin<nbins;ibin++)
{
density_temp[ibin]=0.0;
density_all[ibin]=0.0;
@@ -287,7 +287,7 @@ void ComputePressureCyl::compute_array()
double sqrtD;
double lower_z,upper_z;
- for (ii = 0; ii < inum; ii++)
+ for (ii = 0; ii < inum; ii++)
{
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
@@ -302,7 +302,7 @@ void ComputePressureCyl::compute_array()
r1=x[i][0]*x[i][0]+x[i][1]*x[i][1];
- for (jj = 0; jj < jnum; jj++)
+ for (jj = 0; jj < jnum; jj++)
{
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
@@ -313,21 +313,21 @@ void ComputePressureCyl::compute_array()
// itag = jtag is possible for long cutoffs that include images of self
// do calculation only on appropriate processor
- if (newton_pair == 0 && j >= nlocal)
+ if (newton_pair == 0 && j >= nlocal)
{
jtag = tag[j];
- if (itag > jtag)
+ if (itag > jtag)
{
if ((itag+jtag) % 2 == 0) continue;
- }
- else if (itag < jtag)
+ }
+ else if (itag < jtag)
{
if ((itag+jtag) % 2 == 1) continue;
- }
- else
+ }
+ else
{
if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp)
+ if (x[j][2] == ztmp)
{
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
@@ -458,7 +458,7 @@ void ComputePressureCyl::compute_array()
xL=xi+alpha*dx;
yL=yi+alpha*dy;
- L2=xL*xL+yL*yL;
+ L2=xL*xL+yL*yL;
if (L2>R2kin[nbins-1]) continue;
@@ -475,7 +475,7 @@ void ComputePressureCyl::compute_array()
}
// calculate pressure (force over area)
- for (ibin=0;ibin<nbins;ibin++)
+ for (ibin=0;ibin<nbins;ibin++)
{
Pr_temp[ibin]*=PrAinv[ibin]*Rinv[ibin];
Pphi_temp[ibin]*=PphiAinv;
@@ -488,7 +488,7 @@ void ComputePressureCyl::compute_array()
MPI_Allreduce(Pz_temp,Pz_all,nbins,MPI_DOUBLE,MPI_SUM,world);
// populate array
- for (ibin=0;ibin<nbins;ibin++)
+ for (ibin=0;ibin<nbins;ibin++)
{
array[ibin][0]=R[ibin];
array[ibin][2]=Pr_all[ibin]*nktv2p;
@@ -504,7 +504,7 @@ memory usage of data
double ComputePressureCyl::memory_usage()
{
- double bytes =
+ double bytes =
(3.0*(double)nphi + 16.0*(double)nbins+5.0*(double)nbins) * sizeof(double);
return bytes;
}
--
GitLab
From a6ba55080fe42a3de8e755df04ceb4bfa184b80e Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 14:33:49 -0400
Subject: [PATCH 318/332] Use MathConst namespace
---
src/USER-MISC/compute_pressure_cylinder.cpp | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index 03331a1b98..917ef75a4a 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -27,8 +27,10 @@
#include "error.h"
#include "citeme.h"
#include "domain.h"
+#include "math_const.h"
using namespace LAMMPS_NS;
+using namespace MathConst;
static const char cite_compute_pressure_cylinder[] =
"compute pressure/cylinder:\n\n"
@@ -152,7 +154,7 @@ void ComputePressureCyl::init()
for (int iphi=0;iphi<nphi;iphi++)
{
- phi=((double)iphi)*3.14159/180.0;
+ phi=((double)iphi)*MY_PI/180.0;
tangent[iphi]=tan(phi);
ephi_x[iphi]=-sin(phi);
ephi_y[iphi]=cos(phi);
@@ -165,16 +167,16 @@ void ComputePressureCyl::init()
R2[iq]=R[iq]*R[iq];
R2kin[iq]=(((double)iq)+1.0)*bin_width;
R2kin[iq]*=R2kin[iq];
- PrAinv[iq]=1.0/(2.0*3.14159*(zhi-zlo)*R[iq]);
+ PrAinv[iq]=1.0/(2.0*MY_PI*(zhi-zlo)*R[iq]);
}
PphiAinv=1.0/((zhi-zlo)*bin_width*2.0*(double)nphi);
- invVbin[0]=1.0/((zhi-zlo)*3.14159*R2kin[0]);
- PzAinv[0]=1.0/(3.14159*R2kin[0]*((double)nzbins));
+ invVbin[0]=1.0/((zhi-zlo)*MY_PI*R2kin[0]);
+ PzAinv[0]=1.0/(MY_PI*R2kin[0]*((double)nzbins));
for (int jq=1;jq<nbins;jq++)
{
- invVbin[jq]=1.0/((zhi-zlo)*3.14159*(R2kin[jq]-R2kin[jq-1]));
- PzAinv[jq]=1.0/(3.14159*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
+ invVbin[jq]=1.0/((zhi-zlo)*MY_PI*(R2kin[jq]-R2kin[jq-1]));
+ PzAinv[jq]=1.0/(MY_PI*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
}
// need an occasional half neighbor list
--
GitLab
From 08b135ce6b3b70b3d3705b4f48687ab5ef196c0b Mon Sep 17 00:00:00 2001
From: ckadding <cody.addington@gmail.com>
Date: Tue, 2 Oct 2018 14:54:09 -0400
Subject: [PATCH 319/332] Apply uniform LAMMPS formatting
---
src/USER-MISC/compute_pressure_cylinder.cpp | 99 ++++++++-------------
1 file changed, 38 insertions(+), 61 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index 917ef75a4a..bdffa32af1 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -152,16 +152,14 @@ void ComputePressureCyl::init()
