From f7e17e97e8f34686e523ab55773f2120767b5864 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 17 Dec 2015 15:46:12 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14379
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/KOKKOS/pair_kokkos.h | 6 +++---
src/KOKKOS/verlet_kokkos.cpp | 4 ++--
src/MANYBODY/pair_comb3.cpp | 2 +-
src/USER-MISC/fix_srp.cpp | 10 ++++++++++
src/USER-PHONON/fix_phonon.cpp | 3 +++
src/USER-PHONON/fix_phonon.h | 4 ----
src/modify.h | 1 +
7 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 5f9b347ddf..eb188f9c14 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -355,12 +355,12 @@ struct PairComputeFunctor<PairStyle,FULLCLUSTER,STACKPARAMS,Specialisation> {
EV_FLOAT compute_item(const typename Kokkos::TeamPolicy<device_type>::member_type& dev,
const NeighListKokkos<device_type> &list, const NoCoulTag& ) const {
EV_FLOAT ev;
- const int i = dev.league_rank()*dev.team_size() + dev.team_rank();
+ int i = dev.league_rank()*dev.team_size() + dev.team_rank();
const X_FLOAT xtmp = c.c_x(i,0);
const X_FLOAT ytmp = c.c_x(i,1);
const X_FLOAT ztmp = c.c_x(i,2);
- const int itype = c.type(i);
+ int itype = c.type(i);
const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = list.d_numneigh[i];
@@ -368,7 +368,7 @@ struct PairComputeFunctor<PairStyle,FULLCLUSTER,STACKPARAMS,Specialisation> {
F_FLOAT3 ftmp;
for (int jj = 0; jj < jnum; jj++) {
- const int jjj = neighbors_i(jj);
+ int jjj = neighbors_i(jj);
Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(dev,NeighClusterSize),[&] (const int& k, F_FLOAT3& fftmp) {
const F_FLOAT factor_lj = c.special_lj[sbmask(jjj+k)];
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index 67e852a7d9..527e10add3 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -458,7 +458,7 @@ void VerletKokkos::force_clear()
size_t nbytes = sizeof(double) * nall;
if (nbytes) {
- if (atomKK->k_f.modified_host > atomKK->k_f.modified_device) {
+ if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) {
memset_kokkos(atomKK->k_f.view<LMPHostType>());
atomKK->modified(Host,F_MASK);
} else {
@@ -475,7 +475,7 @@ void VerletKokkos::force_clear()
} else {
int nall = atomKK->nfirst;
- if (atomKK->k_f.modified_host > atomKK->k_f.modified_device) {
+ if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) {
memset_kokkos(atomKK->k_f.view<LMPHostType>());
atomKK->modified(Host,F_MASK);
} else {
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 255e8a54c4..fc2a805d15 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -604,7 +604,7 @@ void PairComb3::read_file(char *file)
FILE *fp;
if (comm->me == 0) {
- fp = fopen(file,"r");
+ fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open COMB3 potential file %s",file);
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index e5d592d301..88f18e9a7c 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -104,6 +104,16 @@ void FixSRP::init()
if ((bptype < 1) || (bptype > atom->ntypes))
error->all(FLERR,"Illegal bond particle type");
+ // fix SRP should be the first fix running at the PRE_EXCHANGE step.
+ // Otherwise it might conflict with, e.g. fix deform
+
+ if (modify->n_pre_exchange > 1) {
+ char *first = modify->fix[modify->list_pre_exchange[0]]->id;
+ if ((comm->me == 0) && (strcmp(id,first) != 0))
+ error->warning(FLERR,"Internal fix for pair srp defined too late."
+ " May lead to incorrect behavior.");
+ }
+
// setup neigh exclusions for diff atom types
// bond particles do not interact with other types
// type bptype only interacts with itself
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index f2748994f5..d675736179 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -23,8 +23,11 @@
konglt@sjtu.edu.cn; konglt@gmail.com
------------------------------------------------------------------------- */
+#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
#include "fix_phonon.h"
+#include "fft3d_wrap.h"
#include "atom.h"
#include "compute.h"
#include "domain.h"
diff --git a/src/USER-PHONON/fix_phonon.h b/src/USER-PHONON/fix_phonon.h
index 95a9d200e1..ecd3a8ebc9 100644
--- a/src/USER-PHONON/fix_phonon.h
+++ b/src/USER-PHONON/fix_phonon.h
@@ -43,10 +43,6 @@ typedef double FFT_SCALAR;
#include <complex>
#include "fix.h"
#include <map>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "fft3d_wrap.h"
namespace LAMMPS_NS {
diff --git a/src/modify.h b/src/modify.h
index 0367761037..17d409a46e 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -23,6 +23,7 @@ namespace LAMMPS_NS {
class Modify : protected Pointers {
friend class Info;
+ friend class FixSRP;
public:
int nfix,maxfix;
int n_initial_integrate,n_post_integrate,n_pre_exchange,n_pre_neighbor;
--
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