double phi;
- for (int iphi=0;iphi<nphi;iphi++)
- {
+ for (int iphi = 0; iphi < nphi; iphi++) {
phi=((double)iphi)*MY_PI/180.0;
tangent[iphi]=tan(phi);
ephi_x[iphi]=-sin(phi);
ephi_y[iphi]=cos(phi);
}
- for (int iq=0;iq<nbins;iq++)
- {
+ for (int iq = 0; iq < nbins; iq++) {
R[iq]=((double)iq+0.5)*bin_width;
Rinv[iq]=1.0/R[iq];
R2[iq]=R[iq]*R[iq];
@@ -173,8 +171,8 @@ void ComputePressureCyl::init()
invVbin[0]=1.0/((zhi-zlo)*MY_PI*R2kin[0]);
PzAinv[0]=1.0/(MY_PI*R2kin[0]*((double)nzbins));
- for (int jq=1;jq<nbins;jq++)
- {
+
+ for (int jq = 1; jq < nbins; jq++) {
invVbin[jq]=1.0/((zhi-zlo)*MY_PI*(R2kin[jq]-R2kin[jq-1]));
PzAinv[jq]=1.0/(MY_PI*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
}
@@ -185,7 +183,7 @@ void ComputePressureCyl::init()
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
- for (int zzz=0;zzz<nzbins;zzz++) binz[zzz]=(((double)zzz)+0.5)*bin_width+zlo;
+ for (int zzz = 0; zzz < nzbins; zzz++) binz[zzz]=(((double)zzz)+0.5)*bin_width+zlo;
}
@@ -213,8 +211,7 @@ void ComputePressureCyl::compute_array()
int ibin;
// clear pressures
- for (ibin=0;ibin<nbins;ibin++)
- {
+ for (ibin = 0; ibin < nbins; ibin++) {
density_temp[ibin]=0.0;
density_all[ibin]=0.0;
Pr_temp[ibin]=0.0;
@@ -254,17 +251,16 @@ void ComputePressureCyl::compute_array()
// calculate number density (by radius)
double temp_R2;
- for (i=0;i<nlocal;i++) if (x[i][2]<zhi && x[i][2]>zlo)
- {
+ for (i = 0; i < nlocal; i++) if ((x[i][2] < zhi) && (x[i][2] > zlo)) {
temp_R2=x[i][0]*x[i][0]+x[i][1]*x[i][1];
- if (temp_R2>R2kin[nbins-1]) continue; // outside of Rmax
+ if (temp_R2 > R2kin[nbins-1]) continue; // outside of Rmax
- for (j=0;j<nbins;j++) if (temp_R2<R2kin[j]) break;
+ for (j = 0; j < nbins; j++) if (temp_R2 < R2kin[j]) break;
density_temp[j]+=invVbin[j];
}
MPI_Allreduce(density_temp,density_all,nbins,MPI_DOUBLE,MPI_SUM,world);
- for (i=0;i<nbins;i++) array[i][1]=density_all[i]; // NEW
+ for (i = 0; i < nbins; i++) array[i][1]=density_all[i]; // NEW
// loop over neighbors of my atoms
// skip if I or J are not in group
@@ -289,8 +285,7 @@ void ComputePressureCyl::compute_array()
double sqrtD;
double lower_z,upper_z;
- for (ii = 0; ii < inum; ii++)
- {
+ for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
@@ -304,8 +299,7 @@ void ComputePressureCyl::compute_array()
r1=x[i][0]*x[i][0]+x[i][1]*x[i][1];
- for (jj = 0; jj < jnum; jj++)
- {
+ for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
@@ -315,22 +309,17 @@ void ComputePressureCyl::compute_array()
// itag = jtag is possible for long cutoffs that include images of self
// do calculation only on appropriate processor
- if (newton_pair == 0 && j >= nlocal)
- {
+ if (newton_pair == 0 && j >= nlocal) {
jtag = tag[j];
- if (itag > jtag)
- {
+ if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
}
- else if (itag < jtag)
- {
+ else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
}
- else
- {
+ else {
if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp)
- {
+ if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
@@ -344,8 +333,7 @@ void ComputePressureCyl::compute_array()
r2=x[j][0]*x[j][0]+x[j][1]*x[j][1];
// ri is smaller of r1 and r2
- if (r2<r1)
- {
+ if (r2 < r1) {
risq=r2;
rjsq=r1;
xi=x[j][0];
@@ -355,8 +343,7 @@ void ComputePressureCyl::compute_array()
dy=x[i][1]-x[j][1];
dz=x[i][2]-x[j][2];
}
- else
- {
+ else {
risq=r1;
rjsq=r2;
xi=x[i][0];
@@ -377,25 +364,23 @@ void ComputePressureCyl::compute_array()
B=2.0*(xi*dx+yi*dy);
// normal pressure contribution P_rhorho
- for (ibin=0;ibin<nbins;ibin++)
- {
+ for (ibin = 0; ibin < nbins; ibin++) {
// completely inside of R
- if (rjsq<R2[ibin]) continue;
+ if (rjsq < R2[ibin]) continue;
C=risq-R2[ibin];
D=B*B-4.0*A*C;
// completely outside of R
- if (D<0.0) continue;
+ if (D < 0.0) continue;
sqrtD=sqrt(D);
alpha1=0.5*(-B+sqrtD)/A;
alpha2=0.5*(-B-sqrtD)/A;
- if (alpha1>0.0 && alpha1<1.0)
- {
+ if ((alpha1 > 0.0) && (alpha1 < 1.0)) {
zR=zi+alpha1*dz;
- if (zR<zhi && zR>zlo)
+ if ((zR < zhi) && (zR > zlo))
{
xR=xi+alpha1*dx;
yR=yi+alpha1*dy;
@@ -404,11 +389,9 @@ void ComputePressureCyl::compute_array()
Pr_temp[ibin]+=fn;
}
}
- if (alpha2>0.0 && alpha2<1.0)
- {
+ if ((alpha2 > 0.0) && (alpha2 < 1.0)) {
zR=zi+alpha2*dz;
- if (zR<zhi && zR>zlo)
- {
+ if ((zR < zhi) && (zR > zlo)) {
xR=xi+alpha2*dx;
yR=yi+alpha2*dy;
fn=fpair*fabs(xR*dx+yR*dy);
@@ -419,16 +402,15 @@ void ComputePressureCyl::compute_array()
}
// azimuthal pressure contribution (P_phiphi)
- for (int iphi=0;iphi<nphi;iphi++)
- {
+ for (int iphi = 0; iphi < nphi; iphi++) {
alpha=(yi-xi*tangent[iphi])/(dx*tangent[iphi]-dy);
// no intersection with phi surface
- if (alpha>=1.0 || alpha<=0.0) continue;
+ if ((alpha >= 1.0) || (alpha <= 0.0)) continue;
// no contribution (outside of averaging region)
zL=zi+alpha*dz;
- if (zL>zhi || zL<zlo) continue;
+ if ((zL > zhi) || (zL < zlo)) continue;
xL=xi+alpha*dx;
yL=yi+alpha*dy;
@@ -436,24 +418,22 @@ void ComputePressureCyl::compute_array()
L2=xL*xL+yL*yL;
// no intersection (outside of Rmax)
- if (L2>R2kin[nbins-1]) continue;
+ if (L2 > R2kin[nbins-1]) continue;
ftphi=fabs(dx*ephi_x[iphi]+dy*ephi_y[iphi])*fpair;
// add to appropriate bin
- for (ibin=0;ibin<nbins;ibin++) if (L2<R2kin[ibin])
- {
+ for (ibin = 0; ibin < nbins; ibin++) if (L2 < R2kin[ibin]) {
Pphi_temp[ibin]+=ftphi;
break;
}
}
// z pressure contribution (P_zz)
- for (int zbin=0;zbin<nzbins;zbin++)
- {
+ for (int zbin = 0; zbin < nzbins; zbin++) {
// check if interaction contributes
- if (x[i][2]>binz[zbin] && x[j][2]>binz[zbin]) continue;
- if (x[i][2]<binz[zbin] && x[j][2]<binz[zbin]) continue;
+ if ((x[i][2] > binz[zbin]) && (x[j][2] > binz[zbin])) continue;
+ if ((x[i][2] < binz[zbin]) && (x[j][2] < binz[zbin])) continue;
alpha=(binz[zbin]-zi)/dz;
@@ -462,13 +442,12 @@ void ComputePressureCyl::compute_array()
L2=xL*xL+yL*yL;
- if (L2>R2kin[nbins-1]) continue;
+ if (L2 > R2kin[nbins-1]) continue;
ftz=fabs(dz)*fpair;
// add to appropriate bin
- for (ibin=0;ibin<nbins;ibin++) if (L2<R2kin[ibin])
- {
+ for (ibin = 0; ibin < nbins; ibin++) if (L2 < R2kin[ibin]) {
Pz_temp[ibin]+=ftz;
break;
}
@@ -477,8 +456,7 @@ void ComputePressureCyl::compute_array()
}
// calculate pressure (force over area)
- for (ibin=0;ibin<nbins;ibin++)
- {
+ for (ibin = 0; ibin < nbins; ibin++) {
Pr_temp[ibin]*=PrAinv[ibin]*Rinv[ibin];
Pphi_temp[ibin]*=PphiAinv;
Pz_temp[ibin]*=PzAinv[ibin];
@@ -490,8 +468,7 @@ void ComputePressureCyl::compute_array()
MPI_Allreduce(Pz_temp,Pz_all,nbins,MPI_DOUBLE,MPI_SUM,world);
// populate array
- for (ibin=0;ibin<nbins;ibin++)
- {
+ for (ibin = 0; ibin < nbins; ibin++) {
array[ibin][0]=R[ibin];
array[ibin][2]=Pr_all[ibin]*nktv2p;
array[ibin][3]=Pphi_all[ibin]*nktv2p;
--
GitLab
From 590ab1661e0b1773bb02ca29ec922514cd72f4e4 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 15:17:11 -0400
Subject: [PATCH 320/332] convert more system headers to c++ style
---
src/USER-MISC/compute_pressure_cylinder.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index bdffa32af1..b35e851e4b 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <cmath>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_pressure_cylinder.h"
#include "atom.h"
#include "update.h"
--
GitLab
From a549752764a34219f6e07232a886c227d1a6b285 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 2 Oct 2018 15:18:06 -0400
Subject: [PATCH 321/332] reduce compiler warnings and some more whitespace
adjustments
---
src/USER-MISC/compute_pressure_cylinder.cpp | 35 +++++++++------------
1 file changed, 15 insertions(+), 20 deletions(-)
diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp
index b35e851e4b..6fcd343e38 100644
--- a/src/USER-MISC/compute_pressure_cylinder.cpp
+++ b/src/USER-MISC/compute_pressure_cylinder.cpp
@@ -50,10 +50,10 @@ static const char cite_compute_pressure_cylinder[] =
ComputePressureCyl::ComputePressureCyl(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
- R(NULL), Rinv(NULL), R2(NULL), R2kin(NULL), invVbin(NULL),
- density_temp(NULL), density_all(NULL), tangent(NULL), ephi_x(NULL),
- ephi_y(NULL), Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL),
- Pphi_temp(NULL), Pphi_all(NULL), PrAinv(NULL), PzAinv(NULL), binz(NULL)
+ Pr_temp(NULL), Pr_all(NULL), Pz_temp(NULL), Pz_all(NULL), Pphi_temp(NULL),
+ Pphi_all(NULL), R(NULL), Rinv(NULL), R2(NULL), PrAinv(NULL), PzAinv(NULL),
+ R2kin(NULL), density_temp(NULL), invVbin(NULL), density_all(NULL),
+ tangent(NULL), ephi_x(NULL), ephi_y(NULL), binz(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_compute_pressure_cylinder);
if (narg != 7) error->all(FLERR,"Illegal compute pressure/cylinder command");
@@ -171,7 +171,7 @@ void ComputePressureCyl::init()
invVbin[0]=1.0/((zhi-zlo)*MY_PI*R2kin[0]);
PzAinv[0]=1.0/(MY_PI*R2kin[0]*((double)nzbins));
-
+
for (int jq = 1; jq < nbins; jq++) {
invVbin[jq]=1.0/((zhi-zlo)*MY_PI*(R2kin[jq]-R2kin[jq-1]));
PzAinv[jq]=1.0/(MY_PI*(R2kin[jq]-R2kin[jq-1])*((double)nzbins));
@@ -189,7 +189,7 @@ void ComputePressureCyl::init()
/* ---------------------------------------------------------------------- */
-void ComputePressureCyl::init_list(int id, NeighList *ptr)
+void ComputePressureCyl::init_list(int /* id */, NeighList *ptr)
{
list = ptr;
}
@@ -226,10 +226,10 @@ void ComputePressureCyl::compute_array()
int me;
MPI_Comm_rank(world,&me);
- int i,j,n,ii,jj,inum,jnum,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz;
- double rsq,eng,fpair,factor_coul,factor_lj;
+ double rsq,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
@@ -276,14 +276,12 @@ void ComputePressureCyl::compute_array()
double r1=0.0;
double r2=0.0;
double risq,rjsq;
- double ri,rj,rij,fij;
- double A,B,C,Bsq,A2inv,A4,D;
- double alpha1,alpha2,aij;
+ double A,B,C,D;
+ double alpha1,alpha2;
double xi,yi,zi,dx,dy,dz;
- double m,xR,yR,zR,fn;
+ double xR,yR,zR,fn;
double alpha,xL,yL,zL,L2,ftphi,ftz;
double sqrtD;
- double lower_z,upper_z;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -313,11 +311,9 @@ void ComputePressureCyl::compute_array()
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
- }
- else if (itag < jtag) {
+ } else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
- }
- else {
+ } else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
@@ -342,8 +338,7 @@ void ComputePressureCyl::compute_array()
dx=x[i][0]-x[j][0];
dy=x[i][1]-x[j][1];
dz=x[i][2]-x[j][2];
- }
- else {
+ } else {
risq=r1;
rjsq=r2;
xi=x[i][0];
@@ -358,7 +353,7 @@ void ComputePressureCyl::compute_array()
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
- eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
+ pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
A=dx*dx+dy*dy;
B=2.0*(xi*dx+yi*dy);
--
GitLab
From 9e9b97231cfbf6d912c937b49677f4e93d85867a Mon Sep 17 00:00:00 2001
From: Aidan Thompson <athomps@sandia.gov>
Date: Tue, 2 Oct 2018 16:56:27 -0600
Subject: [PATCH 322/332] Fixed sign error on mu for semigrand variant
---
src/MC/fix_atom_swap.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 3e981c5609..12b5d65f4a 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -377,7 +377,7 @@ int FixAtomSwap::attempt_semi_grand()
int success = 0;
if (i >= 0)
if (random_unequal->uniform() <
- exp(-beta*(energy_after - energy_before
+ exp(beta*(energy_before - energy_after
+ mu[jtype] - mu[itype]))) success = 1;
int success_all = 0;
--
GitLab
From fd20eb93b2e7f63b2fb1efda2b81e494b1cdc994 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Thu, 4 Oct 2018 21:30:34 -0600
Subject: [PATCH 323/332] remove listing of extinct special_bonds 'extra'
keyword
---
doc/src/special_bonds.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 283aad6c2d..e90535e65f 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -13,7 +13,7 @@ special_bonds command :h3
special_bonds keyword values ... :pre
one or more keyword/value pairs may be appended :ulb,l
-keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
+keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} :l
{amber} values = none
{charmm} values = none
{dreiding} values = none
@@ -219,7 +219,7 @@ each time the command is issued.
[Default:]
All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
-angle = no, dihedral = no, and extra = 0.
+angle = no, dihedral = no.
:line
--
GitLab
From 7f8302b65b44f7e7f6ee5bfa7827b2defab79bd9 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Thu, 4 Oct 2018 22:08:43 -0600
Subject: [PATCH 324/332] replace extra_special with maxspecial in restarts
---
src/read_restart.cpp | 6 +++---
src/write_restart.cpp | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 9be035e1a1..a57831a5b2 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -64,7 +64,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
- EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM};
+ EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL};
#define LB_FACTOR 1.1
@@ -924,8 +924,8 @@ void ReadRestart::header(int incompatible)
atom->extra_dihedral_per_atom = read_int();
} else if (flag == EXTRA_IMPROPER_PER_ATOM) {
atom->extra_improper_per_atom = read_int();
- } else if (flag == EXTRA_SPECIAL_PER_ATOM) {
- force->special_extra = read_int();
+ } else if (flag == MAXSPECIAL) {
+ atom->maxspecial = read_int();
} else error->all(FLERR,"Invalid flag in header section of restart file");
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index edb6dfa7e8..6e01ab2997 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -63,7 +63,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
- EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM};
+ EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL};
/* ---------------------------------------------------------------------- */
@@ -533,7 +533,7 @@ void WriteRestart::header()
write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom);
write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom);
write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom);
- write_int(EXTRA_SPECIAL_PER_ATOM,force->special_extra);
+ write_int(MAXSPECIAL,atom->maxspecial);
// -1 flag signals end of header
--
GitLab
From 17853aef202c668b4abd976e6fa1d82e74629836 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Oct 2018 09:47:47 +0200
Subject: [PATCH 325/332] modify restart changes, so it stays backward
compatible and does not result in unexpected behavior when reading old
restarts. also use consistent naming conventions for enum entries
---
src/read_restart.cpp | 6 ++++--
src/write_restart.cpp | 4 ++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index a57831a5b2..252c48d251 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -64,7 +64,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
- EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL};
+ EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL};
#define LB_FACTOR 1.1
@@ -924,7 +924,9 @@ void ReadRestart::header(int incompatible)
atom->extra_dihedral_per_atom = read_int();
} else if (flag == EXTRA_IMPROPER_PER_ATOM) {
atom->extra_improper_per_atom = read_int();
- } else if (flag == MAXSPECIAL) {
+ } else if (flag == EXTRA_SPECIAL_PER_ATOM) {
+ force->special_extra = read_int();
+ } else if (flag == ATOM_MAXSPECIAL) {
atom->maxspecial = read_int();
} else error->all(FLERR,"Invalid flag in header section of restart file");
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 6e01ab2997..e0e17cd292 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -63,7 +63,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
- EXTRA_IMPROPER_PER_ATOM,MAXSPECIAL};
+ EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL};
/* ---------------------------------------------------------------------- */
@@ -533,7 +533,7 @@ void WriteRestart::header()
write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom);
write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom);
write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom);
- write_int(MAXSPECIAL,atom->maxspecial);
+ write_int(ATOM_MAXSPECIAL,atom->maxspecial);
// -1 flag signals end of header
--
GitLab
From 61e2cd3f61fc18850e26326eecb86b03576a841c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Oct 2018 16:03:11 +0200
Subject: [PATCH 326/332] avoid requesting threaded neighbor lists that are
both threaded via USER-OMP and USER-INTEL
---
src/USER-INTEL/fix_intel.cpp | 7 ++++++-
src/USER-OMP/fix_omp.cpp | 5 ++++-
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 3a67b60632..37212928df 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -532,8 +532,13 @@ void FixIntel::check_neighbor_intel()
_offload_noghost = 0;
}
#endif
+
+ // avoid flagging a neighbor list as both USER-INTEL and USER-OMP
+ if (neighbor->requests[i]->intel)
+ neighbor->requests[i]->omp = 0;
+
if (neighbor->requests[i]->skip)
- error->all(FLERR, "Cannot yet use hybrid styles with Intel package.");
+ error->all(FLERR, "Hybrid styles with Intel package are unsupported.");
}
}
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 8d54d5b451..8be54caada 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -318,8 +318,11 @@ void FixOMP::set_neighbor_omp()
const int neigh_omp = _neighbor ? 1 : 0;
const int nrequest = neighbor->nrequest;
+ // flag *all* neighbor list requests as USER-OMP threaded,
+ // but skip lists already flagged as USER-INTEL threaded
for (int i = 0; i < nrequest; ++i)
- neighbor->requests[i]->omp = neigh_omp;
+ if (! neighbor->requests[i]->intel)
+ neighbor->requests[i]->omp = neigh_omp;
}
/* ---------------------------------------------------------------------- */
--
GitLab
From 1e9778b81e2e3f58bcd06414a8097b9e33af028f Mon Sep 17 00:00:00 2001
From: mkanski <michal.kanski@live.com>
Date: Fri, 5 Oct 2018 20:34:12 +0200
Subject: [PATCH 327/332] Extend compute pair to handle multiple instances of a
given pair style
---
doc/src/compute_pair.txt | 33 +++++++++++++++++++++++----------
src/compute_pair.cpp | 32 +++++++++++++++++++++++---------
src/compute_pair.h | 2 +-
3 files changed, 47 insertions(+), 20 deletions(-)
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index b309019e30..751ea2c340 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -10,17 +10,22 @@ compute pair command :h3
[Syntax:]
-compute ID group-ID pair pstyle evalue :pre
+compute ID group-ID pair pstyle keyword value :pre
-ID, group-ID are documented in "compute"_compute.html command
-pair = style name of this compute command
-pstyle = style name of a pair style that calculates additional values
-evalue = {epair} or {evdwl} or {ecoul} or blank (optional setting) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+pair = style name of this compute command :l
+pstyle = style name of a pair style that calculates additional values :l
+zero or more keyword/value pairs may be appended :l
+keyword = {evalue} or {nsub}
+ {evalue} arg = {epair} or {evdwl} or {ecoul}
+ {nsub} n = use {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre
+:ule
[Examples:]
compute 1 all pair gauss
-compute 1 all pair lj/cut/coul/cut ecoul
+compute 1 all pair lj/cut/coul/cut evalue ecoul
+compute 1 all pair tersoff nsub 2
compute 1 all pair reax :pre
[Description:]
@@ -33,15 +38,23 @@ NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
-hybrid/overlay"_pair_hybrid.html command.
+hybrid/overlay"_pair_hybrid.html command. If the sub-style is
+used more than once, additional keyword {nsub} has to be specified in
+order to choose a single instance.
-The {evalue} setting is optional; it may be left off the command. All
+NOTE: The {nsub} keyword should be used only if the sub-style occurs
+multiple times. Its value must be an integer from 1 to M, where M is
+the number of times the sub-style is listed in the "pair_style hybrid
+or hybrid/overlay"_pair_hybrid.html" command. If the pair style is
+used once, {nsub} must remain zero.
+
+The {evalue} setting is optional. All
pair styles tally a potential energy {epair} which may be broken into
two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}.
If the pair style calculates Coulombic interactions, their energy will
be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones
style van der Waals interaction or not) is tallied in {evdwl}. If
-{evalue} is specified as {epair} or left out, then {epair} is stored
+{evalue} is specified as {epair}, then {epair} is stored
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
@@ -82,4 +95,4 @@ the doc page for the pair style for details.
[Default:]
-The default for {evalue} is {epair}.
+The keyword defaults are {evalue} = {epair}, nsub = 0.
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index 444395bae5..6129f192e2 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -29,7 +29,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
pstyle(NULL), pair(NULL), one(NULL)
{
- if (narg < 4 || narg > 5) error->all(FLERR,"Illegal compute pair command");
+ if (narg < 4) error->all(FLERR,"Illegal compute pair command");
scalar_flag = 1;
extscalar = 1;
@@ -41,19 +41,33 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
pstyle = new char[n];
strcpy(pstyle,arg[3]);
- if (narg == 5) {
- if (strcmp(arg[4],"epair") == 0) evalue = EPAIR;
- if (strcmp(arg[4],"evdwl") == 0) evalue = EVDWL;
- if (strcmp(arg[4],"ecoul") == 0) evalue = ECOUL;
- } else evalue = EPAIR;
+ int iarg = 4;
+ nsub = 0;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"evalue") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command");
+ if (strcmp(arg[iarg+1],"epair") == 0) evalue = EPAIR;
+ else if (strcmp(arg[iarg+1],"evdwl") == 0) evalue = EVDWL;
+ else if (strcmp(arg[iarg+1],"ecoul") == 0) evalue = ECOUL;
+ else error->all(FLERR, "Unrecognized energy type");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"nsub") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command");
+ nsub = force->inumeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else error->all(FLERR,"Illegal compute pair command");
+
+ }
+
// check if pair style with and without suffix exists
- pair = force->pair_match(pstyle,1);
+ pair = force->pair_match(pstyle,1,nsub);
if (!pair && lmp->suffix) {
strcat(pstyle,"/");
strcat(pstyle,lmp->suffix);
- pair = force->pair_match(pstyle,1);
+ pair = force->pair_match(pstyle,1,nsub);
}
if (!pair)
@@ -84,7 +98,7 @@ void ComputePair::init()
{
// recheck for pair style in case it has been deleted
- pair = force->pair_match(pstyle,1);
+ pair = force->pair_match(pstyle,1,nsub);
if (!pair)
error->all(FLERR,"Unrecognized pair style in compute pair command");
}
diff --git a/src/compute_pair.h b/src/compute_pair.h
index 9f2678aaab..57d52a5bab 100644
--- a/src/compute_pair.h
+++ b/src/compute_pair.h
@@ -33,7 +33,7 @@ class ComputePair : public Compute {
void compute_vector();
private:
- int evalue,npair;
+ int evalue,npair,nsub;
char *pstyle;
class Pair *pair;
double *one;
--
GitLab
From 8960774b166119fbdf58d54b65cbca142e9e0c29 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 5 Oct 2018 14:55:18 -0400
Subject: [PATCH 328/332] correct typo in USER-SMD introduced by doc-adjust PR
---
src/USER-SMD/compute_smd_triangle_vertices.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp
index 67ec27778a..b24223b8b5 100644
--- a/src/USER-SMD/compute_smd_triangle_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp
@@ -28,7 +28,7 @@
#include <cstring>
#include <iostream>
#include <Eigen/Eigen>
-#include "compute_smd_triangle_mesh_vertices.h"
+#include "compute_smd_triangle_vertices.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
--
GitLab
From 8b944e06f015a391c2d9b773768488d950edfe5e Mon Sep 17 00:00:00 2001
From: mkanski <michal.kanski@live.com>
Date: Fri, 5 Oct 2018 21:08:18 +0200
Subject: [PATCH 329/332] Small changes in doc file
---
doc/src/compute_pair.txt | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index 751ea2c340..1a3ec06508 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -18,7 +18,7 @@ pstyle = style name of a pair style that calculates additional values :l
zero or more keyword/value pairs may be appended :l
keyword = {evalue} or {nsub}
{evalue} arg = {epair} or {evdwl} or {ecoul}
- {nsub} n = use {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre
+ {nsub} n = use the {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre
:ule
[Examples:]
@@ -39,14 +39,15 @@ NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html command. If the sub-style is
-used more than once, additional keyword {nsub} has to be specified in
-order to choose a single instance.
+used more than once, an additional keyword {nsub} has to be
+specified in order to choose which instance of the sub-style will
+be used by the compute.
NOTE: The {nsub} keyword should be used only if the sub-style occurs
multiple times. Its value must be an integer from 1 to M, where M is
the number of times the sub-style is listed in the "pair_style hybrid
or hybrid/overlay"_pair_hybrid.html" command. If the pair style is
-used once, {nsub} must remain zero.
+used only once, {nsub} must remain zero.
The {evalue} setting is optional. All
pair styles tally a potential energy {epair} which may be broken into
--
GitLab
From 3c41295e7077b592351676c19e0ff45779553f91 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 8 Oct 2018 17:23:22 +0200
Subject: [PATCH 330/332] change implementation to be consistent with
pair_coeff and remain backward compatible
---
doc/src/compute_pair.txt | 27 ++++++++++-----------------
src/compute_pair.cpp | 32 +++++++++++++++++---------------
2 files changed, 27 insertions(+), 32 deletions(-)
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index 1a3ec06508..b36d61f71c 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -10,22 +10,20 @@ compute pair command :h3
[Syntax:]
-compute ID group-ID pair pstyle keyword value :pre
+compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
pair = style name of this compute command :l
pstyle = style name of a pair style that calculates additional values :l
-zero or more keyword/value pairs may be appended :l
-keyword = {evalue} or {nsub}
- {evalue} arg = {epair} or {evdwl} or {ecoul}
- {nsub} n = use the {n}-th instance of a sub-style in a pair_style hybrid or hybrid/overlay command :pre
+nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l
+{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l
:ule
[Examples:]
compute 1 all pair gauss
-compute 1 all pair lj/cut/coul/cut evalue ecoul
-compute 1 all pair tersoff nsub 2
+compute 1 all pair lj/cut/coul/cut ecoul
+compute 1 all pair tersoff 2 epair
compute 1 all pair reax :pre
[Description:]
@@ -39,15 +37,10 @@ NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
hybrid/overlay"_pair_hybrid.html command. If the sub-style is
-used more than once, an additional keyword {nsub} has to be
-specified in order to choose which instance of the sub-style will
-be used by the compute.
-
-NOTE: The {nsub} keyword should be used only if the sub-style occurs
-multiple times. Its value must be an integer from 1 to M, where M is
-the number of times the sub-style is listed in the "pair_style hybrid
-or hybrid/overlay"_pair_hybrid.html" command. If the pair style is
-used only once, {nsub} must remain zero.
+used more than once, an additional number {nsub} has to be specified
+in order to choose which instance of the sub-style will be used by
+the compute. Not specifying the number in this case will cause the
+compute to fail.
The {evalue} setting is optional. All
pair styles tally a potential energy {epair} which may be broken into
@@ -55,7 +48,7 @@ two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}.
If the pair style calculates Coulombic interactions, their energy will
be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones
style van der Waals interaction or not) is tallied in {evdwl}. If
-{evalue} is specified as {epair}, then {epair} is stored
+{evalue} is blank or specified as {epair}, then {epair} is stored
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index 6129f192e2..9690f140c5 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -13,6 +13,7 @@
#include <mpi.h>
#include <cstring>
+#include <cctype>
#include "compute_pair.h"
#include "update.h"
#include "force.h"
@@ -43,23 +44,24 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
int iarg = 4;
nsub = 0;
+ evalue = NPAIR;
+
+ if (narg > iarg) {
+ if (isdigit(arg[iarg][0])) {
+ nsub = force->inumeric(FLERR,arg[iarg]);
+ ++iarg;
+ if (nsub <= 0)
+ error->all(FLERR,"Illegal compute pair command");
+ }
+ }
- while (iarg < narg) {
- if (strcmp(arg[iarg],"evalue") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command");
- if (strcmp(arg[iarg+1],"epair") == 0) evalue = EPAIR;
- else if (strcmp(arg[iarg+1],"evdwl") == 0) evalue = EVDWL;
- else if (strcmp(arg[iarg+1],"ecoul") == 0) evalue = ECOUL;
- else error->all(FLERR, "Unrecognized energy type");
- iarg += 2;
- } else if (strcmp(arg[iarg],"nsub") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal compute pair command");
- nsub = force->inumeric(FLERR,arg[iarg+1]);
- iarg += 2;
- } else error->all(FLERR,"Illegal compute pair command");
-
+ if (narg > iarg) {
+ if (strcmp(arg[iarg],"epair") == 0) evalue = EPAIR;
+ else if (strcmp(arg[iarg],"evdwl") == 0) evalue = EVDWL;
+ else if (strcmp(arg[iarg],"ecoul") == 0) evalue = ECOUL;
+ else error->all(FLERR, "Illegal compute pair command");
+ ++iarg;
}
-
// check if pair style with and without suffix exists
--
GitLab
From dc6123fafcb63d1dab91b7e831d91d7cd5fa8464 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 8 Oct 2018 17:26:21 +0200
Subject: [PATCH 331/332] fix stupid typo
---
src/compute_pair.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index 9690f140c5..df4f3a1ddb 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -44,7 +44,7 @@ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
int iarg = 4;
nsub = 0;
- evalue = NPAIR;
+ evalue = EPAIR;
if (narg > iarg) {
if (isdigit(arg[iarg][0])) {
--
GitLab
From 70bee266418851e036fb47c952d2d855218cc006 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 9 Oct 2018 12:59:12 -0400
Subject: [PATCH 332/332] update version number
---
doc/src/Manual.txt | 4 ++--
src/version.h | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ecee17269a..dab2ea385e 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="18 Sep 2018 version">
+<META NAME="docnumber" CONTENT="10 Oct 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
-18 Sep 2018 version :c,h2
+10 Oct 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/src/version.h b/src/version.h
index 469d74fed7..d9d93cac0e 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "18 Sep 2018"
+#define LAMMPS_VERSION "10 Oct 2018"
--
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